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
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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.
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SciScore for 10.1101/2021.03.01.21252705: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The first was tested with BinaxNOW™, immediately followed by a separate bilateral swab for SARS-CoV-2 genomic sequencing[8,9]. BinaxNOW™suggested: NoneTo do this, we built a Bayesian phylogeny for each lineage in BEAST v. BEASTsuggested: (BEAST, RRID:SCR_010228)SARS-CoV-2 consensus genome generation: Raw .fastq files were imported into IDseq and consensus genomes were generated automatically using the embedded SARS-CoV-2 pipeline [6]. SARS-CoV-2suggested: (Active Motif Cat# 91351, RRID:AB_2847848)Specifically, minimap2 was used to align raw reads to the reference genome MN908947.2 [7], … SciScore for 10.1101/2021.03.01.21252705: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The first was tested with BinaxNOW™, immediately followed by a separate bilateral swab for SARS-CoV-2 genomic sequencing[8,9]. BinaxNOW™suggested: NoneTo do this, we built a Bayesian phylogeny for each lineage in BEAST v. BEASTsuggested: (BEAST, RRID:SCR_010228)SARS-CoV-2 consensus genome generation: Raw .fastq files were imported into IDseq and consensus genomes were generated automatically using the embedded SARS-CoV-2 pipeline [6]. SARS-CoV-2suggested: (Active Motif Cat# 91351, RRID:AB_2847848)Specifically, minimap2 was used to align raw reads to the reference genome MN908947.2 [7], then the consensus sequence was generated using samtools [8], mpileup and ivar [9]. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)For subsampled genomes, we aligned them against the reference genome (Genbank accession: MN996528.1) using MAFFT v7.471 [15] with default settings. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Each multi-sequence alignment was used to build a separate maximum likelihood tree in IQ-TREE v. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has several limitations. First, testing was conducted at a walk-up testing site, and thus these are inherently convenience samples; however, this would not be expected to impose a differential selection bias for those with or without any particular variant. Second, clear classification of the index case was not always possible, particularly when multiple adults from a household tested positive on the same date; further, secondary household attack rate calculations do not account for potential external sources of infection other than the index case. However, the relative risk of secondary infection from household exposure to West Coast versus non-West Coast variants was similar among children, a group less likely to have been misclassified as non-index or to be exposed to external infection. Third, household testing coverage was incomplete; this might contribute to an over (or under) estimate of secondary attack rate, and while we again have no reason to suspect differential ascertainment by strain, this could bias estimates of relative risk. The occurrence of variants in SARS-CoV-2 was always expected; however, it is often difficult to understand the importance of any given single or co-occurring mutations. While further epidemiological and laboratory experiments will be required to fully understand the community impact and mechanistic underpinnings of each variant, it is clear that enhanced genomic surveillance, paired with community engagement, testing, and respo...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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