Virus World
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Virus World
Virus World provides a daily blog of the latest news in the Virology field and the COVID-19 pandemic. News on new antiviral drugs, vaccines, diagnostic tests, viral outbreaks, novel viruses and milestone discoveries are curated by expert virologists. Highlighted news include trending and most cited scientific articles in these fields with links to the original publications. Stay up-to-date with the most exciting discoveries in the virus world and the last therapies for COVID-19 without spending hours browsing news and scientific publications. Additional comments by experts on the topics are available in Linkedin (https://www.linkedin.com/in/juanlama/detail/recent-activity/)
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Analysis of SARS-CoV-2 Mutations in the United States Suggests Presence of Four Substrains and Novel Variants

Analysis of SARS-CoV-2 Mutations in the United States Suggests Presence of Four Substrains and Novel Variants | Virus World | Scoop.it

SARS-CoV-2 has been mutating since it was first sequenced in early January 2020. Here, we analyze 45,494 complete SARS-CoV-2 geneome sequences in the world to understand their mutations. Among them, 12,754 sequences are from the United States. Our analysis suggests the presence of four substrains and eleven top mutations in the United States. These eleven top mutations belong to 3 disconnected groups. The first and second groups consisting of 5 and 8 concurrent mutations are prevailing, while the other group with three concurrent mutations gradually fades out. Moreover, we reveal that female immune systems are more active than those of males in responding to SARS-CoV-2 infections. One of the top mutations, 27964C > T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we uncover that two of four SASR-CoV-2 substrains in the United States become potentially more infectious. Rui Wang et al. report a comprehensive analysis of nearly 13,000 SARS-CoV-2 genome sequences isolated from patients in the United States, comprising more than 7000 single mutations. They show that SARS-CoV-2 genomes cluster into four distinct groups and that two of these groups are potentially more infectious, underlining the urgent need for viral control strategies in the US.

 

Findings Published in Communications Biology (Feb. 15, 2021):

https://www.nature.com/articles/s42003-021-01754-6

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Some People Can Get the Pandemic Virus Twice, a Study Suggests. That is No Reason to Panic

Some People Can Get the Pandemic Virus Twice, a Study Suggests. That is No Reason to Panic | Virus World | Scoop.it

A man in Hong Kong was found to be reinfected with COVID-19, but what that means for vaccines and immunity is unclear. Scientists have found the first solid evidence that people can be reinfected with the virus that causes COVID-19. A new study shows a 33-year-old man who was treated at the hospital for a mild case in March harbored the virus again when he was tested at the Hong Kong airport after returning from Europe on 15 August, less than 5 months later. He had no symptoms this time. Researchers had sequenced the virus, SARS-CoV-2, from the first infection; they did so again after the patient’s second diagnosis and found numerous differences between the two, bolstering the case that the patient had been infected a second time. “This case proves that at least some patients do not have life-long immunity,” Kelvin To, a clinical microbiologist at the University of Hong Kong (HKU) and one of the authors of a paper on the case, told Science today. Exactly what that finding means is unclear, however. To and his colleagues make some sweeping statements in their paper, parts of which Science has seen. “It is unlikely that herd immunity can eliminate SARS-CoV-2,” the authors write, referring to the idea that the epidemic will peter out once enough people have been infected and become immune. “Second, vaccines may not be able to provide life-long protection against COVID-19.”

 

But it’s too early to draw those conclusions, says Columbia University virologist Angela Rasmussen. “I disagree that this has huge implications across the board for vaccines and immunity,” she wrote in an email, because the patient described in the study may be a rare example of people not mounting a good immune response to the first infection. Mark Slifka, a viral immunologist at Oregon Health & Science University, says his takeaway from the paper is the opposite of what the authors write: “Even though [the patient] got infected with a very different strain that’s distinct from the first time around, they were protected from disease,” he says. “That is good news.” Fueling the debate over the importance of the case is that the paper on it isn’t public yet, which means scientists can’t scrutinize its data in full. HKU put out a press release about the study today and said the paper had been accepted for publication by the journal Clinical Infectious Diseases. To confirmed that a few pages of the manuscript circulating online were from the paper but said he could not make the full text available. “This is why I loathe data disclosure by press release,” Rasmussen wrote. “It seems designed to stoke sensationalism by leaving all these provocative questions unanswered, some of which could probably be answered by just reading the paper and examining the figures.” There have been several reports of COVID-19 patients testing positive for SARS-CoV-2 again after apparently clearing their infection, but in those cases there was less time between the tests and researchers did not have sequences of the viruses to confirm there were two different infections. Many of these cases were likely testing errors, says Jeffrey Barrett, a genomic epidemiologist at the Wellcome Sanger Institute: “I wasn’t convinced by any of them.” 

 

In the current case, the press release and paper excerpts say, the HKU scientists found 24 differences between the first and second viral genome, including one in the first virus that truncates a gene known as ORF8. “There’s sort of no chance that it’s the same infection twice,” Barrett says. “It is much more convincing than any other anecdotal reports that have come out so far,” agrees virologist Charlotte Houldcroft of the University of Cambridge. Even if the finding settles the question of whether people can be reinfected with the pandemic virus, it raises many additional questions: How often does this happen? Do people have milder infections, or no symptoms at all, the second time around? Can they still infect others? If natural infection does not always confer solid protection, will that be true for vaccines as well? To says he believes reinfections are not rare—just difficult to find. “This case is very special because he was screened at the airport,” he says. “Under normal circumstances, he may not even have been aware that he was infected again.” If reinfections are more likely to lead to asymptomatic cases, To notes, they may be tougher to spot. In a press conference on Monday morning, epidemiologist Maria Van Kerkhove of the World Health Organization warned against jumping to conclusions. “We need to look at this at a population level,” she said. Given that there have been more than 24 million reported SARS-CoV-2 infections worldwide, a single reinfection report may signal a very rare event, Barrett says. “Biology is complicated. You always find some strange exceptions.” He hopes efforts like the COVID-19 Genomics UK Consortium, which is sequencing viral samples from tens of thousands of patients, will provide data on how often reinfection occurs. Houldcroft says studies in health care workers may be key, because they are most likely to be exposed repeatedly....

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