SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing
ABSTRACT Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-08-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.00493-23 |
| _version_ | 1797741729317650432 |
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| author | Pauline Trémeaux Justine Latour Noémie Ranger Vénicia Ferrer Agnès Harter Romain Carcenac Pauline Boyer Sofia Demmou Florence Nicot Stéphanie Raymond Jacques Izopet |
| author_facet | Pauline Trémeaux Justine Latour Noémie Ranger Vénicia Ferrer Agnès Harter Romain Carcenac Pauline Boyer Sofia Demmou Florence Nicot Stéphanie Raymond Jacques Izopet |
| author_sort | Pauline Trémeaux |
| collection | DOAJ |
| description | ABSTRACT Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance. |
| first_indexed | 2024-03-12T14:30:50Z |
| format | Article |
| id | doaj.art-e7b903e0fb68408fa8347215bd3689d5 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-03-12T14:30:50Z |
| publishDate | 2023-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-e7b903e0fb68408fa8347215bd3689d52023-08-17T13:04:15ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-08-0111410.1128/spectrum.00493-23SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time SequencingPauline Trémeaux0Justine Latour1Noémie Ranger2Vénicia Ferrer3Agnès Harter4Romain Carcenac5Pauline Boyer6Sofia Demmou7Florence Nicot8Stéphanie Raymond9Jacques Izopet10Virology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceVirology Laboratory, Toulouse University Hospital, Toulouse, FranceABSTRACT Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance.https://journals.asm.org/doi/10.1128/spectrum.00493-23SARS-CoV-2co-infectiongenomic surveillancelong-read sequencingquasispeciesrecombination |
| spellingShingle | Pauline Trémeaux Justine Latour Noémie Ranger Vénicia Ferrer Agnès Harter Romain Carcenac Pauline Boyer Sofia Demmou Florence Nicot Stéphanie Raymond Jacques Izopet SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing Microbiology Spectrum SARS-CoV-2 co-infection genomic surveillance long-read sequencing quasispecies recombination |
| title | SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing |
| title_full | SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing |
| title_fullStr | SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing |
| title_full_unstemmed | SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing |
| title_short | SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing |
| title_sort | sars cov 2 co infections and recombinations identified by long read single molecule real time sequencing |
| topic | SARS-CoV-2 co-infection genomic surveillance long-read sequencing quasispecies recombination |
| url | https://journals.asm.org/doi/10.1128/spectrum.00493-23 |
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