Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil
With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recomb...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Vaccines |
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| Online Access: | https://www.mdpi.com/2076-393X/11/2/212 |
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| author | Fernando Hayashi Sant’Anna Tiago Finger Andreis Richard Steiner Salvato Ana Paula Muterle Varela Juliana Comerlato Tatiana Schäffer Gregianini Regina Bones Barcellos Fernanda Marques de Souza Godinho Paola Cristina Resende Gabriel da Luz Wallau Thaís Regina y Castro Bruna Campestrini Casarin Andressa de Almeida Vieira Alexandre Vargas Schwarzbold Priscila de Arruda Trindade Gabriela Luchiari Tumioto Giannini Luana Freese Giovana Bristot Carolina Serpa Brasil Bruna de Oliveira Rocha Paloma Bortolini Martins Francine Hehn de Oliveira Cock van Oosterhout Eliana Wendland |
| author_facet | Fernando Hayashi Sant’Anna Tiago Finger Andreis Richard Steiner Salvato Ana Paula Muterle Varela Juliana Comerlato Tatiana Schäffer Gregianini Regina Bones Barcellos Fernanda Marques de Souza Godinho Paola Cristina Resende Gabriel da Luz Wallau Thaís Regina y Castro Bruna Campestrini Casarin Andressa de Almeida Vieira Alexandre Vargas Schwarzbold Priscila de Arruda Trindade Gabriela Luchiari Tumioto Giannini Luana Freese Giovana Bristot Carolina Serpa Brasil Bruna de Oliveira Rocha Paloma Bortolini Martins Francine Hehn de Oliveira Cock van Oosterhout Eliana Wendland |
| author_sort | Fernando Hayashi Sant’Anna |
| collection | DOAJ |
| description | With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5′ genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3′ genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel. |
| first_indexed | 2024-03-11T08:02:46Z |
| format | Article |
| id | doaj.art-527da89d83ae4bd79fe95113caf27147 |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-11T08:02:46Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-527da89d83ae4bd79fe95113caf271472023-11-16T23:41:19ZengMDPI AGVaccines2076-393X2023-01-0111221210.3390/vaccines11020212Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South BrazilFernando Hayashi Sant’Anna0Tiago Finger Andreis1Richard Steiner Salvato2Ana Paula Muterle Varela3Juliana Comerlato4Tatiana Schäffer Gregianini5Regina Bones Barcellos6Fernanda Marques de Souza Godinho7Paola Cristina Resende8Gabriel da Luz Wallau9Thaís Regina y Castro10Bruna Campestrini Casarin11Andressa de Almeida Vieira12Alexandre Vargas Schwarzbold13Priscila de Arruda Trindade14Gabriela Luchiari Tumioto Giannini15Luana Freese16Giovana Bristot17Carolina Serpa Brasil18Bruna de Oliveira Rocha19Paloma Bortolini Martins20Francine Hehn de Oliveira21Cock van Oosterhout22Eliana Wendland23Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilCentro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilLaboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre 90450-190, RS, BrazilCentro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, BrazilCentro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, BrazilLaboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, BrazilDepartamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz Pernambuco (FIOCRUZ-PE), Recife 50740-465, PE, BrazilDepartamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, BrazilDepartamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, BrazilDepartamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, BrazilDepartamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, BrazilDepartamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilSchool of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UKHospital Moinhos de Vento, Porto Alegre 90035-000, RS, BrazilWith the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5′ genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3′ genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.https://www.mdpi.com/2076-393X/11/2/212COVID-19SARS-CoV-2 genomesgene flowrecombinationgenetic introgressionadaptive landscape |
| spellingShingle | Fernando Hayashi Sant’Anna Tiago Finger Andreis Richard Steiner Salvato Ana Paula Muterle Varela Juliana Comerlato Tatiana Schäffer Gregianini Regina Bones Barcellos Fernanda Marques de Souza Godinho Paola Cristina Resende Gabriel da Luz Wallau Thaís Regina y Castro Bruna Campestrini Casarin Andressa de Almeida Vieira Alexandre Vargas Schwarzbold Priscila de Arruda Trindade Gabriela Luchiari Tumioto Giannini Luana Freese Giovana Bristot Carolina Serpa Brasil Bruna de Oliveira Rocha Paloma Bortolini Martins Francine Hehn de Oliveira Cock van Oosterhout Eliana Wendland Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil Vaccines COVID-19 SARS-CoV-2 genomes gene flow recombination genetic introgression adaptive landscape |
| title | Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil |
| title_full | Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil |
| title_fullStr | Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil |
| title_full_unstemmed | Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil |
| title_short | Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil |
| title_sort | incipient parallel evolution of sars cov 2 deltacron variant in south brazil |
| topic | COVID-19 SARS-CoV-2 genomes gene flow recombination genetic introgression adaptive landscape |
| url | https://www.mdpi.com/2076-393X/11/2/212 |
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