Evidence map›Paper›PMID 33688689›Full record

ArticlemedRxiv : the preprint server for health sciences2021

Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco.

James Peng, Sabrina A Mann, Anthea M Mitchell, Jamin Liu, Matthew T Laurie, Sara Sunshine, Genay Pilarowski, Patrick Ayscue, Amy Kistler, Manu Vanaerschot and 20 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 11 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

30 authors at 6 institutions in 1 country.

James PengDivision of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Sabrina A MannChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Anthea M MitchellChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Jamin LiuDepartment of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA.
Matthew T LaurieDepartment of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA.
Sara SunshineDepartment of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA.
Genay PilarowskiDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Patrick AyscueChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Amy KistlerChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Manu VanaerschotChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Lucy M LiChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Aaron McGeeverChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Eric D ChowDepartment of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA.
IDseq TeamChan Zuckerberg Initiative, Redwood City, CA 94063, USA.
Carina MarquezDivision of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Robert NakamuraCalifornia Department of Public Health, Richmond, CA 94804, USA.
Luis RubioDivision of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Gabriel ChamieDivision of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Diane JonesUnidos en Salud, San Francisco, CA 94143, USA.
Jon JacoboUnidos en Salud, San Francisco, CA 94143, USA.
Susana RojasUnidos en Salud, San Francisco, CA 94143, USA.
Susy RojasUnidos en Salud, San Francisco, CA 94143, USA.
Valerie Tulier-LaiwaUnidos en Salud, San Francisco, CA 94143, USA.
Douglas BlackDivision of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Jackie MartinezUnidos en Salud, San Francisco, CA 94143, USA.
Jamie NasoUnidos en Salud, San Francisco, CA 94143, USA.
Joshua SchwabDivision of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA.
Maya PetersenDivision of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA.
Diane HavlirDivision of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Joseph DeRisiChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
University of California, San Francisco · USUnited in Health · USChan Zuckerberg Initiative (United States) · USUniversity of California, Berkeley · USCalifornia Department of Public Health · USStanford University · US

Funding

San Francisco Vaccine and Prevention UnitUM1AI069496 · NIAID · PUBLIC HEALTH FOUNDATION ENTERPRISES · PI Susan Buchbinder, Diane V Havlir · 2012 to 2026
$30.5M
GENETICS OF EUCARYOTIC AND PROCARYOTIC ORGANISMST32GM007810 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ASHRAFI, KAVEH, NARLIKAR, GEETA J · 1985 to 2020
$15.1M
Identification and Characterization of the Antiviral Response to RSV Infection: A Single Cell ApproachF31AI150007 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SUNSHINE, SARA · 2020 to 2022
$116k
NIAID NIH HHS F31 AI150007NIAID NIH HHS UM1 AI069496NIGMS NIH HHS T32 GM007810
6 · The paper itself

Abstract

backgroundSequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities.

methodsSARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants.

resultsA total of 12,124 tests were performed yielding 1,099 positives. From these, 811 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to "West Coast" variants were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.357 vs 0.294, RR=1.29; 95% CI:1.01-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.1%).

conclusionsThe increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants; however, additional laboratory and epidemiological studies are required to better understand differences between these variants. SUMMARY: We observed a growing prevalence and elevated attack rate for "West Coast" SARS-CoV-2 variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.

Identifiers

PMID33688689
PMCPMC7941666
OpenAlexW3134414549

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.