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SARS-CoV-2 potential recombinants in Brazil, Belgium, France, Netherlands, US, Finland, Puerto Rico, Spain

America, BA.1, BA.1.1, BA.2, Belgium, Brazil, Coronavirus, Delta, Deltacron, Denmark, Finland, France, Genome, Infection, Netherlands, Omicron, Recombination, South Africa, Spain, Testing, Transmission, UK, USA, Wales

SARS_CoV-2 recombinants seem to have been popping up across the globe recently. We have listed some of the most recent examples below, with links to their various Github issue pages.

  • Brazil: Recombinant between: BA.1* & BA.2 Earliest sequence: 2022/03/07 (Brazil) Countries circulating: Brazil Likely breakpoint: before 10028 (NSP4). Found Nuc mutations and AA changes. This sample was collected in the city of São Paulo. We are currently investigating if more sequences with this pattern emerges in our genomic surveillance network. Github link
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  • US: Nine samples belonging to this potential lineage, resulting from recombination between AY.119.2 and BA.1.1. Github link  & Preprint
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  •  US: Recombinant between: AY.x (my guess is AY.44, based on Nuc mutation A4015G) & BA.1.1 Earliest sequence: 2021/12/24 (US-MA) Most recent sequence: 2022/1/18 (US-UT) Countries circulating: US, MA and UT (6 sequences). Likely breakpoint: between 5585 and 6511 (NSP3), which is different from other potential Delta/Omicron recombinant lineages. Github link
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  • Belgium, Netherlands, France: Potential recombined BA.2-BA.1.1 lineage in 22 (1.4%) sequences in Roeselare, Belgium characterized by ORF1b:Q866R and ORF1a:R1628C with BA.2 background and ORF1a (2832-10029) and ORF1b (160464-18163) from BA.1.1 (ORF1b:Q866R) Github link
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  • Finland: Eight potential BA.1/BA.2 recombinant sequences with epidemiological linkage were detected in Finland. The recombination breakpoint seems to be downstream from those reported from Denmark. Github link
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  • Puerto Rico: Potential Delta/BA.1 or BA.1.1 Recombinant with Likely Breakpoint at NSP15 or NSP16 (1 seq in Puerto Rico as of 2022-03-18) #476. Recombinant between: AY.x & BA.1 or BA.1.1 (sequence has gap in the G22599A region). Github link
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  • UK/Wales: Potential BA.1.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (43 Seqs in Wales as of 2022-03-11). Github link
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  • South Africa: Potential BA.2/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (5 Seqs in South Africa as of 2022-03-17) #478. Recombinant between: BA.2 & BA.1* Earliest sequence: 2021/12/13 (South Africa). Github link
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  • Spain:Potential BA.2/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (13 Seqs in Spain-Balearic Islands as of 2022-03-21) #482. Recombinant between: BA.2 & BA.1* Earliest sequence: 2022/2/25 (Spain-Balearic Islands) Most recent sequence: 2022/3/11 (Spain-Balearic Islands). Github link
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  • Denmark:Potential BA.1/BA.2 Recombinant with Likely Breakpoint at NSP10/NSP12 (18 Sequences in Denmark as of 2022-03-12) #463. Recombinant between: BA.1* & BA.2 Earliest sequence: 2022/1/31 (Denmark) Most recent sequence: 2022/3/4 Denmark). Github link

 

China CDC: Deltacron is a “Grey Rhino” event