Reviews of "Emergence of a novel SARS-CoV-2 strain in Southern California, USA"

Takahiko Koyama; François Balloux; Lee W Riley

doi:doi:10.1162/2e3983f5.8fd75134

Reviews of "Emergence of a novel SARS-CoV-2 strain in Southern California, USA"

Reviewers: Takahiko Koyama (IBM Research) | 📗📗📗📗◻️ • François Balloux (University College London) | 📕◻️◻️◻️◻️ • Lee W Riley (UC Berkeley) | 📕◻️◻️◻️◻️

by Takahiko Koyama, François Balloux, and Lee W Riley

Published onFeb 11, 2021

This Pub is a Review of

Emergence of a novel SARS-CoV-2 strain in Southern California, USA

by Wenjuan Zhang, Brian D Davis, Stephanie S Chen, Jorge M Sincuir Martinez, Jasmine T Plummer, and Eric Vail

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dx.doi.org

Description

AbstractSince October 2020, novel strains of SARS-CoV-2 including B.1.1.7, have been identified to be of global significance from an infection and surveillance perspective. While this strain (B.1.1.7) may play an important role in increased COVID rates in the UK, there are still no reported strains to account for the spike of cases in Los Angeles (LA) and California as a whole, which currently has some of the highest absolute and per-capita COVID transmission rates in the country. From the early days of the pandemic when LA only had a single viral genome uploaded onto GISAID we have been at the forefront of generating and analyzing the SARS-CoV-2 sequencing data from the LA region. We report a novel strain emerging in Southern California. Most current cases in the catchment population in LA fall into two distinct subclades: 1) 20G (24% of total) is the predominant subclade currently in the United States 2) a relatively novel strain in clade 20C, CAL.20C strain (∼36% of total) is defined by five concurrent mutations. After an analysis of all of the publicly available data and a comparison to our recent sequences, we see a dramatic growth in the relative percentage of the CAL.20C strain beginning in November of 2020. The predominance of this strain coincides with the increased positivity rate seen in this region. Unlike 20G, this novel strain CAL.20C is defined by multiple mutations in the S protein, a characteristic it shares with both the UK and South African strains, both of which are of significant clinical and scientific interest

Statement from the RR:C19 Editorial Office (February 24, 2020)

RR:C19 solicits reviews to assess cutting-edge research that has not formally undergone peer review before being publicly posted to preprint servers. On February 11 and 15, 2021, RR:C19 published three expert peer reviews of “Emergence of a novel SARS-CoV-2 strain in Southern California, USA.” These reviewers found that this research opened up multiple questions that should be further pursued regarding the prevalence and features of the new CAL20C (20C/S452R/B.1.429) variant identified in Southern California, but also highlighted multiple areas of concern with the manuscript. Most notably, two of the reviewers found that the study methods on their own are not conclusive or robust enough to support its claims.

More research has since come out regarding this emerging variant, adding nuance to and concern about the findings presented. Viral mutations are bound to occur in the context of widespread person-to-person transmission, and, as RR:C19 reviewers initially noted, are not in and of themselves necessarily clinically nor epidemiologically relevant. Journalists should exercise caution in reporting the results of the increasing (and important) genomic surveillance conducted throughout the world, as “variants” are entirely inevitable, occur whether or not they are surveilled, and the implications of emerging variants require careful interpretation. Surveillance capacity across the United States and globally is also highly variable, making the situation even more complex.

Additional studies are needed to better understand the roles that variants such as Cal20 have on prevention, policy, and practice. Since RR:C19 published its peer reviews, the areas of concern identified by our reviewers were also addressed by JAMA on February 11, 2021, Science on February 23, 2021, andby scientists in many media outlets. In a landscape where emerging Sars-CoV2 variants are increasingly being identified, thus raising concerns to the public, increased surveillance and timely engagement and response by the scientific community are critical to assess the validity and implications of the research.

To read the original manuscript, click the link above.

Summary of Reviews: This preprint, for which additional peer reviews are pending, identifies a CAL20C variant, which has spread throughout southern California. Additional epidemiological research is needed to determine if this variant could be responsible for increased transmissibility state-wide.

Reviewer 1 (Takahiko Koyama) | 📗📗📗📗◻️

Reviewer 2 (François Balloux) | 📕◻️◻️◻️◻️

Reviewer 3 (Lee W Riley) | 📕◻️◻️◻️◻️

RR:C19 Strength of Evidence Scale Key

📕 ◻️◻️◻️◻️ = Misleading

📙📙 ◻️◻️◻️ = Not Informative

📒📒📒 ◻️◻️ = Potentially Informative

📗📗📗📗◻️ = Reliable

📘📘📘📘📘 = Strong

To read the reviews, click the links below.

Connections

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A Supplement to this Pub

Review 1: "Emergence of a novel SARS-CoV-2 strain in Southern California, USA"

by Takahiko Koyama

Show Description
Published on Feb 11, 2021
rrid.mitpress.mit.edu

Description

This preprint, for which additional peer reviews are pending, identifies a CAL20C variant, which has spread throughout southern California. Additional epidemiological research is needed to determine if this variant could be responsible for increased transmissibility state-wide.