Genomic epidemiology of SARS-CoV-2 within households in coastal Kenya: a case ascertained cohort study

Abstract Analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences from household infections may provide useful epidemiological information for future control measures. Between December 2020 and July 2022, we conducted a case-ascertained household cohort study whereby households were recruited if a member was either a SARS-CoV-2 case or contact of a confirmed case. A total of 765 members of 214 households were prospectively monitored for SARS-CoV-2 infection and transmission. Follow-up visits collected a nasopharyngeal/oropharyngeal (NP/OP) swab on days 1, 4 and 7 for RT-PCR diagnosis. If any of these were positive, further swabs were collected on days 10, 14, 21 and 28. Of 2,780 NP/OP swabs collected, 540 (19.4%) tested SARS-CoV-2 positive and viral genome sequences were recovered for 288 (53.3%) positive samples. The genomes belonged to 23 different Pango lineages. Phylogenetic analysis including contemporaneous Coastal Kenya data estimated 233 putative transmission events involving 162 members of the 89 households, of which 60 (25%) were intra-household transmission events while 173 (75%) were infections that likely occurred outside the households. In 34 (38%) households, multiple virus introductions were observed (up to six) within the one-month follow-up period, in contrast to high-income settings, where a single introduction seemed to occur during epidemic waves. Our findings suggests that in this setting control of respiratory virus spread by household member isolation will be ineffective.