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.

Autor:	Peng J; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Mann SA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA., Mitchell AM; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA., Liu J; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA.; University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA., Laurie MT; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA., Sunshine S; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA., Pilarowski G; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Ayscue P; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Kistler A; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Vanaerschot M; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Li LM; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., McGeever A; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Chow ED; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA., Team I; Chan Zuckerberg Initiative, Redwood City, CA 94063, USA., Marquez C; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Nakamura R; California Department of Public Health, Richmond, CA 94804, USA., Rubio L; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Chamie G; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Jones D; Unidos en Salud, San Francisco, CA 94143, USA., Jacobo J; Unidos en Salud, San Francisco, CA 94143, USA., Rojas S; Unidos en Salud, San Francisco, CA 94143, USA., Rojas S; Unidos en Salud, San Francisco, CA 94143, USA., Tulier-Laiwa V; Unidos en Salud, San Francisco, CA 94143, USA., Black D; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Martinez J; Unidos en Salud, San Francisco, CA 94143, USA., Naso J; Unidos en Salud, San Francisco, CA 94143, USA., Schwab J; Division of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA., Petersen M; Division of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA., Havlir D; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., DeRisi J; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA.
Jazyk:	angličtina
Zdroj:	MedRxiv : the preprint server for health sciences [medRxiv] 2021 Mar 03. Date of Electronic Publication: 2021 Mar 03.
DOI:	10.1101/2021.03.01.21252705
Abstrakt:	Background: Sequencing 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. Methods: SARS-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. Results: A 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%). Conclusions: The 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.
Databáze:	MEDLINE
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