New Coronavirus News from 12 Jul 2022

Tour de France: COVID concerns loom [DW, 12 Jul 2022]

by Tom Mustroph

COVID-19 is accompanying the 2022 Tour de France. But if you test positive and have no symptoms you're allowed to ride. This approach has saved the competition, but it's also a medical and social test.

The fear of getting COVID-19 has spread around the peloton at the Tour de France. "Of course you have concerns," Cofidis rider Max Walscheid told DW.

Cofidis team captain Guillaume Martin had to leave the Tour on Sunday after testing positive.
"Bryan Coquard had a positive test before the Tour started so, of course, it goes through your mind. With Coquard it was worse, because the race hadn't even started and so, of course, you worry that all that preparation, the sweat, blood and tears, will suddenly mean nothing before you even start," Walscheid explained.

Compulsory tests on days off
It has been more than a week since the Tour started, and there have been a few but not many cases. On the day off on Monday, anxiety reached a high point because the obligatory tests from the UCI (International Cycling Union) were on the agenda.

"I want to wear the polka dot jersey during the stage and I hope that corona doesn't rule me out," Walscheid's teammate Simon Geschke said.

Other than the fear of actually getting COVID-19, riders are also wary of being ruled out of the race.

Just before the start of the tenth stage on Tuesday, most drivers breathed easy. Team BikeExchange reported however, that Australian Luke Dirbridge was out after a positive test and mild symptoms.

In the UAE team, defending champion Tadej Pogacar had a similar situation as to the one at Cofidis. Ahead of the start, a rider who tested positive was replaced by a rider who had recovered, and in the middle of the race Norwegian Vegard Stake Laengen had to depart because of the virus. Later on, UAE rider George Bennett was ruled out after a positive test.
Lead rider Pogacar was relieved to have tested negative.

"I hope that's it for our team and we're spared all the way until the end," said the Slovenian.

Change of rules
But a lack of clarity remains. Walscheid, who studied medicine before his cycling career, is fearful of more cases during the Tour.

Firstly, because the virus is already in the peloton - there have been positive tests and rider exclusions. Secondly, the UCI changed their coronavirus regulations shortly before the Tour. Whoever tests positive isn't automatically excluded. More important is the decision of the UCI medical director, the Tour's doctor and the team doctor, who decide whether the viral load is small enough for the cyclist to stay in the race.

"We have orientated ourselves with the current situation, the high vaccination rate in the peloton and the less severe process due to the virus variants currently in circulation," UCI President David Lappartient told DW at the Grand Départ.

The decision has been widely well-received by those taking part because the risk of a rider or an entire team being excluded is minimal. The old rules would have seen entire teams removed in the event of two positive cases.

Fear of mini peloton in Paris
"The new rules are good because they remove the possibility of a situation like the one at the Tour de Suisse," Richard Plugge, team manager of Jumbo-Visma, told DW.

"More than 50 riders had to head home because of corona either because they tested positive or because entire teams withdrew out of precaution. For the Tour, that would mean just five cyclists arriving in Paris."

Of course, Plugge cannot rule out that riders in the peloton won't infect each other. They ride too closely together. One is breathing in the air of another.

"It's chaotic out there. It's not easy to pick out whose rear wheel you're following," said Gabriel Rasch, former pro and current sporting director of Team Ineos Grenadiers.

Risk: Air of screaming fans
Even the fear of catching the virus during the race is a concern in the heads of riders.

"Every day there are so many people on the course, especially in the mountains. I like it, the way they scream, but that increases the chances of getting the virus," Pogacar said.

The rules made for the Tour are nevertheless very popular because they make competition possible.

"We don't want to fight against COVID, we want to fight against other riders. COVID is not my biggest rival," Pogacar said.

Plugge, whose team Jumbo-Visma finished second in 2020 and 2021 with Primoz Roglic and Jonas Vingegaard, also doesn't want the Tour to be decided by the virus. The Dutchman even had figures to hand that could give cause for cautious optimism.

"There are lots of big concerts in the Netherlands at the moment. Around 20 percent of people attending have contracted COVID. That is more than a few, but it does mean that 80 percent are not getting infected, so the chances of not getting the virus are really high," he told DW.

"We should currently look at COVID like a flu, of course with all the known precautions regarding hygiene, masks and keeping your distance. But only those who are sick and have symptoms should be excluded. They won't be able to make it over the mountains in that state anyway."

