The Big Cuboid
Chung van Gog, 07 April 2022
This is the Big Cuboid. In this Cuboid I will try to understand world problems big and small.
I hear new news every day, and those ordinary rumours of war, plagues, fires, inundations, thefts, murders, massacres, meteors, comets, spectrums, prodigies, apparitions, of towns taken, cities besieged in France, Germany, Turkey, Persia, Poland, &c., daily musters and preparations, and such-like, which these tempestuous times afford, battles fought, so many men slain, monomachies, shipwrecks, piracies, and sea-fights, peace, leagues, stratagems, and fresh alarms. A vast confusion of vows, wishes, actions, edicts, petitions, lawsuits, pleas, laws, proclamations, complaints, grievances are daily brought to our ears. New books every day, pamphlets, corantoes, stories, whole catalogues of volumes of all sorts, new paradoxes, opinions, schisms, heresies, controversies in philosophy, religion, &c. Now come tidings of weddings, masquings, mummeries, entertainments, jubilees, embassies, tilts and tournaments, trophies, triumphs, revels, sports, plays: then again, as in a new shifted scene, treasons, cheating tricks, robberies, enormous villainies in all kinds, funerals, burials, death of Princes, new discoveries, expeditions; now comical, then tragical matters.
Robert Burton, The Anatomy of Melancholy
Like a seedling, the Big Cuboid will grow over time and eventually address all of the problems below.
Table of Contents
- Table of Contents
- 34. Pandemics
- 34.1. Current Pandemics
- 34.1.1. The COVID-19 Pandemic
- A) Origin
- B) Death
- C) Disease
- D) Evolution
- D1) Future variants will have unpredictable severity
- D2) There is a significant risk of anthroponisis-reverse anthroponisis induced mutations
- D3) Evolutionary pressures in chronic infection might allow a VOC (Variant of Concern) to emerge.
- D4) BA.5: this Omicron sub-variant is the worst version of the virus that we’ve seen
- E) Impact
- F) Bright spots
- 34.1.2. 2022 Monkeypox virus (MPXV) outbreak
- 34.1.1. The COVID-19 Pandemic
- 34.2. Other current public heatlh emergencies of international concern (PHEICs)
- 34.3. Current outbreaks
- 34.1. Current Pandemics
34. Pandemics
Last updated: July 2022.
Also includes epidemics and smaller outbreaks.
34.1. Current Pandemics
34.1.1. The COVID-19 Pandemic
This is what Wikipedia has to say about the COVID-19 pandemic in the introduction to their article. Wikipedia is far from the best source on most topics, but at least it’s a somewhat decent starting point. Wikipedia introductions tend to capture something resembling a consensus—modulo predictable biases. This makes sense, since Wikipedia articles originate as a compromise between many different editors.
The COVID-19 pandemic, also known as the coronavirus pandemic, is an ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The novel virus was first identified from an outbreak in Wuhan, China, in December 2019. Attempts to contain it there failed, allowing the virus to spread to other areas of China and later worldwide. The World Health Organization (WHO) declared a Public Health Emergency of International Concern on 30 January 2020 and a pandemic on 11 March 2020. As of 24 July 2022, the pandemic had caused more than 569 million cases and 6.38 million confirmed deaths, making it one of the deadliest in history.
COVID-19 symptoms range from undetectable to deadly, but most commonly include fever, dry cough, and fatigue. Severe illness is more likely in elderly patients and those with certain underlying medical conditions. COVID-19 transmits when people breathe in air contaminated by droplets and small airborne particles containing the virus. The risk of breathing these in is highest when people are in close proximity, but they can be inhaled over longer distances, particularly indoors. Transmission can also occur if contaminated fluids reach the eyes, nose or mouth, and, rarely, via contaminated surfaces. Infected persons are typically contagious for 10 days, and can spread the virus even if they do not develop symptoms. Mutations have produced many strains (variants) with varying degrees of infectivity and virulence.[5][6]
COVID-19 vaccines have been approved and widely distributed in various countries since December 2020. Other recommended preventive measures include social distancing, wearing masks, improving ventilation and air filtration, and quarantining those who have been exposed or are symptomatic. Treatments include monoclonal antibodies,[7] novel antiviral drugs, and symptom control. Governmental interventions include travel restrictions, lockdowns, business restrictions and closures, workplace hazard controls, quarantines, testing systems, and tracing contacts of the infected.
The pandemic has triggered severe social and economic disruption around the world, including the largest global recession since the Great Depression.[8] Widespread supply shortages, including food shortages, were caused by supply chain disruption. The resultant near-global lockdowns saw an unprecedented pollution decrease. Educational institutions and public areas were partially or fully closed in many jurisdictions, and many events were cancelled or postponed. Misinformation circulated through social media and mass media, and political tensions intensified. The pandemic raised issues of racial and geographic discrimination, health equity, and the balance between public health imperatives and individual rights.
Wang et al. (2021) provide one of the best overviews of the virus and associated disease. It is worth reading their article in full to understand how SARS-CoV-2 works and how it spreads. Note in particular that small aerosols can stay in the air for hours, so wear your mask indoors even if you are alone. I am grateful to Mitchell Tsai for first pointing me towards this article and to other relevant sources.
Airborne transmission of respiratory viruses
Mechanisms of airborne transmission The COVID-19 pandemic has highlighted controversies and unknowns about how respiratory pathogens spread between hosts. Traditionally, it was thought that respiratory pathogens spread between people through large droplets produced in coughs and through contact with contaminated surfaces (fomites). However, several respiratory pathogens are known to spread through small respiratory aerosols, which can float and travel in air flows, infecting people who inhale them at short and long distances from the infected person. Wang et al. review recent advances in understanding airborne transmission gained from studying the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and other respiratory pathogens. The authors suggest that airborne transmission may be the dominant form of transmission for several respiratory pathogens, including SARS-CoV-2, and that further understanding of the mechanisms underlying infection from the airborne route will better inform mitigation measures. —GKA
Structured Abstract
BACKGROUND Exposure to droplets produced in the coughs and sneezes of infected individuals or contact with droplet-contaminated surfaces (fomites) have been widely perceived as the dominant transmission modes for respiratory pathogens. Airborne transmission is traditionally defined as involving the inhalation of infectious aerosols or “droplet nuclei” smaller than 5 μm and mainly at a distance of >1 to 2 m away from the infected individual, and such transmission has been thought to be relevant only for “unusual” diseases. However, there is robust evidence supporting the airborne transmission of many respiratory viruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome (MERS)–CoV, influenza virus, human rhinovirus, and respiratory syncytial virus (RSV). The limitations of traditional views of droplet, fomite, and airborne transmission were illuminated during the COVID-19 pandemic. Droplet and fomite transmission of SARS-CoV-2 alone cannot account for the numerous superspreading events and differences in transmission between indoor and outdoor environments observed during the COVID-19 pandemic. Controversy surrounding how COVID-19 is transmitted and what interventions are needed to control the pandemic has revealed a critical need to better understand the airborne transmission pathway of respiratory viruses, which will allow for better-informed strategies to mitigate the transmission of respiratory infections.
ADVANCES Respiratory droplets and aerosols can be generated by various expiratory activities. Advances in aerosol measurement techniques, such as aerodynamic and scanning mobility particle sizing, have shown that the majority of exhaled aerosols are smaller than 5 μm, and a large fraction are <1 μm for most respiratory activities, including those produced during breathing, talking, and coughing. Exhaled aerosols occur in multiple size modes that are associated with different generation sites and production mechanisms in the respiratory tract. Although 5 μm has been used historically to distinguish aerosols from droplets, the size distinction between aerosols and droplets should be 100 μm, which represents the largest particle size that can remain suspended in still air for more than 5 s from a height of 1.5 m, typically reach a distance of 1 to 2 m from the emitter (depending on the velocity of airflow carrying the aerosols), and can be inhaled. Aerosols produced by an infected individual may contain infectious viruses, and studies have shown that viruses are enriched in small aerosols (<5 μm). The transport of virus-laden aerosols is affected by the physicochemical properties of aerosols themselves and environmental factors, including temperature, relative humidity, ultraviolet radiation, airflow, and ventilation. Once inhaled, virus-laden aerosols can deposit in different parts of the respiratory tract. Larger aerosols tend to be deposited in the upper airway; however, smaller aerosols, although they can also be deposited there, can penetrate deep into the alveolar region of the lungs. The strong effect of ventilation on transmission, the distinct difference between indoor and outdoor transmission, well-documented long-range transmission, the observed transmission of SARS-CoV-2 despite the use of masks and eye protection, the high frequency of indoor superspreading events of SARS-CoV-2, animal experiments, and airflow simulations provide strong and unequivocal evidence for airborne transmission. Fomite transmission of SARS-CoV-2 has been found to be far less efficient, and droplets are only dominant when individuals are within 0.2 m of each other when talking. Although both aerosols and droplets can be produced by infected individuals during expiratory activities, droplets fall quickly to the ground or surfaces within seconds, leaving an enrichment of aerosols over droplets. The airborne pathway likely contributes to the spread of other respiratory viruses whose transmission was previously characterized as droplet driven. The World Health Organization (WHO) and the US Centers for Disease Control and Prevention (CDC) have officially acknowledged the inhalation of virus-laden aerosols as a main transmission mode in spreading COVID-19 at both short and long ranges in 2021.
