Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco
| Autor: | Patrick Ayscue, Sabrina A Mann, Jon Jacobo, Douglas Black, Susana Rojas, Jackie Martinez, Sara Sunshine, Anthea M Mitchell, Carina Marquez, Eric D. Chow, Diane Jones, Manu Vanaerschot, IDseq Team, Diane V. Havlir, Valerie Tulier-Laiwa, Jamin Liu, James Peng, Joshua Schwab, Joseph L. DeRisi, Gabriel Chamie, Aaron McGeever, Susy Rojas, Robert Nakamura, Amy Kistler, Luis Rubio, Lucy M Li, Maya L. Petersen, Matthew T. Laurie, Jamie Naso, Genay Pilarowski |
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| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Microbiology (medical) medicine.medical_specialty Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) secondary attack rates 030106 microbiology Medical and Health Sciences Microbiology Article Vaccine Related 03 medical and health sciences 0302 clinical medicine Biodefense Epidemiology Pandemic spike mutation household transmission medicine IDseq Team Humans 030212 general & internal medicine West coast Lung Estimation Community based business.industry SARS-CoV-2 Risk of infection Prevention Incidence COVID-19 Genomics Biological Sciences Emerging Infectious Diseases Infectious Diseases Good Health and Well Being variant Pneumonia & Influenza San Francisco business Infection Viral load Demography |
| Zdroj: | medRxiv article-version (status) pre article-version (number) 1 Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, vol 74, iss 1 |
| ISSN: | 1537-6591 |
| Popis: | 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: | OpenAIRE |
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