Recombination between SARS-CoV-2 Omicron BA.1 and BA.2 variants identified in a traveller from Nepal at the airport quarantine facility in Japan

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Abstract
We conducted a sentinel genome surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with assistance from airport quarantine stations. 1 Until 14 March 2022, the whole-genome sequences of 8030 quarantine and 224 582 domestic SARS-CoV-2 isolates in Japan have been deposited in the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. During quarantine surveillance, by pre-entry SARS-CoV-2 screening, at international airports, we identified a unique isolate IC-5720 (collection date: 22 February 2022; GISAID ID: EPI_ISL_11057288; short-read archive: DRX340596) from a traveller visiting from Nepal, exhibiting prominent genomic recombination between the Omicron variants BA.1 and BA.2. Initially, IC-5720 was not adequately assigned as BA.2 owing to the recombination and a low-quality assignment (‘not determined’ or ‘none’) in the PANGO lineage. 2 Detailed genome alignment using the Nextclade tool suggested that despite belonging to the 21 L (Omicron, BA.2) clade, the IC-5720 isolate has mutation profiles in the whole ORF1a gene identical to those in 21 K (Omicron, BA.1). This revealed a possible breakpoint at the end of the ORF1a gene between BA.1 and BA.2 variants ( Figure 1A). Heterogeneous mixed alleles were not identified during deep sequencing (2013 × mean read depth), suggesting that the isolate did not originate from a mixed infection. IC-5720 carries a spike protein identical to that in the BA.2 variant, eliminating concerns for further risks of infectivity and immune escape. Collectively, a recombinant isolate similar to IC-5720, although not entirely identical, has been identified in the UK and USA ( Figures 1B and C).
Funding Information
  • Ministry of Health and Welfare (20HA2007, 19HA1001)
  • Development Research Program on Emerging and Re-emerging Infectious Diseases (JP21fk0108103)