Post by Nadica (She/Her) on Oct 3, 2024 2:38:36 GMT
A novel SARS-CoV-2 recombinant transmitted from a patient with an acute co-infection - Published Oct 1, 2024
Correspondence
Recombination occurs in typical coronavirus replication1 and has shaped the SARS-CoV-2 landscape, as shown by the global spread of the recombinant XBB-lineage during 2022 and 2023; however, the generation of recombinants has not been documented previously. Chronic infections in immunocompromised patients have been indicated as a factor in the evolution of SARS-CoV-2 through point mutations.2,3 In this Correspondence, we report on a patient with an acute co-infection of two SARS-CoV-2 lineages, who transmitted a novel recombinant variant in a hospital setting.
In October, 2023, a novel omicron (B.1.1.529) recombinant variant was detected in a patient during SARS-CoV-2 genomic surveillance in Stockholm, Sweden (appendix). The variant had the 5′-part of the genome derived from HV.1 (a sublineage of XBB) and the 3′-part from BA.2.86.1, with a breakpoint approximately at the juncture of the orf1b and S genes. The patient had tested negative for SARS-CoV-2 by PCR 5 days before the detection of the variant. A contemporaneous patient was also identified to have a HV.1–BA.2.86.1 co-infection based on 70 mixed nucleotides at sequence positions that distinguish the HV.1 and BA.2.86.1 variants, with the minor BA.2.86.1 component accounting for approximately 30% of the sequencing depth. The two patients were hospitalised in the same ward for 8 days. Additional evidence for direct transmission of the recombinant variant from the patient with the co-infection is provided by the closely related viral sequences in the two patients, which shared six rare mutations. The patient with the co-infection had no previous negative test result for SARS-CoV-2 that would ascertain the duration of the infection; nevertheless, the viral sequences indicated an acute infection as the HV.1 component was zero mutations and the BA.2.86.1 component was two mutations away from contemporary Swedish sequences. Both patients received five or more doses of a SARS-CoV-2 vaccine, with the last dose administered more than 6 months earlier, and both patients were admitted to inpatient care for reasons other than COVID-19. The novel recombinant variant was also not detected in other SARS-CoV-2 sequences from patients in Sweden.
This Correspondence shows that acute co-infections with two or more SARS-CoV-2 variants in vaccinated individuals provide sufficient conditions for generating transmissible recombinants; the unprecedented extent of the SARS-CoV-2 surveillance allowed for the identification and characterisation of this occurrence. To the best of our knowledge, an epidemiological linkage between the source co-infection and resultant recombinant has been established for the first time, effectively capturing the origin of a recombinant variant.
Correspondence
Recombination occurs in typical coronavirus replication1 and has shaped the SARS-CoV-2 landscape, as shown by the global spread of the recombinant XBB-lineage during 2022 and 2023; however, the generation of recombinants has not been documented previously. Chronic infections in immunocompromised patients have been indicated as a factor in the evolution of SARS-CoV-2 through point mutations.2,3 In this Correspondence, we report on a patient with an acute co-infection of two SARS-CoV-2 lineages, who transmitted a novel recombinant variant in a hospital setting.
In October, 2023, a novel omicron (B.1.1.529) recombinant variant was detected in a patient during SARS-CoV-2 genomic surveillance in Stockholm, Sweden (appendix). The variant had the 5′-part of the genome derived from HV.1 (a sublineage of XBB) and the 3′-part from BA.2.86.1, with a breakpoint approximately at the juncture of the orf1b and S genes. The patient had tested negative for SARS-CoV-2 by PCR 5 days before the detection of the variant. A contemporaneous patient was also identified to have a HV.1–BA.2.86.1 co-infection based on 70 mixed nucleotides at sequence positions that distinguish the HV.1 and BA.2.86.1 variants, with the minor BA.2.86.1 component accounting for approximately 30% of the sequencing depth. The two patients were hospitalised in the same ward for 8 days. Additional evidence for direct transmission of the recombinant variant from the patient with the co-infection is provided by the closely related viral sequences in the two patients, which shared six rare mutations. The patient with the co-infection had no previous negative test result for SARS-CoV-2 that would ascertain the duration of the infection; nevertheless, the viral sequences indicated an acute infection as the HV.1 component was zero mutations and the BA.2.86.1 component was two mutations away from contemporary Swedish sequences. Both patients received five or more doses of a SARS-CoV-2 vaccine, with the last dose administered more than 6 months earlier, and both patients were admitted to inpatient care for reasons other than COVID-19. The novel recombinant variant was also not detected in other SARS-CoV-2 sequences from patients in Sweden.
This Correspondence shows that acute co-infections with two or more SARS-CoV-2 variants in vaccinated individuals provide sufficient conditions for generating transmissible recombinants; the unprecedented extent of the SARS-CoV-2 surveillance allowed for the identification and characterisation of this occurrence. To the best of our knowledge, an epidemiological linkage between the source co-infection and resultant recombinant has been established for the first time, effectively capturing the origin of a recombinant variant.