OUTLOOK Airborne transmission of pathogens has been vastly underappreciated, mostly because of an insufficient understanding about the airborne behavior of aerosols and at least partially because of the misattribution of anecdotal observations. Given the lack of evidence for droplet and fomite transmission and the increasingly strong evidence for aerosols in transmitting numerous respiratory viruses, we must acknowledge that airborne transmission is much more prevalent than previously recognized. Given all that we have learned about SARS-CoV-2 infection, the aerosol transmission pathway needs to be reevaluated for all respiratory infectious diseases. Additional precautionary measures must be implemented for mitigating aerosol transmission at both short and long ranges, with particular attention to ventilation, airflows, air filtration, UV disinfection, and mask fit. These interventions are critical tools for ending the current pandemic and preventing future outbreaks.
Abstract The COVID-19 pandemic has revealed critical knowledge gaps in our understanding of and a need toupdate the traditional view of transmission pathways for respiratory viruses. The long-standingdefinitions of droplet and airborne transmission do not account for the mechanisms by which virus-ladenrespiratory droplets and aerosols travel through the air and lead to infection. In this Review, wediscuss current evidence regarding the transmission of respiratory viruses by aerosols—how they aregenerated, transported, and deposited, as well as the factors affecting the relative contributions ofdroplet-spray deposition versus aerosol inhalation as modes of transmission. Improved understanding ofaerosol transmission brought about by studies of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) infection requires a reevaluation of the major transmission pathways for other respiratoryviruses, which will allow better-informed controls to reduce airborne transmission.
Virus-laden aerosols (<100 I1/4m) are first generated by an infected individual through expiratory activities, through which they are exhaled and transported in the environment. They may be inhaled by a potential host to initiate a new infection, provided that they remain infectious. In contrast to droplets (>100 I1/4m), aerosols can linger in air for hours and travel beyond 1 to 2 m from the infected individual who exhales them, causing new infections at both short and long ranges.
The Swiss Cheese Respiratory Virus Pandemic Defense, thanks to virologist Ian M. Mackay.
Here are the different lineages. This diagram was made by Nextstrain.
While indoors, always wear masks: NH95, FFP2, FFP3, or else a surgical mask if you don’t have anything else.
What follows are some of my personal notes, shared in the spirit of responsible communication.
A) Origin
The novel virus was first identified from an outbreak in Wuhan, China, in December 2019
It is more likely than not that the COVID-19 pandemic began in a wet market in Wuhan. Here are the abstracts of three 2022 papers that provide evidence for the latter.
SARS-CoV-2 emergence very likely resulted from at least two zoonotic events
Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversity prior to February 2020 comprised only two distinct viral lineages—denoted A and B—with no transitional haplotypes. Novel phylodynamic rooting methods, coupled with epidemic simulations, indicate that these two lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses and occurred in late-November/early-December 2019 and no earlier than the beginning of November 2019, while the introduction of lineage A likely occurred within weeks of the first event. These findings define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. Hence, as with SARS-CoV-1 in 2002 and 2003, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.
Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market
Emerging in December 2019, coronavirus disease 2019 (COVID-19) eventually became a pandemic and has posed a tremendous threat to global public health. However, the origins of SARS-CoV-2, the causative agent of COVID-19, remain to be determined. It has reported that a certain number of the early case clusters had a contact history with Huanan Seafood Market. Therefore, surveillance of SARS-CoV-2 within the market is of vital importance. Herein, we presented the SARS-CoV-2 detection results of 1380 samples collected from the environment and the animals within the market in early 2020. By SARS-CoV-2-specific RT-qPCR, 73 environmental samples tested positive for SARS-CoV-2 and three live viruses were successfully isolated. The viruses from the market shared nucleotide identity of 99.980% to 99.993% with the human isolate HCoV/Wuhan/IVDC-HB-01. In contrast, no virus was detected in the animal swabs covering 18 species of animals in the market. The SARS-COV-2 nucleic acids in the positive environmental samples showed significant correlation of abundance of Homo sapiens with SARS-CoV-2. In summary, this study provided convincing evidence of the prevalence of SARS-CoV-2 in the Huanan Seafood Market during the early stage of COVID-19 outbreak.
The Huanan market was the epicenter of SARS-CoV-2 emergence
Despite strong epidemiological links and the documented presence of SARS-CoV-2 susceptible animals, the role of the Huanan Seafood Wholesale Market in the COVID-19 pandemic remains controversial. Using spatial analyses we show that the earliest known COVID-19 cases diagnosed in December 2019 were geographically distributed near to, and centered on, this market. This distribution cannot be explained by high densities of elderly people at greater risk of symptomatic COVID-19. This pattern was stronger in cases without, rather than with, identified epidemiological links to the Huanan market, consistent with SARS-CoV-2 community transmission starting in the surrounding area. By combining spatial and genomic data, we show that both the two early lineages of SARS-CoV-2 have a clear association with the Huanan market. We also report that live mammals, including raccoon dogs, were sold at the market in late 2019 and geospatial analyses within the market show that SARS-CoV-2-positive environmental samples were strongly associated with vendors selling live animals. Together, these analyses provide dispositive evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic.
One sentence summary: Geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was the site of origin of the COVID-19 pandemic.
The New York Times ran a good interactive article about the initial spread of SARS-CoV-2.
One year earlier, the New York Times published an interview with Shi Zhengli, a top virologist at the Wuhan Institute of Virology. Based on this interview, Chung never considered the lab leak hypothesis as likely has the seafood market zoonosis.
There are a number of other relevant aspects with regard to the origin of SARS-CoV-2.
A1) Experts and scientists have been warning of a pandemic for decades
In my obsessive reading about the coronavirus pandemic, I’ve avoided articles that focus on the early missteps that could have stopped COVID-19 if only we’d been more attentive, organized, and responsive. Those articles were wreaking havoc with my anxiety level. The time for “coulda, woulda, shoulda” would be later, I figured; what matters now is whatever needs to be done in the next few days, and the next few days after that.
There’s also a personal reason why I’ve boycotted articles about early warning signs: Scientists were detailing those early warning signs decades ago, and a handful of science journalists were writing about their work. I was one of those journalists.
When I started researching A Dancing Matrix in 1990, the term “emerging viruses” had just been coined by a young virologist named Stephen Morse, who would become the main character in my book. I wrote about how experts were identifying conditions that could lead to the introduction of new, potentially devastating pathogens—climate change, massive urbanization, the proximity of humans to farm or forest animals that serve as viral reservoirs—with the worldwide spread of those microbes accelerated by war, the global economy, and international air travel. Too many of us, I wrote, were blithely going about our business despite the growing threat. Sound familiar?
“The single biggest threat to man’s continued dominance on the planet is the virus.” I used that searing quote from Nobel laureate Joshua Lederberg, who was president of Rockefeller University and Morse’s boss, in the introduction to my book. Back then I thought it was a little bit melodramatic. Now it strikes me as terrifyingly accurate.
Here is the blob for A Dancing Matrix. We will hear more about Creutzfeldt-Jakob later.
Even as humanity reels beneath the assault of AIDS, epidemiologists are gearing themselves up for the plague’s successor. It might be dengue fever, whose carrier, the Asian tiger mosquito, has recently appeared in the United States, or Creutzfeldt-Jakob disease, which has been transmitted by contaminated human growth hormone. The next pandemic might be caused by any of a dozen viruses that were once confined to other species or territories but now place human beings at risk as we increasingly cross their boundaries.
Updated to include the latest research and developments, this fascinating and sometimes unsetting book sums up all that we currently know about viruses: what they are, how they spread, and how scientists are trying to outwit them. Interweaving theory and real-life medical drama, A Dancing Matrix is science reportage at its most suspenseful and informative
A2) ASFV, African swine fever virus, might have led to SARS-CoV-2
This is what Xia et al. (2021) have to say:
How One Pandemic Led To Another: Asfv, the Disruption Contributing To Sars-Cov-2 Emergence in Wuhan
The spillover of a virus from one host species to another requires both molecular and ecological risk factors to align. While extensive research both before and after the emergence of SARS-CoV-2 in 2019 implicates horseshoe bat as the significant reservoir genus for the new coronavirus, it remains unclear why it emerged at this time. One massive disruption to human-animal contact in 2019 is linked to the on-going African swine fever virus (ASFV) pandemic. This began in Georgia in 2007 and was introduced to China in 2018. Pork is the major meat source in the Chinese diet. Severe fluctuations in the pork market prior to December 2019, may have increased the transmission of zoonotic pathogens, including severe acute respiratory syndrome–related coronaviruses, from wildlife to humans, wildlife to livestock and non-local animals to local animals. The major production and consumption regions for pork are geographically separated in China. The dramatic shortage of pork following restrictions of pig movement and culling resulted in price increases, leading to alternative sources of meat and unusual animal and meat movements nationwide often involving wildlife and thus greatly increased opportunities for human-Sarbecovirus contacts. Pork prices were particularly high in southern provinces (Guangdong, Guangxi, Fujian, Jiangxi, Hunan, and Hubei), where wildlife is farmed on different scales and more frequently consumed. Shandong experienced the biggest losses in pork production (~1.7 million metric tons), which is also the largest mink farming province. Hence, human exposure to SARS-CoV-2 from wildlife or infected animals are more likely to have taken place in 2019, when China was experiencing the worst effects of the ASFV pandemic.
