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

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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the National Institute for Health and Care Research (NIHR) (project reference 17/63/82) using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office and Wellcome Trust (grant# 220985). Members of COVID-19 Testing Team at KWTRP are supported by multiple funding sources including UNITAD (BOHEMIA study received by Dr Marta Maia funded UNITAID), EDCTP (Senior Fellowship and Research and Innovation Action (RIA) grants received by Dr Francis Ndungu), GAVI (PCIVS grant received by Prof. Anthony Scott). Dr Simon Dellicour acknowledges support from the Fonds National de la Recherche Scientifique (F.R.S.-FNRS, Belgium; grant nF.4515.22), from the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen, FWO, Belgium; grant nG098321N), and from the European Union Horizon 2020 project MOOD (grant agreement n874850).The views expressed in this publication are those of the author (s) and not necessarily those of NIHR, the Department of Health and Social Care, Foreign Commonwealth and Development Office, Wellcome Trust or the UK government. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study protocol was reviewed and approved by both the Scientific and Ethics Research Unit (SERU) at Kenya Medical Research Institute (KEMRI), Nairobi, Kenya (SERU protocol # 4077) and the University of Warwick, Biomedical and Scientific Research Ethics Committee, Coventry, United Kingdom (REF: BSREC 150/19-20 AM01). Prior to data and sample collection, written informed consent was obtained from all participants aged 18 years or older, while for participants aged less than 18 years consent was obtained from their parents or legal guardians. Assent was also sought for adolescents (11-17 years of age). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The consensus genome sequences obtained in this study that passed our quality control filters have been submitted to both GISAID and GenBank database (accession numbers available in appendix pages of the supplementary material). The raw data files have been prepared for deposition in Harvard DataVerse. For more detailed information beyond the metadata used in the paper, there is a process of managed access requiring submission of a request form for consideration by our Data Governance Committee (http://kemri-wellcome.org/about-us/#ChildVerticalTab_15).