First Documented Transmission of a Newly Minted Hybrid SARS-CoV-2 Variant

In a recent case report, Swedish scientists documented the first known transmission of a novel recombinant SARS-CoV-2 variant. The case highlights how a patient co-infected with two different strains—sublineages of XBB (HV.1) and BA.2.86.1—generated and transmitted a hybrid variant to another patient within a hospital setting.

In October 2023, routine genomic surveillance in Stockholm identified a recombinant variant in a patient (Patient B). This hybrid virus combined genetic material from two distinct lineages: the 5′ part of the genome from HV.1 and the 3′ part from BA.2.86.1. The recombination occurred at the orf1b and S gene junction, producing a novel variant not observed in other Swedish patients.

Meanwhile, another patient (Patient A), co-hospitalized in the same ward, was found to be co-infected with both HV.1 and BA.2.86.1. Sequencing revealed that about 30% of the virus in Patient A came from the BA.2.86.1 lineage. The two patients shared six rare mutations, confirming that Patient A transmitted the recombinant variant to Patient B during their 8-day stay.

HV.1 (EG.5.1.6.1) is part of the Eris (EG.5) family, first identified in China in February 2023 as a descendant of the XBB variant dubbed Gryphon, which spread widely in Singapore and India in 2022. BA.2.86.1 is a descendent of Pirola (BA.2.86), first detected in Israel and Denmark in August 2023. Another offshoot of Pirola, JN.1, first detected in Luxembourg in August 2023, caused last winter’s wave and is expected to be followed by XEC, a recombinant of BA.2.86 sublineages (KS.1.1 (BA.2.86.1.1.13.1.1.1 and KP.3.3 (BA.2.86.1.1.11.1.3.3)), in this year’s winter wave.

Both patients had received five or more COVID-19 vaccine doses, with their most recent dose administered over six months before hospitalization. Despite being admitted for reasons unrelated to COVID-19, this case has provided valuable insight into real-time viral recombination within human hosts.


REFERENCE

Robert Dyrdak, Sofia Stamouli, Shambhu Ganeshappa Aralaguppe, Martin Ekman, Hamzah Safari, Carlo Berg, Elin Movert, Neus Latorre-Margalef, Emmi Andersson, Magnus Gisslén, Joanna Nederby-Öhd, Åsa Sjödin Leufvén, Josette Schoenmakers, Sandra Broddesson, Ben Murrell, Jan Albert, A novel SARS-CoV-2 recombinant transmitted from a patient with an acute co-infection, The Lancet Microbe, 2024, 100998, ISSN 2666-5247,https://doi.org/10.1016/j.lanmic.2024.100998.

(https://www.sciencedirect.com/science/article/pii/S2666524724002660)

Published October 1, 2024



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