Flu or deadly threat?
With 164 athletes, 450 staff, 480 members of the advertising caravans, around 4,000 journalists and officials, 300 police officers involved in each stage, as well as approximately 28,000 police officers and firefighters on the sidelines, the Tour de France is currently a large-scale test.

It's not just the best rider, climber or sprinter being recorded this year. It's also exploring the theory that COVID-19 is now more like a flu and no longer needs to be countered as if it were a deadly threat.

New Coronavirus News from 3 Aug 2022

Global COVID cases trend down, with surges in Japan, Korea [CIDRAP, 3 Aug 2022]

by Lisa Schnirring

Global COVID-19 cases dropped again last week, as the BA.5-fueled disease burden shifts to some Asian nations, including Japan and South Korea, the World Health Organization (WHO) said in its latest weekly update.

In US developments, the Biden administration today released two new reports on long COVID, one on a research action plan and the other on services and support for people experiencing the long-term effects of the disease.

Cases still high as subvariants increase
After global cases rose through June, COVID activity appears to be declining, with a 9% drop last week compared to the week before, the WHO said. Two regions, however, reported increases, the Western Pacific, where cases rose 20%, and Africa, where illnesses were up 5%.

The WHO has urged caution in interpreting trends based on cases, due to declines in testing and surveillance.

In the Western Pacific region, the highest jumps were in Japan, which reported a 42% increase, and South Korea, which reported a 25% rise compared to the week before.

Japan's cases are averaging more than 200,000 per day, with healthcare systems feeling pressure in some areas, partly due to COVID-19 illnesses in staff, according to the Japan Times. South Korea is reporting more than 100,000 cases a day, the highest since the middle of April, according to the Korea Herald.

In Africa, the biggest proportional increases were reported from Liberia, Seychelles, and Rwanda.

Of more than 6.5 million cases reported to the WHO last week, the five countries with the most cases were Japan, the United States, South Korea, Germany, and Italy.

Deaths were stable last week after rising the previous week, with about 14,000 reported to the WHO, with the United States reporting the most.

The proportions of more transmissible BA.4 and BA.5 Omicron subvariants continue to increase. BA.5 prevalence rose from 63.8% to 69.6%, and BA.4 levels rose slightly, from 10.9% to 11.8%.

Biden administration unveils long-COVID reports
In April, President Joe Biden issued a memorandum calling for two reports in 120 days, both addressing the challenge of long COVID, in which patients infected with SARS-CoV-2 experience symptoms—some serious—for months or even years.

The Department of Health and Human Services (HHS) released the two reports today, one on a research action plan and the other on federal services and support for people with long COVID. HHS Secretary Xavier Becerra, JD, said, "As our nation continues to make strides in the fight against COVID-19, these reports are critical to shine a light on Long COVID’s impact and how to match people to resources."

HHS estimates that 7.7 million to 23 million Americans are experiencing long COVID, and that about 1 million are out of the workforce at any given time, amounting to $50 billion in lost earnings each year.

In other COVID developments:
• President Biden, who is experiencing a rebound after Paxlovid treatment, tested positive for COVID again today for the fifth day in a row, according to a statement from his physician, Kevin O'Connor, DO. He noted that the president has a light cough but finished a light workout today. Biden will continue to isolate and work from the executive residence.
• The European Medicines Agency today recommended that pericarditis and myocarditis be listed as new side effects in the product information for the Novavax COVID-19 vaccine, owing to a small number of reported cases.
• Cattle can occasionally be infected with SARS-CoV-2, though it's not clear if the animals can transmit the virus, German researchers reported in a research letter in Emerging InfectiousDiseases. They based their findings on serology tests from samples from German cattle in late 2021.

Covid cases have halved in three weeks, but a record-breaking wave is expected in the Autumn [iNews, 3 Aug 2022]

By Tom Bawden

Covid cases have tumbled by more than half in just three weeks as the schools holidays and warmer weather mean people spend less time indoors together.

But experts warn that with further record-breaking waves expected in the Autumn and Spring we are still nowhere near witnessing the end of Covid.

Daily Symptomatic infections fell from a record 351,546 cases on 10 July to 164,427 on Monday – a decline of 52 per cent, or 181,455 daily infections, according to the ZOE Covid study app.

