tetano
Editor, Senior Moderator
Med (N Y)
. 2022 Oct 20;S2666-6340(22)00449-4.
doi: 10.1016/j.medj.2022.10.002. Online ahead of print.
Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination
Alexandre Bolze[SUP] 1 [/SUP], Tracy Basler[SUP] 1 [/SUP], Simon White[SUP] 1 [/SUP], Andrew Dei Rossi[SUP] 1 [/SUP], Dana Wyman[SUP] 1 [/SUP], Hang Dai[SUP] 1 [/SUP], Pavitra Roychoudhury[SUP] 2 [/SUP], Alexander L Greninger[SUP] 2 [/SUP], Kathleen Hayashibara[SUP] 3 [/SUP], Mark Beatty[SUP] 4 [/SUP], Seema Shah[SUP] 4 [/SUP], Sarah Stous[SUP] 4 [/SUP], John T McCrone[SUP] 1 [/SUP], Eric Kil[SUP] 1 [/SUP], Tyler Cassens[SUP] 1 [/SUP], Kevin Tsan[SUP] 1 [/SUP], Jason Nguyen[SUP] 1 [/SUP], Jimmy Ramirez[SUP] 1 [/SUP], Scotty Carter[SUP] 1 [/SUP], Elizabeth T Cirulli[SUP] 1 [/SUP], Kelly Schiabor Barrett[SUP] 1 [/SUP], Nicole L Washington[SUP] 1 [/SUP], Pedro Belda-Ferre[SUP] 1 [/SUP], Sharoni Jacobs[SUP] 1 [/SUP], Efren Sandoval[SUP] 1 [/SUP], David Becker[SUP] 1 [/SUP], James T Lu[SUP] 1 [/SUP], Magnus Isaksson[SUP] 1 [/SUP], William Lee[SUP] 1 [/SUP], Shishi Luo[SUP] 5 [/SUP]
Affiliations
Abstract
Background: Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.
Methods: We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.
Findings: We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.
Conclusions: Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.
Funding: This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).
Keywords: BA.1; Delta; Omicron; RNA virus; SARS-CoV-2; Translation to patients; alternative allele fraction; breakpoint; co-infection; recombination; sequencing.
. 2022 Oct 20;S2666-6340(22)00449-4.
doi: 10.1016/j.medj.2022.10.002. Online ahead of print.
Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination
Alexandre Bolze[SUP] 1 [/SUP], Tracy Basler[SUP] 1 [/SUP], Simon White[SUP] 1 [/SUP], Andrew Dei Rossi[SUP] 1 [/SUP], Dana Wyman[SUP] 1 [/SUP], Hang Dai[SUP] 1 [/SUP], Pavitra Roychoudhury[SUP] 2 [/SUP], Alexander L Greninger[SUP] 2 [/SUP], Kathleen Hayashibara[SUP] 3 [/SUP], Mark Beatty[SUP] 4 [/SUP], Seema Shah[SUP] 4 [/SUP], Sarah Stous[SUP] 4 [/SUP], John T McCrone[SUP] 1 [/SUP], Eric Kil[SUP] 1 [/SUP], Tyler Cassens[SUP] 1 [/SUP], Kevin Tsan[SUP] 1 [/SUP], Jason Nguyen[SUP] 1 [/SUP], Jimmy Ramirez[SUP] 1 [/SUP], Scotty Carter[SUP] 1 [/SUP], Elizabeth T Cirulli[SUP] 1 [/SUP], Kelly Schiabor Barrett[SUP] 1 [/SUP], Nicole L Washington[SUP] 1 [/SUP], Pedro Belda-Ferre[SUP] 1 [/SUP], Sharoni Jacobs[SUP] 1 [/SUP], Efren Sandoval[SUP] 1 [/SUP], David Becker[SUP] 1 [/SUP], James T Lu[SUP] 1 [/SUP], Magnus Isaksson[SUP] 1 [/SUP], William Lee[SUP] 1 [/SUP], Shishi Luo[SUP] 5 [/SUP]
Affiliations
- PMID: 36332633
- PMCID: PMC9581791
- DOI: 10.1016/j.medj.2022.10.002
Abstract
Background: Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.
Methods: We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.
Findings: We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.
Conclusions: Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.
Funding: This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).
Keywords: BA.1; Delta; Omicron; RNA virus; SARS-CoV-2; Translation to patients; alternative allele fraction; breakpoint; co-infection; recombination; sequencing.