Reviews of "Evidence for SARS-CoV-2 Delta and Omicron Co-infections and Recombination"

Fernando Spilki; Kenneth Stedman

doi:doi:10.1162/2e3983f5.054997fa

Reviews of "Evidence for SARS-CoV-2 Delta and Omicron Co-infections and Recombination"

Reviewers: F Spilki (Universidade Feevale) | 📗📗📗📗◻️ • K Stedman (Portland State University) | 📗📗📗📗◻️

by Fernando Spilki and Kenneth Stedman

Published onMar 30, 2022

This Pub is a Review of

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

by Alexandre Bolze, Tracy Basler, Simon White, Andrew Dei Rossi, Dana Wyman, Pavitra Roychoudhury, Alexander L. Greninger, Kathleen Hayashibara, Eric Kil, Hang Dai, Tyler Cassens, Kevin Tsan, Jason Nguyen, Jimmy Ramirez, Scotty Carter, Elizabeth T. Cirulli, Kelly Schiabor Barrett, Nicole L Washington, Pedro Belda-Ferre, Sharoni Jacobs, Efren Sandoval, David Becker, James T Lu, Magnus Isaksson, William Lee, and Shishi Luo

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dx.doi.org

Description

Between November 2021 and February 2022, SARS-CoV-2 Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5'-end of the viral genome was from the Delta genome, and the 3'-end from Omicron including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared to the circulating Omicron lineages.

To read the original manuscript, click the link above.

Summary of Reviews: This preprint examines the potential evidence for SARS-CoV-2 Delta and Omicron co-infection and consequential recombination. Such events have been demonstrated several times already over the course of the pandemic, however, not every recombinant becomes a viable virus. Though it’s bibliographic citations and discussion section could be refined, reviewers agree that this paper provides strong evidence of co-infection, utilizes robust and appropriate methods, and addresses any caveats in their data.

Reviewer 1 (Fernando S…) | 📗📗📗📗◻️

Reviewer 2 (Kenneth S…) | 📗📗📗📗◻️

RR:C19 Strength of Evidence Scale Key

📕 ◻️◻️◻️◻️ = Misleading

📙📙 ◻️◻️◻️ = Not Informative

📒📒📒 ◻️◻️ = Potentially Informative

📗📗📗📗◻️ = Reliable

📘📘📘📘📘 = Strong

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A Supplement to this Pub

Review 1: "Evidence for SARS-CoV-2 Delta and Omicron Co-infections and Recombination"

by Fernando Spilki

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Published on Mar 30, 2022
rrid.mitpress.mit.edu

Description

Though it’s bibliographic citations and discussion section could be refined, reviewers agree that this paper provides strong evidence of co-infection, utilizes robust and appropriate methods, and addresses any caveats in their data.