COVID-19 Vaccine Effectiveness against SARS-CoV-2 Infections with the Delta Variant among Ages >=12 Years in Utah

We conducted weekly surveillance for SARS-CoV-2 infection among a sample of households with [≥]1 child aged 0-17 years from selected Utah counties. A Cox proportional hazards model approach was used to calculate infection hazard rate and vaccine effectiveness. Findings show that the recommended primary series of COVID-19 vaccine was effective against circulating variants during a Delta-predominant wave in Utah.

SARS-CoV-2 genomic diversity in households highlights the challenges of sequence-based transmission inference

BackgroundThe reliability of sequence-based inference of SARS-CoV-2 transmission is not clear. Sequence data from infections among household members can define the expected genomic diversity of a virus along a defined transmission chain. MethodsSARS-CoV-2 cases were identified prospectively among 2,369 participants in 706 households. Specimens with an RT-PCR cycle threshold [≤]30 underwent whole genome sequencing. Intrahost single nucleotide variants (iSNV) were identified at [≥]5% frequency. Phylogenetic trees were used to evaluate the relationship of household and community sequences. ResultsThere were 178 SARS-CoV-2 cases in 706 households. Among 147 specimens sequenced, 106 yielded a whole genome consensus with coverage suitable for identifying iSNV. Twenty-six households had sequences from multiple cases within 14 days. Consensus sequences were indistinguishable among cases in 15 households, while 11 had [≥]1 consensus that differed by 1-2 mutations. Sequences from households and the community were often interspersed on phylogenetic trees. Identification of iSNV improved inference in 2 of 15 households with indistinguishable consensus sequences and 6 of 11 with distinct ones. ConclusionsIn multiple infection households, whole genome consensus sequences differed by 0-1 mutations. Identification of shared iSNV occasionally resolved linkage, but the low genomic diversity of SARS-CoV-2 limits the utility of "sequence-only" transmission inference. SummaryHigh depth of coverage whole genome sequencing can identify SARS-CoV-2 transmission chains in settings where there is strong epidemiologic linkage but is not reliable as a stand-alone method for transmission inference.