A3) We created the pandemicene
This is what Carlson et al. (2022) writes in Nature:
Climate change increases cross-species viral transmission risk
At least 10,000 virus species have the ability to infect humans but, at present, the vast majority are circulating silently in wild mammals1,2. However, changes in climate and land use will lead to opportunities for viral sharing among previously geographically isolated species of wildlife3,4. In some cases, this will facilitate zoonotic spillover—a mechanistic link between global environmental change and disease emergence. Here we simulate potential hotspots of future viral sharing, using a phylogeographical model of the mammal–virus network, and projections of geographical range shifts for 3,139 mammal species under climate-change and land-use scenarios for the year 2070. We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, causing the cross-species transmission of their associated viruses an estimated 4,000 times. Owing to their unique dispersal ability, bats account for the majority of novel viral sharing and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Notably, we find that this ecological transition may already be underway, and holding warming under 2 °C within the twenty-first century will not reduce future viral sharing. Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking the range shifts of species, especially in tropical regions that contain the most zoonoses and are experiencing rapid warming.
B) Death
As of 24 July 2022, the pandemic had caused more than 569 million cases and 6.38 million confirmed deaths, making it one of the deadliest in history.
Tragically, the true death toll is significantly higher. Here are the current best estimates of excess mortality.
The Economist model: 95%CI lower bound: 14.68 million, central estimate: 22.02 million, 95%CI upper bound: 25.51 million. World Health Organization: 95%CI lower bound: 13.32 million, mean estimate: 14.91 million, 95%CI upper bound: 16.65 million.
For comparison, the total number of World War I casualties was about 40 million. When thinking about such tragedies, I always find it important to keep in mind the following words by Professor Timothy Snyder about the individuality of each victim when he writes about mass killing under Hitler and Stalin. Don’t get me wrong: I am not comparing the coronavirus pandemic with the Holocaust.
Each record of death suggests, but cannot supply, a unique life. We must be able not only to reckon the number of deaths but to reckon with each victim as an individual. The one very large number that withstands scrutiny is that of the Holocaust, with its 5.7 million Jewish dead, 5.4 million of whom were killed by the Germans. But this number, like all of the others, must be seen not as 5.7 million, which is an abstraction few of us can grasp, but as 5.7 million times one. This does not mean some generic image of a Jew passing through some abstract notion of death 5.7 million times. It means countless individuals who nevertheless have to be counted, in the middle of life: Dobcia Kagan, the girl in the synagogue at Kovel, and everyone with her there, and all the individual human beings who were killed as Jews in Kovel, in Ukraine, in the East, in Europe.
Cultures of memory are organized by round numbers, intervals of ten; but somehow the remembrance of the dead is easier when the numbers are not round, when the final digit is not a zero. So within the Holocaust, it is perhaps easier to think of 780,863 different people at Treblinka: where the three at the end might be Tamara and Itta Willenberg, whose clothes clung together after they were gassed, and Ruth Dorfmann, who was able to cry with the man who cut her hair before she entered the gas chamber. Or it might be easier to imagine the one person at the end of the 33,761 Jews shot at Babi Yar: Dina Pronicheva’s mother, let us say, although in fact every single Jew killed there could be that one, must be that one, is that one.
Within the history of mass killing in the bloodlands, recollection must include the one million (times one) Leningraders starved during the siege, 3.1 million (times one) distinct Soviet prisoners of war killed by the Germans in 1941– 1944, or the 3.3 million (times one) distinct Ukrainian peasants starved by the Soviet regime in 1932– 1933. These numbers will never be known with precision, but they hold individuals, too: peasant families making fearful choices, prisoners keeping each other warm in dugouts, children such as Tania Savicheva watching their families perish in Leningrad.
Each of the 681,692 people shot in Stalin’s Great Terror of 1937– 1938 had a different life story: the two at the end might be Maria Juriewicz and Stanisław Wyganowski, the wife and husband reunited “under the ground.” Each of the 21,892 Polish prisoners of war shot by the NKVD in 1940 was in the midst of life. The two at the end might be Dobiesław Jakubowicz, the father who dreamed about his daughter, and Adam Solski, the husband who wrote of his wedding ring on the day that the bullet entered his brain.
The Nazi and Soviet regimes turned people into numbers, some of which we can only estimate, some of which we can reconstruct with fair precision. It is for us as scholars to seek these numbers and to put them into perspective. It is for us as humanists to turn the numbers back into people. If we cannot do that, then Hitler and Stalin have shaped not only our world, but our humanity
Here are some of those who lost their life to COVID-19.
Of Kious ‘James’ Kelly, Brenda Perryman and Pearlie Louie, and Clint and Carla Smith.
Here are the survivor stories.
Of Rita Delorais Coleman, Daniel B. Estrada, Noemi Garcia, and many others.
And here is the Survivor Diaries project.
About the Covid-19 Survivor Diaries Project
We started Covid-19 Survivor Diaries in April 2020 when Covid-19 started spreading where we lived, New York City. But, it’s not the first time we’ve been in an outbreak. This project is inspired by our time living through the world’s largest Ebola outbreak in West Africa in 2014. I helped PCI Media share Ebola survivor stories through radio, TV, and social media reaching nearly 10 million people. It helped curb the spread of the virus by driving change in attitudes and behaviors.
Through that project, I learned that survivors stories can provide vital health information, dispel myths, offer truths, reduce stigma, and educate first responders through the voices of people that communities know and trust. To those watching from the outside, they bring humanity to an otherwise ominous disease. Just as importantly, they offer hope to all.
When we found ourselves in the middle of another outbreak, I decided to start this personal project to chronicle and share the stories of Covid-19 survivors. We started by interviewing and photographing survivors in the New York metro area. Then, we decided we want to document survivors in all 50 states, so we moved out of our apartment and moved into a trailer so we could safely drive around the country. So far, we’ve interviewed and photographed over 140 survivors in 29 states. Our goal is to get to all 50 states by the end of 2021. You can check out our current filming schedule here. Help us get there by becoming a monthly patron here.
We are currently sharing these stories through social media and our website. Sometimes we pitch or provide them to media outlets. We are also working on a book and a documentary film series to document this moment in history.
The three websites linked above are all primarily based in the United States. But each country has survivors with their story to tell. So many of them are experiencing grief. Their world collapses as they will never see a loved one who succumbed to coronavirus disease again. This is what Ed Yong, who introduced us earlier to the pandemicene, has to tell us
By upending the entire world, COVID could have created a shared experience that countered the loneliness of grief. But most of the people I’ve been speaking with feel profoundly lonely—detached from society, from their support network, and especially from their loved ones at the moment of their death.
C) Disease
This is what the Wikipedia article on Long COVID has to say in the introduction:
Long COVID or Long-haul COVID[1] is a condition characterized by long-term consequences persisting or appearing after the typical convalescence period of COVID-19. It is also known as post-COVID-19 syndrome, post-COVID-19 condition,[2][3] post-acute sequelae of COVID-19 (PASC), or chronic COVID syndrome (CCS).[4][5][6] Long COVID can affect nearly every organ system, with sequelae including respiratory system disorders, nervous system and neurocognitive disorders, mental health disorders, metabolic disorders, cardiovascular disorders, gastrointestinal disorders, musculoskeletal pain, and anemia.[7] A wide range of symptoms are commonly reported, including fatigue, malaise, headaches, shortness of breath, anosmia (loss of smell), parosmia (distorted smell), muscle weakness, low fever and cognitive dysfunction.[8]
The exact nature of symptoms and the number of people who experience long-term symptoms are unknown; these vary according to the definition used, the population being studied, and the time period used in the study. A survey by the UK Office for National Statistics estimated that about 14% of people who tested positive for SARS-CoV-2 experienced one or more symptoms for longer than three months.[9] A study from the University of Oxford of 273,618 survivors of COVID-19, mainly from the United States, showed that about 37% experienced one or more symptoms between three and six months after diagnosis.[10]
While studies into various aspects of long COVID are under way,[11][12] as of November 2021, the definition of the illness is still unclear, as is its mechanism. Health systems in some countries and jurisdictions have been mobilized to deal with this group of patients by creating specialized clinics and providing advice.[13][14][15] Overall, however, it is considered by default to be a diagnosis of exclusion.[16]
A review suggests that global prevalence of long COVID conditions after infection could be as high as 43%, with the most common symptoms being fatigue and memory problems.[17][18]
Should it be surprising that so many suffer from Long COVID? Not at all, as Laura Spinney explains in “Pandemics disable people — the history lesson that policymakers ignore“.
