Current COVID-19 infections include worrying future variants

Whole-genome sequencing of 140 COVID samples from individuals infected between April 2020 and August 2021 showed infectious signatures consistent with the dominant strain at the time represented by different colored partitions. I’m here. Each horizontal line represents a sequenced sample, with lineage-specific positions displayed vertically. Credit: Ernest (Ricky) Chan

Today the question is not so much “Have you ever had COVID-19?” but rather “Do you know which variant you have been infected with?” If you weren’t infected early in the pandemic, you may be able to guess which variant found you, as researchers have found and reported massive surges.

But now, researchers at Case Western Reserve University (CWRU) say it’s not so black and white. They used gene sequencing to show that among 360 patients, all infections contained multiple variants of his SARS-CoV-2. More importantly, they found that genetic mutations observed at low frequency in older infections mutated into new strains responsible for later surges in infections.

Ernest (Ricky) Chan said: At the Case Western Reserve School of Medicine he is Director of Bioinformatics His Core at the Cleveland Institute for Computational Biology.

According to their paper published in PLOS Geneticsthe CWRU team performed complete genome sequencing of the SARS-CoV-2 virus from 250 patients in northeastern Ohio and another 110 with complete gene sequences of the infectious virus provided by research collaborators. We used similar data from patients with

These data were developed early in the COVID-19 pandemic, where alpha and then delta variants were of great concern. The study suggests that mutations found in Omicron BA.1 and BA.2 have made Omicron and its repeats a worrying subspecies, leading to a major resurgence of COVID-19 last winter at least a year ago. showed that it already existed as a relatively small mutation.

While the research team recognizes the importance of focusing on the majority variant for the development of effective diagnostics, therapeutics, and vaccines, it is important to the research community that the We strongly urge you to quantify and report variants for this purpose.

For example, their study pinpointed two individuals who carried a B.1.1.7/B.1.617.2 co-infection in mid-May 2021. The collection of these samples is from Ohio B. 1.617.2 is present in the Cleveland area, where the city lifted its civil emergency declaration (May 28, 2021) and the state imposed masking mandates and social distancing orders. It happened when I withdrew (June 2, 2021).

“Transferring knowledge of B.1.617.2 transmission and transmission in Cleveland before easing mitigation measures may have contributed to a more prudent public health strategy,” the study authors explained. I’m here.

During gene sequencing, the researchers observed numerous examples of alternative alleles that did not clear the 50% threshold for inclusion in the conventional consensus sequence, but there were concerns, including multiple Omicron strains. is now a variant.

“These observations suggest that minority alleles in previous SARS-CoV-2 infections may contribute to the continued evolution of worrying new variants. To confirm this, a broader genome-wide analysis of SARS-CoV-2 should consider minor alternative alleles, as proposed,” the authors wrote in a recently published paper. I’m here.

Finally, the authors point out that SARS-CoV-2 is not the only case of underreported genetic diversity. They say it occurs with most, if not all, infectious agents. Yersinia pestisMarburg virus, Ebola virus, malaria parasite When Mycobacterium tuberculosis.

“Appropriately addressing the under-reporting of the complexity of infectious diseases represented by data repositories would be a major change in the very important characteristics of infectious diseases, including the assessment of drug treatment efficacy and resistance, and vaccine escape.” It has potential,” the study authors conclude.