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

Abstract

Background: Sequencing of the severe acute respiratory syndrome coronavirus 2 (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 22 November to 1 December, 2020, and 10-29 January 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 1099 positives. From these, 928 high-quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to the "California" or "West Coast" variants (B.1.427 and B.1.429) were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.36 vs 0.29, risk ratio [RR] = 1.28; 95% confidence interval [CI]: 1.00-1.64). 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 64.3%).

Conclusions: The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants. Summary: We observed a growing prevalence and modestly elevated attack rate for "West Coast" severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.

Keywords: SARS-CoV-2; household transmission; secondary attack rates; spike mutation; variant.

Figure 1.

Testing catchment area. The location of the 24th & Mission testing site is denoted by the yellow symbol. Negative tests are in gray, and positive tests are shown in red. Household locations shown have a random offset of up to 750 meters to obfuscate the precise addresses of individuals. The testing catchment area encompasses a substantial number of individuals in the surrounding 8 Bay Area counties (A). The greatest concentration of individuals reside within San Francisco county (B), Map tiles by Stamen Design and data by OpenStreetMap.

Figure 2.

Variants observed at 24th & Mission. A, Proportion of daily cases belonging to West Coast and non-West Coast variants. B, Total number of samples per day. C, D, Area maps [22] showing the relative proportion of PANGO lineages acquired from full length genomes from the November (N = 191) and January (N = 737) time periods, respectively. E, Genome maps for variants detected in this study. Dominant mutations (filled black circles), and nonsynonymous mutations detected at lower frequency in combination with existing lineages (filled gray circles) are shown in gray. Abbreviation: PANGO, Phylogenetic Assignment of Named Global Outbreak.