When Ashley Shew turned up for an appointment at a medical centre in spring 2020, a member of staff told her she could remove her mask because only people with pre-existing conditions were vulnerable to COVID-19. Shew was surprised. “A hard-of-hearing amputee battered by chemotherapy and more”, as she describes herself, she is a regular at the centre — the appointment that day concerned her prosthetic leg. Who, she wondered, did the staff member think counted as a person with pre-existing conditions?
The invisibility of disability is not new, says Shew, a 38-year-old philosopher who explores the intersection of technology and disability at Virginia Polytechnic Institute and State University in Blacksburg. “But it is particularly deadly that we don’t frame COVID-19 as a disability issue,” she says. “Even linguistically we’re pointed away from it. ‘Pre-existing conditions’ is a way of not saying ‘disability’.”
From the beginning of this pandemic, people with disabilities understood that the disease would target them and would swell their ranks. Disability historians knew that there was a penumbra of ill health to previous mass-death events. Health economists warned that, as with tuberculosis, HIV and other diseases, morbidity would stalk mortality. Too many others have clung stubbornly to a belief that COVID-19 is something from which a minority of people die, and that most bounce back quickly and intact, with only their immune system updated. The longer the pandemic drags on, the harder it is to maintain that fiction.
Two years in, the debilitating tail of the pandemic has revealed itself in the form of tens of millions of people living with long COVID1. It is high time to ask whether attitudes to disability will change as a result. Will society grasp that the body can be altered for a long period — even permanently — by infectious disease, just as it seems to have accepted that the body politic will never be the same again? And will it make the necessary accommodations?
Here is the blurb of her book Pale Rider:
In 1918, the Italian-Americans of New York, the Yupik of Alaska and the Persians of Mashed had almost nothing in common except for a virus–one that triggered the worst pandemic of modern times and had a decisive effect on the history of the twentieth century. The Spanish flu of 1918-1920 was one of the greatest human disasters of all time. It infected a third of the people on Earth–from the poorest immigrants of New York City to the king of Spain, Franz Kafka, Mahatma Gandhi and Woodrow Wilson. But despite a death toll of between 50 and 100 million people, it exists in our memory as an afterthought to World War I. In this gripping narrative history, Laura Spinney traces the overlooked pandemic to reveal how the virus travelled across the globe, exposing mankind’s vulnerability and putting our ingenuity to the test. As socially significant as both world wars, the Spanish flu dramatically disrupted–and often permanently altered–global politics, race relations and family structures, while spurring innovation in medicine, religion and the arts. It was partly responsible, Spinney argues, for pushing India to independence, South Africa to apartheid and Switzerland to the brink of civil war. It also created the true “lost generation.” Drawing on the latest research in history, virology, epidemiology, psychology and economics, Pale Rider masterfully recounts the little-known catastrophe that forever changed humanity.
The New York times wrote a series of insightful articles about the mechanism and consequences of Long COVID a while back.
Note: vaccines only provide partial protection against Long COVID.
C1) Disease Breeds Disease
Sadly, one disease leads to another.
C1.1) The COVID-19 Infodemic
Perhaps not technically a disease, the COVID-19 infodemic is nevertheless infectious and dangerous.
False information, including intentional disinformation and conspiracy theories, about the scale of the COVID-19 pandemic and the origin, prevention, diagnosis, and treatment of the disease has been spread through social media, text messaging,[1] and mass media. False information has been propagated by celebrities, politicians, and other prominent public figures. Many countries have passed laws against “fake news”, and thousands of people have been arrested for spreading COVID-19 misinformation. The spread of COVID-19 misinformation by governments has also been significant.
Commercial scams have claimed to offer at-home tests, supposed preventives, and “miracle” cures.[2] Several religious groups have claimed their faith will protect them from the virus.[3] Without evidence, some people have claimed the virus is a bioweapon accidentally or deliberately leaked from a laboratory, a population control scheme, the result of a spy operation, or the side effect of 5G upgrades to cellular networks.[4]
The World Health Organization (WHO) declared an “infodemic” of incorrect information about the virus that poses risks to global health.[5] While belief in conspiracy theories is not a new phenomenon, in the context of the COVID-19 pandemic, this can lead to adverse health effects. Cognitive biases, such as jumping to conclusions and confirmation bias, may be linked to the occurrence of conspiracy beliefs.[6] In addition to health effects, harms resulting from the spread of misinformation and endorsement of conspiracy theories include increasing distrust of news organizations and medical authorities as well as divisiveness and political fragmentation.[7]
From How to Talk to a Science Denier, the five common elements of science denial:
After spending enough time around Flat Earthers, anti-vaxxers, intelligent designers, and climate change deniers, one begins to sense a pattern. Their strategies are all the same.1 Although the content of their belief systems differs, all science denial seems grounded in the same few mistakes in human reasoning. This has been studied by previous researchers such as Mark and Chris Hoofnagle, Pascal Diethelm and Martin McKee, John Cook, and Stephan Lewandowsky, who have come to consensus on five common factors:2
(1) Cherry-picking evidence
(2) Belief in conspiracy theories
(3) Reliance on fake experts (and the denigration of real experts)
(4) Committing logical errors
(5) Setting impossible expectations for what science can achieve
Together, these provide a common blueprint for science deniers to create a counter-narrative on any topic where they wish to challenge the scientific consensus.
C1.1.1) The anti-vaxx industry
In particular, the COVID-19 infodemic and its patrons add more fuel to the anti-vaxx trash fire.
C1.2) COVID-19 associated mucormycosis (2021-present)
This is what Hoenigl et al. (2022) have to say in their review:
The emergence of COVID-19 associated mucormycosis: a review of cases from 18 countries
Reports of COVID-19-associated mucormycosis have been increasing in frequency since early 2021, particularly among patients with uncontrolled diabetes. Patients with diabetes and hyperglycaemia often have an inflammatory state that could be potentiated by the activation of antiviral immunity to SARS-CoV2, which might favour secondary infections. In this Review, we analysed 80 published and unpublished cases of COVID-19-associated mucormycosis. Uncontrolled diabetes, as well as systemic corticosteroid treatment, were present in most patients with COVID-19-associated mucormycosis, and rhino-orbital cerebral mucormycosis was the most frequent disease. Mortality was high at 49%, which was particularly due to patients with pulmonary or disseminated mucormycosis or cerebral involvement. Furthermore, a substantial proportion of patients who survived had life-changing morbidities (eg, loss of vision in 46% of survivors). Our Review indicates that COVID-19-associated mucormycosis is associated with high morbidity and mortality. Diagnosis of pulmonary mucormycosis is particularly challenging, and might be frequently missed in India.
As one of the challenges, they name that there is little awareness of COVID-19-associated mucormycosis, as well as challenges regarding diagnosis and treatment.
C1.3) COVID-19-associated encephalitis or Creutzfeldt–Jakob disease (2021-present)
This is worrying. A mild COVID-19 infection in a young patient led to Creutzfeldt-Jakob disease. Read what Bernandini et al. (2022) write in Prion:
Creutzfeldt-Jakob disease after COVID-19: infection-induced prion protein misfolding? A case report
Creutzfeldt-Jakob disease (CJD) is a rare, fatal disease presenting with rapidly progressive neurological deficits caused by the accumulation of a misfolded form (PrPSc) of prion protein (PrPc). Coronavirus disease 2019 (COVID-19) is a primarily respiratory syndrome caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); many diverse neurological complications have been observed after COVID-19. We describe a young patient developing CJD two months after mild COVID-19. Presenting symptoms were visuospatial deficits and ataxia, evolving into a bedridden state with preserved consciousness and diffuse myoclonus. Diagnostic work-up was suggestive of CJD. The early age of onset and the short interval between respiratory and neurological symptoms might suggest a causal relationship: a COVID-19-related neuroinflammatory state may have induced the misfolding and subsequent aggregation of PrPSc. The present case emphasizes the link between neuroinflammation and protein misfolding. Further studies are needed to establish the role of SARS-CoV-2 as an initiator of neurodegeneration.
C1.4) Back with a Vengeance
Viruses that were on hiatus during Covid are back — and behaving in unexpected ways.
Here is one example of a virus which may start to behave eratically in Fall: enterovirus D68.
