6,000-plus tests bring down Covid positivity ratio in Pakistan

NIH data shows 87 infections: Chinese researchers release genomic data that could help clarify origin of Covid-19 pandemic

April 1, 2023 10:34 AM

Pakistan has diagnosed 87 more Covid-19 infections with no fatality but the daily number of test have crossed 6,000 mark during the last 24 hours (Friday), showed the statistics released by the National Institute of Health (NIH) on Saturday morning, reported 24NewsHD TV channel.

According to the NIH data, the death toll in the country remained the same at 30,649 whereas the number of total infections now went up to 1,579,704 after adding the fresh 87 cases.

During the last 24 hours (Friday), 6,011 tests as compared to previous day’s 4,639 were conducted throughout Pakistan whereas the positivity ratio stood at 1.45%. The number of patients in critical care stood at 25.

China releases genomic data that could help clarify origin of Covid-19 pandemic

In the face of intense pressure and criticism from many in the scientific community, Chinese researchers have released a trove of new genetic data that may offer fresh clues to the origin of the Covid-19 pandemic. They also substantially revised a related study they first posted online 13 months ago to include this evidence, which some scientists say gives more credibility to the thesis that SARS-CoV-2 could have jumped into humans from raccoon dogs or other mammals illegally sold at a Wuhan market.

The Chinese team’s initial preprint argued that the market data, consisting of genetic sequences found in 923 samples collected in or near the market in early 2020, “highly suggests” humans brought the coronavirus there--and made no mention of evidence showing that SARS-CoV-2 susceptible mammals were present. Their updated preprint acknowledges the genetic evidence of the animals and now says the collected samples don’t resolve whether infected animals or humans, or even contaminated food, introduced the virus into the market, where the first cluster of COVID-19 cases surfaced.

“I'm pleased that the data have been updated and made available on different platforms and that [the researchers] have made their updated manuscript available on a preprint server,” says Maria Van Kerkhove, an epidemiologist at the World Health Organization (WHO) who last week urged the Chinese group to share the market data after another research team stumbled on some of it. “I reiterate that any and all data related to the origins of SARS-CoV-2 needs to be made available immediately.”

Written by researchers primarily affiliated with the Chinese Center for Disease Control and Prevention (CCDC), the preprint focuses on “environmental samples”—from drains, containers, tables, doors, the ground—that the authors took at the Huanan Seafood Wholesale Market in January to March of 2020. After COVID-19 cases began popping up there in December 2019, the market was quickly shut down by Chinese authorities on 1 January 2020. Initially, CCDC researchers, including preprint co-author George Gao (who then headed the agency), said they suspected animals at the market triggered the outbreak. But they later denied that the market sold illegal mammals, arguing that imported fish or people from other countries brought the virus there.

The CCDC preprint was posted in February 2022 on Research Square, which hosts papers under review at the Nature family of journals. It did not discuss any sequences of wildlife found at the market and concluded that “no animal host of SARS-CoV-2 can be deduced.” Outside China, questions swirled around yet another possibility: That the virus was brought to the market by an infected person after it somehow leaked from the relatively nearby Wuhan Institute of Virology, which has a longstanding effort to study coronaviruses found in bats.

Now Gao and his co-authors have made a great deal more of their data available on databases including GISAID, which many researchers use to share genetic sequences of SARS-CoV-2. In their revised preprint, which they posted on 29 March on the server ChinaXiv, they note that “environmental samples showed the abundance of different vertebrata genera.” Some of these same samples also had traces of SARS-CoV-2. However, “[T]hese environmental samples cannot prove the infection of the animals,” caution Gao, William Liu, Guizhen Wu, and their co-authors.

“Furthermore, even if the animals were infected, it could not still rule out that the human-to-animal transmission occurred, considering the sampling time was at least one month after the human-to-human transmission within the market. Thus, the possibility of potential introduction of the virus through human or cold chain product into the market cannot yet be ruled out,” they conclude.

Greg Tucker-Kellogg, a systems biologist at the National University of Singapore who thinks infected animals sparked the pandemic, says the revised preprint makes clear that Chinese authorities who insisted that the market did not sell wildlife “were not being truthful—ever” and that there was “no remotely adequate effort that we know of” to trace those wildlife back to their sources.  Even with this update, he adds, “there is still a lot of essential data that we don't now have.”

The genetic sequences from the Wuhan market took an unusual journey into the spotlight. Florence Débarre, an evolutionary biologist at the French national research agency, CNRS, was surprised to find a subset of the data 3 weeks ago while combing through GISAID. When she collaborated with a team of scientists from outside of China to analyze the sequences, they found the evidence that the market had the mammals, which they took to WHO. The finding first became public on 16 March in an Atlantic story titled “The Strongest Evidence Yet That an Animal Started the Pandemic.”

Explaining that they did not want to scoop a journal publication by Chinese researchers, Débarre and her colleagues posted a report online on 20 March that analyzed the data but did not provide the sequences. A miniflap erupted with GISAID, which temporarily suspended their access, asserting that the team had violated the database’s terms of access. But GISAID restored the access when the group provided evidence of having offered to collaborate with the Chinese researchers.

For several of Débarre’s collaborators, the new data simply add support to what they consider even more compelling evidence of a market origin, which they published in papers in the 26 July 2022 Science (here and here). But Joel Wertheim, an evolutionary biologist at the University of California, San Diego, who co-authored the 20 March report with Débarre, says he is “thrilled” the data are now publicly available. “The data are exceptionally valuable for further understanding the origins of the COVID-19 pandemic,” Wertheim says. “Better late than never.

But he remains “befuddled” by how the Chinese authors do not see that their evidence supports an animal origin. Michael Worobey, an evolutionary biologist who is also a co-author on the analysis, suggests it may be possible to find farms that raised the animals sold at the market 3 years ago and still find evidence of SARS-CoV-2 there--“perhaps even dig up pits where I suspect many animals were buried in early 2020 when farms were rapidly liquidated,” he wrote in a tweet.

Marietjie Venter, a virologist at the University of Pretoria who heads WHO’s Scientific Advisory Group for the Origins of Novel Pathogens (SAGO), agrees the new data open up important avenues to explore. "The SAGO encourages the China CDC to investigate the upstream source of these animals at the markets and vendors that were present at the time,” Venter says.

The Chinese researchers close their revised preprint the same way they did the original: “Definitely, more work involving international coordination is needed to investigate the potential origins of SARS-CoV-2.”–

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