The drop was fuelled by the huge number of cases in June and early July which have left far fewer people to infect – with a prior infection thought to offer significant protection against reinfection for around 28 days (and reasonable protection for about 100 days) against the dominant BA.5 variant.

That compares to around 200 days of protection against earlier variants of Covid as BA.5 is better at getting around immunity built up by vaccination and prior infection – meaning it will be even harder to keep a lid on the virus.

“It appears that BA.5 is more resistant to the innate immune response,” said Professor Lawrence Young, a virologist at Warwick University.

“The hope is that that frequent reinfection will continue to provide a wall of immunity that protects from severe disease. Booster jabs, particularly if modified to target omicron, should also provide some protection from infection and transmission.

“But I fear that we will be confronted with new variants over the winter and that the cycle of infection and reinfection will continue for some time – perhaps another couple of years – until we have improved vaccines and better levels of population immunity,” he said.

Professor Karl Friston, a virus modeller at University College London, added: “An increase in the rate at which immunity is lost means that the endemic phase of the pandemic may entail higher levels of circulating virus.”

“This means that ‘getting rid of Covid’ is purely aspirational. The real question is what level of prevalence is tolerable before adjustments to our behaviour are required,” he said.

Professor Friston’s modelling suggests the UK is facing two separate Covid waves in the next eight months that will each see case numbers soaring above anything seen so far in the pandemic.

He predicts that the current decline will continue at a similar rate until early October as the school holidays and warmer weather bring infections down sharply.

This will take cases to a trough in just over two months time, with about 1.5 per cent of the population forecast to be infected at that point, he says.

But, as schools go back and the weather cools, infections will begin to spread more rapidly.
And within a few weeks cases will start shooting up – on or around 6 October – to the point where they hit an unprecedented high in late November, Professor Friston says.

At that point, about eight per cent of the UK population would be infected – compared to about 5.5 per cent during the current record.

While cases will then come down, he forecasts a further wave in March 2023 that will see about 6.5 per cent of the population infected – making it smaller than the expected autumn wave but still bigger than anything seen up to this point.

Simon Williams, of Swansea University, said: “One of the big challenges going forward, especially since the removal of free testing is whether people are able to recognise COVID symptoms – which will help determine what actions they might take to help prevent spreading it on.”

The top five symptoms of the BA.5 Omicron subvariant are sore throat, headache, cough without phlegm, a blocked nose and a runny nose.

Cross-Border Transmissions of the Delta Substrain AY.29 During Tokyo Olympic and Paralympic Games [Front. Microbiology, 3 Aug 2022]

Authored by Takahiko Koyama, Reitaro Tokumasu, Kotoe Katayama, Ayumu Saito,
Michiharu Kudo and Seiya Imoto

Tokyo Olympic and Paralympic Games, postponed for the COVID-19 pandemic, were finally held in the summer of 2021. Just before the games, the Alpha variant was being replaced with the more contagious Delta variant. AY.4 substrain AY.29, which harbors two additional characteristic mutations of 5239C > T (NSP3 Y840Y) and 5514T > C (NSP3 V932A), emerged in Japan and became dominant in Tokyo by the time of the Olympic Games. Variants of SARS-CoV-2 genomes were performed to extract AY.29 Delta substrain samples with 5239C > T and 5514T > C. Phylogenetic analysis was performed to illustrate how AY.29 strains evolved and were introduced into countries abroad. Simultaneously, ancestral searches were performed for the overseas AY.29 samples to identify their origins in Japan using the maximum variant approach. As of January 10, 2022, 118 samples were identified in 20 countries. Phylogenetic analysis and ancestral searches identified 55 distinct introductions into those countries. The United States had 50 samples with 10 distinct introductions, and the United Kingdom had 13 distinct strains introduced in 18 samples. Other countries or regions with multiple introductions were Canada, Germany, South Korea, Hong Kong, Thailand, and the Philippines. Among the 20 countries, most European and North American countries have vaccination rates over 50% and sufficient genomic surveillances are conducted; transmissions seem contained. However, propagation to unvaccinated regions might have caused unfathomable damages. Since samples in those unvaccinated countries are also undersampled with a longer lead time for data sharing, it will take longer to grasp the whole picture. More rigorous departure screenings for the participants from the unvaccinated countries might have been necessary.