All eyes will be trained this fall on children’s hospitals to see whether there will be a surge in cases of a polio-like condition called acute flaccid myelitis, or AFM, which is thought to be caused by infection with enterovirus D68. … “Now we have four years of children who haven’t seen that virus. We don’t know what’s going to happen. We don’t know when it comes back. But when it does come back, there are more susceptible children out there that would not be expected to have immunity,” [Kevin Messacar] said. “That’s what we’re watching with a variety of different viruses.”
D) Evolution
Sars-CoV-2 is constantly evolving. A few considerations.
D1) Future variants will have unpredictable severity
Peter V. Markov, Aris Katzourakis, and Nikolaos I. Stilianakis explain:
The comparatively milder infections with the Omicron variant and higher levels of population immunity have raised hopes for a weakening of the pandemic. We argue that the lower severity of Omicron is a coincidence and that ongoing rapid antigenic evolution is likely to produce new variants that may escape immunity and be more severe.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is set for continuous circulation in humans owing to its ease of transmission, waning immunity, antigenic evolution and an array of potential animal reservoirs1. A key question is predicting the epidemiological and clinical parameters of this continuous circulation2 and the future population burden of coronavirus disease 2019 (COVID-19).
The comparatively milder levels of disease produced by Omicron, the most recent variant of concern (VOC), in relation to previous VOCs rekindled a variety of wishful narratives about the epidemiology and evolution of the virus. These ideas range from misconceived and premature theories about ‘harmless’ endemicity3, to expectations that widespread immunity renders epidemic waves safe and to hopes that the virus will evolve to be benign.
The notion that viruses will evolve to be less virulent to spare their hosts is one of the most persistent myths surrounding pathogen evolution. Unlike viral immune escape and transmissibility, which are under strong evolutionary pressure, virulence is typically a by-product, fashioned by complex interactions between factors in both the host and the pathogen. Viruses evolve to maximize their transmissibility and sometimes this may correlate with higher virulence, for example, if high viral loads promote transmission but also increase severity. If so, pathogens may evolve towards higher virulence. If severity manifests late in infection, only after the typical transmission window, as in SARS-CoV-2, but also influenza virus, HIV, hepatitis C virus and many others, it plays a limited role in viral fitness and may not be selected against. Forecasting virulence evolution is a complex task, and the lower severity of Omicron is hardly a good predictor for future variants. The prospect of future VOCs featuring the potentially disastrous combination of the ability to reinfect due to immune escape along with high virulence is unfortunately very real.
Another common belief banks on widespread vaccine or infection-induced immunity to guarantee mild SARS-CoV-2 infections in the future. This idea, however, ignores a central feature of SARS-CoV-2 biology — antigenic evolution, that is, an ongoing modification of the viral antigenic profile in response to host immune pressures. High rates of antigenic evolution can result in immune escape, that is, reduced capacity of the immune system to prevent reinfection and potentially severe disease thereupon. On a population level, antigenic evolution and escape can increase burden through increasing the rates of reinfections and rates of severe illness (Fig. 1).
As BA.5 and Centaurus are sweeping the world, we have no idea what variant will come next. In all likelihood, Pi will be even more fit than BA.5 and even better at escaping the Great Wall of Immunity.
D2) There is a significant risk of anthroponisis-reverse anthroponisis induced mutations
There is a good discussion about this dynamic in a recent review paper. But unfortunately I can’t find the paper anymore.
In essence, humans can pass on strains of SARS-CoV-2 to wild animals, in which the virus can evolve further, and pass it back on humans again.
D3) Evolutionary pressures in chronic infection might allow a VOC (Variant of Concern) to emerge.
As explained by Harari et al. (2022) in the following Nature Medicine Research Briefing.
From the editor
“The evolutionary origins of SARS-CoV-2 VOCs are unknown, but one possibility is that they emerge in infected and immunocompromised people. Comparing SARS-CoV-2 mutations in globally circulating strains with those of the variants that evolve over time in immunocompromised patients uncovers fascinating hypotheses on the selective pressures driving chronic infection in an individual versus transmission in a population.” Alison Farrell, Senior Editor, Nature Medicine
D4) BA.5: this Omicron sub-variant is the worst version of the virus that we’ve seen
As writes Professor Eric Topol on his substack, Ground Truths. (And see here for Part 2)
The Omicron sub-variant BA.5 is the worst version of the virus that we’ve seen. It takes immune escape, already extensive, to the next level, and, as a function of that, enhanced transmissibility, well beyond Omicron (BA.1) and other Omicron family variants that we’ve seen (including BA.1.1, BA.2, BA.2.12.1, and BA.4). You could say it’s not so bad because there hasn’t been a marked rise in hospitalizations and deaths as we saw with Omicron, but that’s only because we had such a striking adverse impact from Omicron, for which there is at least some cross-immunity (BA.1 to BA.5). Here I will review (1) what we know about its biology; (2) its current status around the world; and (3) the ways we can defend against it.
To recap, BA.5 is quite distinct and very fit
E) Impact
Pandemics take an unequall toll.
E0) Privilege
Having good health is a privilege. As is not being immunocompromised or otherwise vulnerable to respiratory infectious diseases. As are having access to good health care, to high-quality vaccins, to anti-viral drugs and medication. It is a privilege not to suffer from COVID-19 yourself and not to lose a loved one to COVID-19. Being able to self-quarantine and work from home are privileges. And this is just the tip of the privilege iceberg.
Not everyone will have those priviliges. Not caring about those who are less privileged than you is apathetic. Putting vulnerable people at risk because you do not want to take basic precautions can lead to negligent assault and negligent homicide.
E0.1) Vaccine Inequity
As Amy Maxmen notes in her dicussion of the radical plan for vaccine equity :
COVID demonstrated the folly of relying on goodwill & the West.
Nearly 80% of people in rich countries have been vaccinated & fewer than 20% in poor countries. This is cruel AND dumb. Economies are connected. Variants spread.
E1) The Sisyphean cycle of panic and neglect
Another fantastic article by Ed Young.
It’s not just the US. It’s us. Humanity. After a panic phase in which toilet paper sold out, people have now turned to neglect and minimization under the credo of “living with COVID”.
That “the pandemic is over” and that we are now “living with COVID” might be the biggest lie of all. For many, “living with COVID” means “getting disabled by COVID” and “dying of COVID”.
Here is what Eric Topol has to write about COVID capitulation.
E2) Impact on health care systems
The coronavirus pandemic has a major adverse impact on health care systems worldwide. Here is one example recently published in BMJ regarding the UK’s National Health Service.
The NHS is not living with covid, it’s dying from it
The government must be honest about the threat the pandemic still poses
Today may be the most difficult day the NHS has ever experienced. The headlines will focus on the pressures created by the heatwave and that most visible sign of healthcare failure—ambulances queuing outside hospitals.1 But, as readers of The BMJ and HSJ know all too well, this brutal situation is the culmination of many factors, which include but are not limited to prolonged periods of underfunding in the past decade,2 lack of an adequate workforce plan,34 and a cowardly and shortsighted failure to undertake social care reform.5
There is one more problem. Most people (including many in the NHS) are so tired of it that they are wilfully pushing it to the back of their minds, but now is the time to face the fact that the nation’s attempt to “live with covid” is the straw that is breaking the NHS’s back. In 2020 and 2021 the NHS coped with pandemic peaks by stopping or slowing much of its routine work. 2022 was meant to be the year of full speed recovery, when we would build back better and fairer, when record waiting lists in elective care, cancer diagnosis and treatment, and mental health would begin to reduce, and the workload on primary care would begin to ease.
One of the assumptions underpinning this hope was that covid-19 would be nothing more than an irritant for most of the year, with perhaps a winter wave in December. It is now July, and not counting the first omicron surge that peaked in January, the UK and the NHS have experienced two further covid waves,6 with gaps of just under three months between peaks (https://coronavirus.data.gov.uk/). The current wave of hospital admissions78 driven by the BA.4 and BA.5 variants is likely to peak in the next few days, but other variants will be ready for global distribution soon.9
Weekly hospital admissions to English hospitals, for those who test positive for covid-19, have averaged just over 9000 in the first six and half months of the year. In 2021 the number was just under 6000, with most admissions concentrated in the first two months of the year. The average in 2020 was just under 7000.10
The omicron variant is less severe, and just under 40% of hospital patients are being treated “primarily” for the disease.10 But a covid-19 diagnosis is a complicating factor for many conditions, worsening outcomes and lengthening recovery times. The need to keep people with covid-19, uninfected people, and contacts apart means an increase in effort. Higher rates of covid-19 in hospitals and the community also result in more staff sickness, further hollowing out an already overstretched11 and exhausted workforce.12
What the hospital admissions figures hide is a rising tide of people with long covid, now at two million13 and likely to be a major burden on the health service14 and the nation’s productivity, for a generation. And there are many other much less recognised but still deeply disturbing effects of the continuing pandemic, including endangering the NHS’s supply of blood.15
E2.1) Delayed care
As health care systems are strained in caring for COVID-19 patients, delayed and missed health care is a major problem and disease burden.
