The circulation of contagious variants of SARS-CoV-2 and suboptimal protection of the vaccine create the conditions for simultaneous infections with multiple strains, which could generate recombinant SARS-CoV-2 between lineages with new unpredictable characteristics.1
- Jackson B
- Good MF
- Toro MJ
- et al.
Generation and transmission of interlinear recombinants in the SARS-CoV-2 pandemic.2
- VanInsberghe D
- Neish AS
- Lowen AC
- Koelle K
Currently, the recombinant genomes of SARS-CoV-2 are circulating at low levels. Mixed infections have been reported since the first epidemic waves.3
- Samoilov AE
- Kaptelova VV
- Bukharina AY
- et al.
Case report: dominant strain change during dual SARS-CoV-2 infection.4
- Pere N
- Silva CN
- Magallanes AC
- et al.
Dynamics of a SARS-CoV-2 double-lineage coinfection in a prolonged case of COVID-19 viral spread: information on the clinical severity and duration of the disease. Co-infection with omicron and delta has been found in immunocompetent and immunocompromised patients living in different geographical areas.5
- Combes P
- Bisseux M
- Bal A
- et al.
Evidence of coinfection during delta and omicron variants of co-circulation concern, weeks 49-2021 to 02-2022, France.6
- Rockett RJ
- Draper J
- Gal M
- et al.
Coinfection with omicron and delta SARS-COV-2 variants revealed by genomic surveillance. Because these variants are characterized by different genomic sequences, their co-presence can be quickly identified. However, recombination between closely related variants is difficult to identify, but it can also occur. To date, a total of 637 cases of recombinant omicron BA.1 and BA.2, known as XE, have been confirmed in the UK, and the number is increasing. under investigation in England. Technical information 39. These data also suggest that intralignment recombination generates highly transmissible chimeric strains. All coinfections must be detected to minimize the risk of recombination. Here we report a 63-year-old unvaccinated woman with mild respiratory symptoms who was given a nasopharyngeal swab on January 31, 2022. The sample was positive. for E, N, and RdRp or genes using the Allplex SARS-CoV-2 assay (Arrow and Seegene, Seoul, South Korea; Appendix p 3). This case was found by chance, as it was randomly selected along with 68 other acute infections for a molecular survey requested by the Istituto Superiore di Sanità. All isolates were preliminarily examined with multiple PCR to detect mutation signatures of the major circulating variants and were found to belong to the omicron variant (Appendix p 2). 54 samples were then selected at random, 24 of which were sequenced with the entire genome and 30 of which were sequenced by Sanger in the Spike gene region. The case sample fell into the Sanger group and the resulting electroperogram showed several illegible polymorphisms and sequences close to the suppression of 142-144 amino acids of the omicron variant BA.1. The sample was then examined by genome-wide sequencing and showed 67 mutations defining omicron variants. Of these, 15 were underlined BA.1 and 20 were underlined BA.2 (Appendix p. 2). Nextclade analysis (version 1.14.0) confirmed the presence of two different isolates (Appendix p 2).
The woman quickly isolated herself, had no other contacts since then and resolved the infection within 9 days. These results suggest that omicron coinfection induces mild symptoms, even in unvaccinated individuals, and may go unnoticed. This work underscores the need for effective genomic surveillance to reduce the risk of generating recombinant SARS-CoV-2 with novel pathogenic and immunological properties.
We do not declare contrary interests.
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References
- 1.
- Jackson B
- Good MF
- Toro MJ
- et al.
Generation and transmission of interlinear recombinants in the SARS-CoV-2 pandemic.
Cell. 2021; 184: 5179-5188
- 2.
- VanInsberghe D
- Neish AS
- Lowen AC
- Koelle K
Currently, the recombinant genomes of SARS-CoV-2 are circulating at low levels.
bioRxiv. 2021; ()
- 3.
- Samoilov AE
- Kaptelova VV
- Bukharina AY
- et al.
Case report: dominant strain change during dual SARS-CoV-2 infection.
BMC Infect Dis. 2021; 21: 959
- 4.
- Pere N
- Silva CN
- Magallanes AC
- et al.
Dynamics of a SARS-CoV-2 double-lineage coinfection in a prolonged case of COVID-19 viral spread: information on the clinical severity and duration of the disease.
Microorganisms. 2021; 9: 300
- 5.
- Combes P
- Bisseux M
- Bal A
- et al.
Evidence of coinfection during delta and omicron variants of co-circulation concern, weeks 49-2021 to 02-2022, France.
medRxiv. 2022; ()
- 6.
- Rockett RJ
- Draper J
- Gal M
- et al.
Coinfection with omicron and delta SARS-COV-2 variants revealed by genomic surveillance.
medRxiv. 2022; ()
- 7.
- UK Health Safety Agency
Worrying variants of SARS-CoV-2 and variants in research in England. Technical information 39.
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DOI: https://doi.org/10.1016/S2666-5247(22)00119-7
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