New Coronavirus News from 27 Jul 2022

New studies suggest Covid-19 likely originated from Wuhan wet market [CNN, 27 Jul 2022]

By Jen Christensen
(CNN)In June, the World Health Organization recommended that scientists continue to research all possible origins of the Covid-19 pandemic, including a lab leak. Two newly published studies take totally different approaches but arrive at the same conclusion: The Huanan Seafood Market in Wuhan, China, was most likely the epicenter for the coronavirus.
The studies were posted online as preprints in February but have now undergone peer review and were published Tuesday in the journal Science.

In one, scientists from around the world used mapping tools and social media reports to do a spatial and environmental analysis. They suggest that although the "exact circumstances remain obscure," the virus was probably present in live animals sold at the market in late 2019. The animals were held close together and could easily have exchanged germs. However, the study does not determine which animals may have been sick.

The researchers determined that the earliest Covid-19 cases were centered at the market among vendors who sold these live animals or people who shopped there. They believe that there were two separate viruses circulating in the animals that spilled over into people.

"All eight COVID-19 cases detected prior to 20 December were from the western side of the market, where mammal species were also sold," the study says. The proximity to five stalls that sold live or recently butchered animals was predictive of human cases.

"The clustering is very, very specific," study co-author Kristian Andersen, a professor in the Department of Immunology and Microbiology at Scripps Research, said Tuesday.

The "extraordinary" pattern that emerged from mapping these cases was very clear, said another co-author, Michael Worobey, department head of Ecology and Evolutionary Biology at the University of Arizona.

The researchers mapped the earliest cases that had no connection to the market, Worobey noted, and those people lived or worked in close proximity to the market.

"This is an indication that the virus started spreading in people who worked at the market but then started that spread ... into the surrounding local community as vendors went into local shops, infected people who worked in those shops," Worobey said.

The other study takes a molecular approach and seems to determine when the first coronavirus infections crossed from animals to humans.

The earliest version of the coronavirus, this research shows, probably came in different forms that the scientists call A and B. The lineages were the result of at least two cross-species transmission events into humans.

The researchers suggest that the first animal-to-human transmission probably happened around November 18, 2019, and it came from lineage B. They found the lineage B type only in people who had a direct connection to the Huanan market.

The authors believe that lineage A was introduced into humans from an animal within weeks or even days of the infection from lineage B. Lineage A was found in samples from humans who lived or stayed close to the market.

"These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported," the study says. "As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events."

The likelihood that such a virus would emerge from two different events is low, acknowledged co-author Joel Wertheim, an associate adjunct professor of medicine at the University of California, San Diego.

"Now, I realize it sounds like I just said that a once-in-a-generation event happened twice in short succession, and pandemics are indeed rare, but once all the conditions are in place -- that is a zoonotic virus capable of both human infection and human transmission that is in close proximity to humans -- the barriers to spillover have been lowered such that multiple introductions, we believe, should actually be expected," Wertheim said.

Andersen said the studies don't definitively disprove the lab leak theory but are extremely persuasive, so much so that he changed his mind about the virus' origins.

"I was quite convinced of the lab leak myself, until we dove into this very carefully and looked at it much closer," Andersen said. "Based on data and analysis I've done over the last decade on many other viruses, I've convinced myself that actually the data points to this particular market."

Worobey said he too thought the lab leak was possible, but the epidemiological preponderance of cases linked to the market is "not a mirage."

"It's a real thing," he said. "It's just not plausible that this virus was introduced any other way than through the wildlife trade."

To reduce the chances of future pandemics, the researchers hope they can determine exactly what animal may have first become infected and how.

"The raw ingredients for a zoonotic virus with pandemic potential are still lurking in the wild," Wertheim said. He believes the world needs to do a much better job doing surveillance and monitoring animals and other potential threats to human health.

Andersen said that although we can't prevent outbreaks, collaboration between the world's scientists could be key to the difference between a disease with a small impact and one that kills millions.

"The big question we need to ask ourselves is -- the next time this happens, because it will happen -- how do we go from detecting that outbreak early and preventing that outbreak so it doesn't become a pandemic?"

Scientists hone argument that coronavirus came from Wuhan market [The Washington Post, 27 Jul 2022]

By Joel Achenbach

The coronavirus pandemic began in separate viral spillovers — at least two but perhaps as many as two dozen — from live animals sold and butchered in late 2019 at the Huanan Seafood Market in Wuhan, China, according to two papers published Tuesday in the journal Science.

