Learning from the past to improve SARS-CoV-2 variant discovery

Many researchers have taken the initiative to collect circulating SARS-CoV-2 sequence data from patient samples, even in the early stages of the SARS-CoV-2 pandemic. This collection of data is an important resource for monitoring viral evolution, or how viruses change over time, and the kinetics of global viral spread of new variants. Dr. Lu Ping Zhao and his collaborator at Fred Hutchinson Cancer Center, Dr. Peter Gilbert, Margaret Madeleine, Dan Geraghty, Keith JeromeWhen Larry Corey, employed a retrospective approach that applied novel strategies to collected sequencing data to identify times when SARS-CoV-2 Omicron variants may have been identified as variants of concern (VOCs). This study analyzed global sequence data submitted to the Global Initiative for Sharing Avian Influenza Data (GISAID). Their findings show that using a new method developed by a collaborative team of researchers, SARS-CoV-2 Omicron was classified as a VOC 22 days earlier than the declaration made on November 30, 2021. This suggests that it may have been predict.Their work was recently published JAMA network open.

The SARS-CoV-2 Omicron will organize each patient sample into a SARS-CoV-2 “family tree” to create VOCs and VOCs based on a phylogenetic approach that classifies viral sequences based on nucleotide and insertional or deletional mutations. was considered. One of the challenges of this approach is the inability to quickly update or modify phylogenetic designations to distinguish new variants. The researchers hypothesized that this delay could be reduced by incorporating a statistical learning strategy (SLS) into the sequence analysis pipeline. This approach identified her SARS-CoV-2 sample of a patient with 10 or more mutations and quantified the frequency of these variants within the sampled global population over time to determine if these variants were present in the local population. Determines if it is expanding within.

To explore this approach, researchers retrospectively applied SLS to SARS-CoV-2 genome sequence data collected from people over a two-year period (January 2020-2022). In total, her 63,000 patient samples from Africa and 530,000 patient samples from the United States were included in the analysis.From sequence data, researchers identified a qualifying SARS-CoV-2 Omicron variant predecessor, a variant characterized by 12 of the 28 Omicron core mutations in the virus. spike Genes, from patient samples collected in South Africa with a submission date of 31 December 2020. Her next Omicron case within South Africa occurred in September 2021 and included a variant with all 28 core Omicron mutations. Furthermore, from their analysis, they estimated that his Omicron caseload rate (OCP) or Omicron variant frequency reached 10% in South Africa by 4 November 2021. This threshold for his Omicron cases in the region was met about 300 days after the Omicron outbreak. The predecessor of Omicron. The next day, the Omicron variant quickly became dominant in South Africa (75% of the SARS-CoV-2 sequence on 18 November 2021) and other African countries. Therefore, the authors suggested that if a viral variant exceeded his OCP threshold of 10%, it might be called a VOC. Such frequencies suggest rapid local expansion, as they tend to be the dominant variant circulating in local populations where they can spread.

When Omicron was declared a VOC on November 30, 2021, no cases of this variant were reported in the United States. However, when researchers analyzed his sequence data from November 21-25, 2021, they found eight cases of his Omicron variant in several US states. All samples from the US contained all 28 core Omicron mutations. Taken together, these findings and those from sequence data from Africa may suggest that the Omicron variant originated in South Africa and that transcontinental spread disseminated him once or more in the United States. there is. Interestingly, by using the SLS approach, the researchers dated November 4, 2021, three weeks before the actual alert date, the first Omicron sequence detected in the retrospectively determined United States. We presume that it would have been declared to be a VOC before . The three weeks could have had a significant impact in slowing the intercontinental spread of the virus. The researchers also calculated the local spread of omicron in US states from SARS-CoV-2 sequence data. Here, they observed rapid local expansion following the initial omicron sequences detected in each state. This is similar to case spread kinetics after 28 mutations containing mutations were detected in several African countries.