E2.2) Vaccination backsliding
The COVID-19 pandemic has fueled the largest backslide in vaccinations in three decades.
The largest sustained decline in childhood vaccinations in approximately 30 years has been recorded in official data published today by WHO and UNICEF.
The percentage of children who received three doses of the vaccine against diphtheria, tetanus and pertussis (DTP3) – a marker for immunization coverage within and across countries – fell 5 percentage points between 2019 and 2021 to 81 per cent.
As a result, 25 million children missed out on one or more doses of DTP through routine immunization services in 2021 alone. This is 2 million more than those who missed out in 2020 and 6 million more than in 2019, highlighting the growing number of children at risk from devastating but preventable diseases. The decline was due to many factors including an increased number of children living in conflict and fragile settings where immunization access is often challenging, increased misinformation and COVID-19 related issues such as service and supply chain disruptions, resource diversion to response efforts, and containment measures that limited immunization service access and availability.
“This is a red alert for child health. We are witnessing the largest sustained drop in childhood immunization in a generation. The consequences will be measured in lives,” said Catherine Russell, UNICEF Executive Director. “While a pandemic hangover was expected last year as a result of COVID-19 disruptions and lockdowns, what we are seeing now is a continued decline. COVID-19 is not an excuse. We need immunization catch-ups for the missing millions or we will inevitably witness more outbreaks, more sick children and greater pressure on already strained health systems.”
E3) Poverty
The COVID-19 pandemic alone has driven tens of millions of people into extreme poverty.
The world’s poorest have faced two extraordinarily difficult years. The pandemic has caused unprecedented reversals in poverty reduction that are further exacerbated by rising inflation and the effects of the war in Ukraine. We estimate that these combined crises will lead to an additional 75 million to 95 million people living in extreme poverty in 2022, compared to pre-pandemic projections. If the more pessimistic scenario plays out, 2022 could be the second-worst year in terms of progress made in reducing extreme poverty this century—behind only 2020, when there was an actual increase in global poverty.
F) Bright spots
F1) Increased empathy F2) Vaccines
34.1.2. 2022 Monkeypox virus (MPXV) outbreak
Here is what Wikipedia has to say about the 2022 Monkeypox outbreak.
An ongoing outbreak of monkeypox, a viral disease, was confirmed in May 2022,[5] beginning with a cluster of cases found in the United Kingdom.[6] The first confirmed case was traced to an individual with travel links to Nigeria (where the disease is endemic) and was detected on 6 May 2022.[7] The outbreak marked the first time monkeypox has spread widely outside Central and West Africa. From 18 May onwards, cases were reported from an increasing number of countries and regions, predominantly in Europe but also in North and South America, Asia, Africa, and Australia.[14] As of 23 July, there have been a total of 17,186 confirmed cases.[15] On 23 July, the World Health Organization (WHO) declared the outbreak a Public Health Emergency of International Concern (PHEIC), raising the status of the outbreak to a global health emergency.[16][17]
Monkeypox is a viral infection that manifests a week or two after exposure with fever and other non-specific symptoms, and then produces a rash with blisters that can last for a couple of weeks before usually clearing up.[7] In infections before the current outbreak, 1–3 percent of people with known infections have died (without treatment). Cases in children are more likely to be severe, and health authorities emphasized that anyone can catch the disease, particularly if they have close contact with a symptomatic person.[5][18][19] As of 23 July 2022, 97% of cases outside endemic regions in Africa have occurred in the community of men who have sex with men, especially those who have multiple sex partners.[20] The Centers for Disease Control and Prevention has emphasized the importance of reducing stigma in communicating about the demographic aspects of monkeypox.[21]
A) Warnings
A1) Bunge et al. (2022)
In February 2022, before the May 2022 outbreak started, Bunge et al. warned us that monkeypox was gradually evolving to become of global relevance. They couldn’t have suspected how right they would turn out to be.
Abstract Monkeypox, a zoonotic disease caused by an orthopoxvirus, results in a smallpox-like disease in humans. Since monkeypox in humans was initially diagnosed in 1970 in the Democratic Republic of the Congo (DRC), it has spread to other regions of Africa (primarily West and Central), and cases outside Africa have emerged in recent years. We conducted a systematic review of peer-reviewed and grey literature on how monkeypox epidemiology has evolved, with particular emphasis on the number of confirmed, probable, and/or possible cases, age at presentation, mortality, and geographical spread. The review is registered with PROSPERO (CRD42020208269). We identified 48 peer-reviewed articles and 18 grey literature sources for data extraction. The number of human monkeypox cases has been on the rise since the 1970s, with the most dramatic increases occurring in the DRC. The median age at presentation has increased from 4 (1970s) to 21 years (2010–2019). There was an overall case fatality rate of 8.7%, with a significant difference between clades—Central African 10.6% (95% CI: 8.4%– 13.3%) vs. West African 3.6% (95% CI: 1.7%– 6.8%). Since 2003, import- and travel-related spread outside of Africa has occasionally resulted in outbreaks. Interactions/activities with infected animals or individuals are risk behaviors associated with acquiring monkeypox. Our review shows an escalation of monkeypox cases, especially in the highly endemic DRC, a spread to other countries, and a growing median age from young children to young adults. These findings may be related to the cessation of smallpox vaccination, which provided some cross-protection against monkeypox, leading to increased human-to-human transmission. The appearance of outbreaks beyond Africa highlights the global relevance of the disease. Increased surveillance and detection of monkeypox cases are essential tools for understanding the continuously changing epidemiology of this resurging disease.
Author summary Monkeypox, a zoonotic disease caused by an orthopoxvirus, results in a smallpox-like disease in humans. We conducted a systematic review to assess how monkeypox epidemiology has evolved since it was first diagnosed in 1970 in the Democratic Republic of the Congo. In total, human monkeypox has now appeared in 10 African countries and 4 countries elsewhere. Examples include Nigeria, where the disease re-emerged in the last decade after a 40-year hiatus, and the United States, where an outbreak occurred in 2003. The number of cases has increased at a minimum of 10-fold and median age at presentation has evolved from young children (4 years old) in the 1970s to young adults (21 years old) in 2010–2019. This may be related to the cessation of smallpox vaccinations, which provided some cross-protection against monkeypox. The case fatality rate for the Central African clade was 10.6% versus 3.6% for the West African clade. Overall, monkeypox is gradually evolving to become of global relevance. Surveillance and detection programs are essential tools for understanding the continuously changing epidemiology of this resurging disease.
A2) NTI 2021 Simulation
In March 2021, the Nuclear Threat Initiative (NTI) partnered with the Munich Security Conference to “conduct a tabletop exercise on reducing high-consequence biological threats”. More specifically, they worked out the following exercise scenario:
Exercise Scenario Developed in consultation with technical and policy experts, the exercise scenario portrayed a deadly, global pandemic involving an unusual strain of monkeypox virus that first emerges in the fictional country of Brinia and eventually spreads globally. Later in the exercise, the scenario reveals that the initial outbreak was caused by a terrorist attack using a pathogen engineered in a laboratory with inadequate biosafety and biosecurity provisions and weak oversight. The exercise scenario concludes with more than three billion cases and 270 million fatalities globally. As part of the scenario development process, NTI conducted a virtual consultation with experts in December 2020. (See Appendix A for the list of participating experts.)
The exercise was designed for participants to:
• Discuss requirements for international architectures related to science-based, early assessment of emerging pandemic risks and timely international warning and alerts for potential pandemics.
• Explore conditions that should trigger national pandemic response actions and discuss strategies and challenges for scaling public health interventions.
• Consider options to reduce biotechnology risks and strengthen oversight of dual-use bioscience research.
• Explore opportunities to strengthen international financing mechanisms to bolster global health security preparedness.
Let’s be crystal clear: there is nothing unusual about this, and it should be obvious to anyone with knowledge in the field of misinformation studies that bad actors will use this simulation to fuel their conspiracy theories. I mention the NTI 2021 simulation because (1) it provided an unheeded warning, and (2) it delineates a scenario in which a highly virulent and infectious strain of MPXV causes great harm. Specifically, regarding (1)
Discussion among exercise participants led to the following key findings:
• Weak global detection, assessment, and warning of pandemic risks. The international community needs a more robust, transparent detection, evaluation, and early warning system that can rapidly communicate actionable information about pandemic risks.
• Gaps in national-level preparedness. National governments should improve preparedness by developing national-level pandemic response plans built upon a coherent system of “triggers” that prompt anticipatory action, despite uncertainty and near-term costs—in other words, on a “no-regrets” basis.
• Gaps in biological research governance. The international system for governing dual-use biological research is neither prepared to meet today’s security requirements, nor is it ready for significantly expanded challenges in the future. There are risk reduction needs throughout the bioscience research and development life cycle.