The publication of the papers, which underwent five months of peer review and revisions by the authors, is unlikely to quell the rancorous debate about how the pandemic began and whether the virus emerged from a Chinese laboratory. And the authors acknowledge there are many unknowns requiring further investigation — most notably, which animals were involved.

“Everything upstream of this — which animals, where did they come from, how it’s all connected — is completely unknown at this stage,” Kristian Andersen, an immunologist at Scripps Research, said in a media briefing Tuesday.

“Have we disproven the lab leak theory? No, we have not. Will we ever be able to? No. But there are ‘possible’ scenarios and there are ‘plausible’ scenarios. … ‘Possible’ does not mean equally likely,” Andersen said.

A natural origin of the pandemic — a “zoonosis” — has long been a favored theory among scientists for the simple reason that most pandemics, including the SARS coronavirus outbreak of 2002-2003, have started that way. Andersen and his colleagues believe multiple lines of evidence, including the clustering of early cases of covid-19 around the market, make a market origin not only a likely scenario but the only one that fits the data.

The “lab leak” conjecture was initially dismissed in most mainstream media as a conspiracy theory. There are numerous lab leak scenarios, and many have focused on the Wuhan Institute of Virology, a major research center that studies coronaviruses.

Scientists there say they never had the virus in their laboratory. But outside experts questioned whether the laboratory adhered sufficiently to safety measures when researching viruses. Chinese authorities limited access to the laboratories by outside investigators.
Amateur sleuths created online communities that steadily raised suspicions about a possible lab leak. Pressure to investigate the hypothesis came amid the struggles of the scientific community to nail down how the virus entered the human population.

In May 2021, the journal Science published a letter from 18 scientists calling for an investigation into the virus’s origin that would include exploration of the lab leak theory. Soon after that, President Biden asked his intelligence agencies to investigate all possible origins of the pandemic. The review concluded that the virus was not an engineered bioweapon, but otherwise failed to reach a conclusion about where it came from.

Among the scientists who signed the letter to Science was Michael Worobey, an evolutionary virologist at the University of Arizona who felt the lab leak thesis deserved attention even if it wasn’t the most likely origin. But Worobey soon became convinced that the virus came out of the market. Worobey is the lead author of the new paper that contends the market was the pandemic’s epicenter.

The researchers scoured data about the earliest patients, many of whom had direct links to the market or lived nearby. The geography of early community spread showed infections radiating outward from the vicinity of the market, Worobey said: “It’s an insane bull’s eye.”

Moreover, when the market was first identified as the site of a cluster of cases, Chinese investigators took environmental samples searching for traces of the virus. A disproportionate number of positive virus traces came from the section of the market where live animals had been sold, the new study reports.

“The virus started spreading in people who worked at the market, but then started spreading in the surrounding local community as vendors went to local shops, and infected people who worked in those shops,” Worobey suggested.

Worobey is not new to this issue. Last year, he wrote a “Perspective” article in Science that said the geographical clustering of cases in and around the market could not be explained away as “ascertainment bias,” meaning the clustering was not simply the result of investigators knocking on doors in that area after the market outbreak was detected.

He believes any alternative scenario — such as a lab leak — is implausible.

“It now puts us at a point where we know that the Huanan market was the epicenter of this pandemic. That much is now established. If others want to argue with that, they’re now essentially taking a pseudoscientific approach,” Worobey said in an interview Tuesday. “Even though you don’t have the smoking gun of, ‘Yes we’ve sampled the raccoon dog with the virus in December,’ when you put it all together, it’s the only theory that actually explains all the data.”

Angela Rasmussen, a virologist at the University of Saskatchewan and co-author of one of the new papers, said in an email that she agreed with Worobey: “There is no alternative explanation that fits the facts, so anyone trying to come up with one will have to become adept at willful ignorance, a logical contortionist, or simply a fabulist.”

The contention by the authors of a natural origin of the pandemic is not new: The same two papers in an earlier form were posted online in February on a “preprint” site. But at that point, they existed in peer-review limbo — something that could be reported in a news story but lacking the stature of studies that have survived scrutiny by knowledgeable outsiders and journal editors.

