Detection of a BA.1/BA.2 recombinant in travelers arriving in Hong Kong, February 2022

We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong from November-2021 to February-2022. Apart from detecting Omicron (BA.1, BA1.1. and BA.2) and Delta variants, we detected a BA.1/BA.2 recombinant in two epidemiologically linked cases. This recombinant has a breakpoint near the 5’ end of Spike gene (nucleotide position 20055-21618). ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work is supported by Research Grants Council of Hong Kong theme-based research schemes (T11-705/21-N) and the Health and Medical Research Fund (COVID190205). ### 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: Ethics committee/IRB at the University of Hong Kong gave ethical approval for this work (IRB number: UW 20-168). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the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 All deduced sequences can be available from GISAID. The GISAID accession number of our sequences are available online at: https://github.com/Leo-Poon-Lab/BA1\_BA2\_recombinant\_HK/blob/main/GISAID\_accessions.txt