• Insufficient financing of international preparedness for pandemics. Many countries around the world lack financing to make essential national investments in pandemic preparedness.
and regarding (2)
The combined global pandemic leads to more than three billion cumulative cases and more than 270 million deaths by the end of December 2023.
Note however, that the current strains of MPXV are nowhere near as virulent and infectious as those in the NTI-MSC tabletop exercise, as NTI explains:
We also do not believe that the current outbreak has the potential to spread as rapidly as the fictional, engineered pathogen in our scenario or to cause such a high case fatality rate.
A3) Confronting 21st-century monkeypox
This warning is different from those above, as it applies to the present, in which MPXV is a pandemic Emphasis mine.
Monkeypox is a zoonotic disease; thus, another critical step is to greatly reduce transmission of the virus from current rodent reservoirs and to prevent spillovers in areas of the world where monkeypox isn’t endemic. Long-term control of monkeypox will require vaccinating as many as possible of the 327 million people 40 years of age and younger living in the 11 African countries where monkeypox is endemic in an animal (rodent) reservoir. This effort should include childhood vaccine programs. Surveillance will be needed to identify new animal reservoirs, which might be established in other countries as a result of infected humans inadvertently transmitting the virus to domestic rodents that have subsequent contact with wild rodents.
The smallpox eradication program was a 12-year effort that involved 73 countries working with as many as 150,000 national staff. Because of its animal reservoir, monkeypox can’t be eradicated. Unless the world develops and executes an international plan to contain the current outbreak, it will be yet another emerging infectious disease that we will regret not containing.
B) Transmission
As it’s early in the MPXV pandemic, we still do not know everything we need to know about monkeypox transmission. Gould et al. (2022) find widespread surface contamination and positive air samples in occupied patient rooms. Thornhill et al. (2022) find that among 582 patients the vast majority (95%) was suspected to have occurred through sexual transmission, though this might party be explained by sampling bias. (See below for the abstracts of both papers.) The WHO has the following information about case profiles:
The following outputs reflect various demographic characteristics in confirmed monkeypox cases. Note that these data are only derived from detailed case data, and as a result, total numbers of cases and deaths may differ from those reported via aggregate case data where reporting is not fully aligned.
As shown below, and stated previously, the ongoing outbreak is largely developing in MSM (Men who have Sex with Men; defined as homosexual or bisexual males in reporting forms) networks. In the following analyses, we have re-coded men reported as bisexual as MSM. Note that reported sexual orientation does not necessarily reflect who the case has had recent sexual history with nor does it imply sexual activity. Generally, severity has been low, with few reported hospitalisations and deaths:
55.8% (7759/13908) of cases with available data are male, the median age is 36 years (IQR: 31 - 43).
Males between 18-44 years old continue to be disproportionately affected by this outbreak as they account for 43.1% of cases.
Of the 13,933 cases where age was available, there were 84 (0.6%) cases reported aged 0-17, out of which 24 (0.2%) were aged 0-4.
Among cases with known data on sexual orientation, 98.3% (5996/6099) identified as MSM. Of those identified as MSM, 54 / 5996 (0.9%) were identified as bisexual men.
Among those with known HIV status 38.0% (2,352/6,197) were HIV-positive. Note that information on HIV status is not available for the majority of cases, and for those for which it is available, it is likely to be skewed towards those reporting positive HIV results.
322 cases were reported to be health workers. However, most were infected in the community and further investigation is ongoing to determine whether the remaining infection was due to occupational exposure.
Of all reported types of transmission, a sexual encounter was reported most commonly, with 3,603 of 3,939 (91.5%) of all reported transmission events.
Of all settings in which cases were likely exposed, the most common was in party setting with sexual contacts, with 569 of 1,380 (41.2%) of all likely exposure categories.
The WHO urges caution in interpreting proportions:
Note that the proportions shown below should be interpreted with caution. When considering some variables, it is more likely that a yes response will be obtained when compared to a no response after consideration of true proportions of these factors. This is most likely to be true for variables where reported answers can only be yes or no, such as HIV status, health worker status, travel history, hospitalisation, ICU, and death.
Monkeypox leads to lots of surface contamination. (Gould et al. 2022).
Important to note that MPXV is a double-stranded DNA virus. This means it’s inherently more stable than RNA viruses and thus survives longer on fomites. It also (presumably) evolves slowly.
Background An unprecedented outbreak of monkeypox virus (MPXV) infections in non-endemic countries has been recognised since 12 May 2022. More than 6000 cases have been identified globally with more than 1500 in the UK by July 2022. Transmission of MPXV is believed to be predominantly through direct contact with lesions or infected body fluids, with possible involvement of fomites and large respiratory droplets. Importantly, a case of monkeypox in a UK healthcare worker in 2018 was suspected to be due to virus exposure while changing bedding.
Methods We investigated environmental contamination with MPXV from infected patients admitted to isolation rooms in the UK, to inform infection prevention and control measures. Surface swabs of high-touch areas in isolation rooms, of healthcare worker personal protective equipment (PPE) in doffing areas, and from air samples collected before and during bedding change were analysed using MPXV qPCR to assess contamination levels. Virus isolation was performed to confirm presence of infectious virus in key positive samples.
Findings We identified widespread surface contamination (66 positive out of 73 samples) in occupied patient rooms (MPXV DNA Ct values 24·7-38·6), on healthcare worker personal protective equipment after use, and in doffing areas (Ct 26·3-34·3). Five out of fifteen air samples taken were positive. Significantly, three of four air samples collected during a bed linen change in one patient’s room were positive (Ct 32·7-35·8). Replication-competent virus was identified in two of four samples selected for viral isolation, including from air samples collected during the bed linen change.
Interpretation These data demonstrate significant contamination in isolation facilities and potential for aerosolisation of MPXV during specific activities. PPE contamination was observed after clinical contact and changing of bed linen. Additionally, contamination of hard surfaces in doffing areas supports the importance of cleaning protocols, PPE use and doffing procedures.
95% of transmission occurres through sexual activity among MSM (Thornhill et al. 2022):
BACKGROUND Before April 2022, monkeypox virus infection in humans was seldom reported outside African regions where it is endemic. Currently, cases are occurring worldwide. Transmission, risk factors, clinical presentation, and outcomes of infection are poorly defined.
METHODS We formed an international collaborative group of clinicians who contributed to an international case series to describe the presentation, clinical course, and outcomes of polymerase-chain-reaction–confirmed monkeypox virus infections.
RESULTS We report 528 infections diagnosed between April 27 and June 24, 2022, at 43 sites in 16 countries. Overall, 98% of the persons with infection were gay or bisexual men, 75% were White, and 41% had human immunodeficiency virus infection; the median age was 38 years. Transmission was suspected to have occurred through sexual activity in 95% of the persons with infection. In this case series, 95% of the persons presented with a rash (with 64% having <10 lesions), 73% had anogenital lesions, and 41% had mucosal lesions (with 54 having a single genital lesion). Common systemic features preceding the rash included fever (62%), lethargy (41%), myalgia (31%), and headache (27%); lymphadenopathy was also common (reported in 56%). Concomitant sexually transmitted infections were reported in 109 of 377 persons (29%) who were tested. Among the 23 persons with a clear exposure history, the median incubation period was 7 days (range, 3 to 20). Monkeypox virus DNA was detected in 29 of the 32 persons in whom seminal fluid was analyzed. Antiviral treatment was given to 5% of the persons overall, and 70 (13%) were hospitalized; the reasons for hospitalization were pain management, mostly for severe anorectal pain (21 persons); soft-tissue superinfection (18); pharyngitis limiting oral intake (5); eye lesions (2); acute kidney injury (2); myocarditis (2); and infection-control purposes (13). No deaths were reported.
CONCLUSIONS In this case series, monkeypox manifested with a variety of dermatologic and systemic clinical findings. The simultaneous identification of cases outside areas where monkeypox has traditionally been endemic highlights the need for rapid identification and diagnosis of cases to contain further community spread.
34.2. Other current public heatlh emergencies of international concern (PHEICs)
See Wilder-Smith & Osman (2021) for a historic overview of PHEICs.
Key findings: Six events were declared PHEIC between 2007 and 2020: the 2009 H1N1 influenza pandemic, Ebola (West African outbreak 2013-2015, outbreak in Democratic Republic of Congo 2018-2020), poliomyelitis (2014 to present), Zika (2016) and COVID-19 (2020 to present). Poliomyelitis is the longest PHEIC. Zika was the first PHEIC for an arboviral disease. For several other emerging diseases a PHEIC was not declared despite the fact that the public health impact of the event was considered serious and associated with potential for international spread.
34.2.2. Polio
Poliomyelitis has been a PHEIC ever since 2014. Cases of Polio still occassionally occur, also in Western countries, as witnessed by the following recent article from the New York Times.
34.3. Current outbreaks
These include outbreaks among humans that have not been declared a PHEIC by the WHO as well as outbreaks among wildlife.