The second paper published Tuesday in Science reports that genetic evidence and computer modeling suggest the virus spilled into the human population not just once, but on multiple occasions in late 2019. Genomic analysis of early cases shows two distinct lineages, called A and B, that had to have come from separate spillovers. Both lineages were found in environmental samples taken in the market, according to a preprint paper from Chinese researchers in February.

Promoters of the lab leak theory counter that the market was more likely a superspreader site. The virus could have been brought there by someone infected at a laboratory, or someone exposed to an infected lab worker, for example.

The argument for a market origin also relies on Chinese data that may be unreliable, Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Institute, said in an interview earlier this year. He said he feels the data are “inconclusive.”

“I feel the data released by the Chinese government should be treated with a healthy grain of salt,” Bloom said.

There is no proof that the virus or its immediate ancestor was in any laboratory before the outbreak in Wuhan. But the ongoing mystery of the pandemic’s origin has called attention to the kind of research on viruses — including “gain of function” experiments — that some critics say is too risky. The U.S. National Institutes of Health, immersed in the controversy because it helped fund some research at the Wuhan Institute of Virology, this year said it was reviewing its policies for ensuring laboratory safety and security.

Sen. Rand Paul (R-Ky.), who favors a laboratory origin explanation, said at an April 30 rally in Kentucky that if Republicans take power in the Senate after the midterm elections, he will use subpoena power to “get to the bottom of where this virus came from.”

Chinese scientists have denied that the virus was present in their lab. The virus, according to Andersen and other virologists who have studied it, does not appear to be manipulated or engineered, and its genetic features could have been produced through evolution.

Still, the controversy about coronavirus research is not likely to fade.

Jeffrey Sachs, a Columbia University economist, heads a commission sponsored by the Lancet journal expected to produce a report this fall on the pandemic, including the origin of the virus.
He recently co-authored an article in the Proceedings of the National Academy of Sciences calling for a probe of the pandemic origin through a “bipartisan congressional inquiry with full investigative powers.”

On Tuesday, after Science published the two papers, Sachs said in an email that he still favors the lab leak theory: “The two competing hypotheses, natural spillover and laboratory creation, are both viable. They should be compared directly against each other. In my view, the laboratory creation hypothesis is the more straightforward and more credible.”

The new papers do not declare “case closed” but are useful, noted David Relman, a professor of medicine and microbiology at Stanford University who was among the signers of the 2021 letter to Science calling for a probe of all possible pandemic origins. He said he would like to see a similarly thorough forensic study of the lab leak hypothesis.

“I don’t think we can say that we now know that it started here. I think we can say that something interesting happened in this part of the city,” Relman said. “We don’t have any [coronavirus] positive animals at the market.”

Andersen, the Scripps Research scientist, has been entangled in the virus origin controversy for more than two years. He was lead author of an early paper, published in Nature Medicine, saying the virus was clearly not engineered. But his first impression of the virus had been that it looked unnatural, and only after doing more research did he conclude that its features could have been produced through evolution.

On Tuesday, Andersen reiterated that he initially thought the novel coronavirus probably came from a laboratory. But all signs now point to the market, he said.

“It’s not a formal proof, again, but it is so strong in my opinion that any other version, a lab leak for example, would have to be able to explain all this evidence,” he said. “It’s just not plausible.”

New Coronavirus News from 26 Jul 2022

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 [Science, 26 Jul 2022]

Authored by JONATHAN E. PEKAR, ANDREW MAGEE, EDYTH PARKER NIEMA MOSHIRI, KATHERINE IZHIKEVICHJENNIFER L. HAVENS, KARTHIK GANGAVARAPU, LORENA MARIANA MALPICA SERRANO, ALEXANDER CRITS-CHRISTOPHNATHANIEL, L. MATTESONMARK ZELLERJOSHUA, I. LEVY, JADE C. WANG, SCOTT HUGHESJUNGMIN LEE, HEEDO PARK, MAN-SEONG PARK , KATHERINE ZI YAN CHING, RAYMOND TZER PIN LIN, MOHD NOOR MAT ISA, YUSUF MUHAMMAD NOOR, TETYANA I. VASYLYEVA, ROBERT F. GARRY, EDWARD C. HOLMES, ANDREW RAMBAUT, MARC A. SUCHARD, KRISTIAN, G. ANDERSEN, MICHAEL WOROBEY AND JOEL O. WERTHEIM

Abstract
Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October–8 December), while the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.