34.3.1. Severe acute hepatitis of unknown aetiology in children
This is what Wikipedia writes:
In 2022, cases of severe sudden hepatitis of unknown origin in children were reported to the World Health Organization (WHO) from several countries.[1][2] Earlier, in October 2021, a cluster of cases of severe hepatitis of unknown origin were identified at a children’s hospital in the U.S. state of Alabama.[3]
Between 5 April and 26 May 2022, 650 likely cases of acute hepatitis of unknown cause in children have been reported to the WHO.[4] The cause remains unknown, although it is not uncommon for the cause of some hepatitis cases in children to remain unknown.[5]
A recent preprint suggests that the acute hepatitis is caused by adeno-associated virus 2 (AAV2).
Summary paragraph
An outbreak of acute hepatitis of unknown aetiology in children was first reported in Scotland in April 2022.1 Cases aged <16 years have since been identified in 35 countries.2 Here we report a detailed investigation of 9 early cases and 58 control subjects. Using next-generation sequencing and real-time PCR, adeno-associated virus 2 (AAV2), was detected in the plasma of 9/9 and liver of 4/4 patients but in 0/13 sera/plasma of age-matched healthy controls, 0/12 children with adenovirus (HAdV) infection and normal liver function and 0/33 children admitted to hospital with hepatitis of other aetiology. AAV2 typically requires a coinfecting ‘helper’ virus to replicate, usually HAdV or a herpesvirus. HAdV (species C and F) and human herpesvirus 6B (HHV6B) were detected in 6/9 and 3/9 affected cases, including 3/4 and 2/4 liver biopsies, respectively. The class II HLA-DRB1*04:01 allele was identified in 8/9 cases (89%), compared with a background frequency of 15.6% in Scottish blood donors, suggestive of increased susceptibility in affected cases. Acute non-A-E paediatric hepatitis is associated with the presence of AAV2 infection, which could represent a primary pathogen or a useful biomarker of recent HAdV or HHV6B infection. Population and mechanistic studies are required to explore these findings further.
Helen Branswell explains what this means in her article for STAT.
Previously the leading hypothesis was that adenovirus 41, which had been found in a number of the infected children, was causing the liver damage. Adenovirus 41 has been known to trigger liver damage in immunocompromised children, but had never been seen to do so in children with intact immune systems.
But the new studies report finding the presence of something called adeno-associated virus 2 — AAV2 for short — in the blood and in liver tissues from a number of affected children. They also found the children were infected with adenoviruses or herpes viruses.
Adeno-associated virus 2 is what is known as a dependoparvovirus. It cannot replicate in a host’s cells unless another virus is present.
If correct, this theory does not rule out the possibility that adenovirus 41 may have played a role in the cases, said Angela Rasmussen, a virologist at the University of Saskatchewan’s Vaccine and Infectious Disease Organization.
“It suggests that AdV 41 (or another helper virus) is necessary but not sufficient,” she told STAT by email.
“If this is correct,” she added, “you need the combination of all three” — a helper virus, such as adenovirus 41, the adeno-associated virus 2, and the genetic predisposition.
34.3.2. Marburg outbreak in Ghana
In July 2022, an outbreak of Marburg virus disease occurred in Ghana. Two positive cases were reported by Ghana on 8 July. After confirmation by the World Health Organization, it is the first such outbreak in Ghana. Two men aged 26 and 51 years old were infected with the disease and both cases resulted in fatalities.
Containment will be extremely important, as Marburg is both contagious and lethal.
34.3.3. Influenza A virus subtype H5N8
As usual, and for better or worse, we will start by reading what Wikipedia has to say.
In the early 2020s, an ongoing outbreak of avian influenza subtype H5N8 has been occurring at poultry farms and among wild bird populations in several countries and continents, leading to the subsequent cullings of millions of birds to prevent a pandemic similar to that of the H5N1 outbreak in 2008. The first case of human transmission was reported by Russian authorities in February 2021, as several poultry farm workers tested positive for the virus.
The H5N8 avian influenza viruses have been widely circulating in wild birds and are responsible for the loss of over 33 million domestic poultry in Europe, Russia, Middle East, and Asia since January 2020. To monitor the invasion and spread of the H5N8 virus in China, we performed active surveillance by analyzing 317 wild bird samples and swab samples collected from 41,172 poultry all over the country. We isolated 22 H5N8 viruses from wild birds and 14 H5N8 viruses from waterfowls. Genetic analysis indicated that the 36 viruses formed two different genotypes: one genotype viruses were widely detected from different wild birds and domestic waterfowls; the other genotype was isolated from a whopper swan. We further revealed the origin and spatiotemporal spread of these two distinct H5N8 virus genotypes in 2020 and 2021. Animal studies indicated that the H5N8 isolates are highly pathogenic to chickens, mildly pathogenic in ducks, but have distinct pathotypes in mice. Moreover, we found that vaccinated poultry in China could be completely protected against H5N8 virus challenge. Given that the H5N8 viruses are likely to continue to spread in wild birds, vaccination of poultry is highly recommended in high-risk countries to prevent H5N8 avian influenza.
34.3.4. Influenza A virus subtype H5N1
Wikipedia:
2021/2022 outbreaks in Europe/Atlantic flyway
Over the winter of 2021 and 2022 avian flu spread among the population of barnacle geese on the Solway Firth, UK, with estimates of up to a third of the Svalbard population being lost; pink-footed geese were also affected there and it seems carried the virus to new sites in northern Scotland. The disease was confirmed in sandwich terns in South Africa in April 2022. In late spring 2022 avian flu outbreaks affected many species of wild bird in the United Kingdom, with heavy losses reported among seabirds returning to breed at colonies in the Northern Isles and Outer Hebrides, including great skuas (bonxie) for which outbreaks had initially been reported in 2021 (Scotland hosts c. 60% of the world’s breeding population) - the 2022 census on St Kilda showed a 64% decline on 2019 with 106 dead birds recorded so far (to 6 June), gannets (1000+ birds reported dead at the Shetlands’ Hermaness colony alone, where there are around 26,000 breeding pairs), with many more gannets being reported dead at other colonies (Troup Head, Bass Rock, and St Kilda); the range of species also seems to be expanding, with reports for many species of wildfowl, seabirds (auks, terns and gulls) and scavenging species (corvids and raptors).Elsewhere in Europe the virus killed hundreds (574+) of Dalmatian pelicans in Greece, and in Israel around 6000 common cranes were found dead at Hula in December 2021. A report by Scientific Task Force on Avian Influenza and Wild Birds on: “H5N1 Highly Pathogenic Avian Influenza in poultry and wild birds: Winter of 2021/2022 with focus on mass mortality of wild birds in UK and Israel” summarises the situation up to 24 January 2022 and mentions that “H5N8 HPAI is still responsible for poultry and wild bird cases mainly in Asia, H5N1 has now in effect replaced this subtype in Africa and Eurasia in both poultry and wild birds”.
2022 outbreaks in New World
In parallel to above reports, similar outbreaks noted from gannet colonies in Canada, with thousands of birds dead in June 2022, as well as common eiders and great black-backed gulls. Prior to that there were reports of spread in wild birds in over 30 states in the US, including major mortalities in a double-crested cormorant colony in Barrington, Illinois, the virus also spreading to scavengers including three bald eagles in Georgia
Brittney J. Miller writes the following for Nature News:
Why unprecedented bird flu outbreaks sweeping the world are concerning scientists
Mass infections in wild birds pose a significant risk to vulnerable species, are hard to contain and increase the opportunity for the virus to spill over into people.
A highly infectious and deadly strain of avian influenza virus has infected tens of millions of poultry birds across Europe, Asia, Africa and North America. But scientists are particularly concerned about the unprecedented spread in wild birds — outbreaks pose a significant risk to vulnerable species, are hard to contain and increase the opportunity for the virus to spill over into people.
Since October, the H5N1 strain has caused nearly 3,000 outbreaks in poultry in dozens of countries. More than 77 million birds have been culled to curb the spread of the virus, which almost always causes severe disease or death in chickens. Another 400,000 non-poultry birds, such as wild birds, have also died in 2,600 outbreaks — twice the number reported during the last major wave, in 2016–17.
Researchers say that the virus seems to be spreading in wild birds more easily than ever before, making outbreaks particularly hard to contain. Wild birds help to transport the virus around the world, with their migration patterns determining when and where it will spread next. Regions in Asia and Europe will probably continue to see large outbreaks, and infections could creep into currently unaffected continents such as South America and Australia.
34.3.5 Foot and Mouth disease outbreak in Indonesia
Wikipedia:
Having succesfully eradicated in 1986, FMD was again detected in Indonesia in May 2022. The Australian government has offered its assistance but remains unconcerned, considering the risk to the country’s biosecurity to be low. The Department of Agriculture (DAWE) is the responsible body and has been monitoring the situation. DAWE has determined there is only a low risk and has stockpiled vaccines since 2004 anyhow.