Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Gutierrez, Bernardo; Castelán-Sánchez, Hugo G; Cândido, Darlan da Silva; Jackson, Ben; Fleishon, Shay; Houzet, Renaud; Ruis, Christopher; Delaye, Luis; Faria, Nuno R.; Rambaut, Andrew; Pybus, Oliver G.; Escalera-Zamudio, Marina

doi:10.1016/j.chom.2022.06.010

Cited by 32 publications

(33 citation statements)

References 52 publications

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“…Over 200 different virus lineages have been detected in Mexico, including all VOC 19,33 . Many lineages also co-circulated across time and space, an observation of particular importance in the context of the recently described recombinant SARS-CoV-2 linages that emerged in North America during 2021 34 .…”

Section: Introductionmentioning

confidence: 99%

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Castelán-Sánchez

Delaye

Inward

et al. 2022

Preprint

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Up to November 2021, over 200 different SARS-CoV-2 lineages circulated in Mexico. To investigate lineage replacement dynamics, we applied a phylodynamic approach to explore the evolutionary trajectories of five dominant lineages that circulated during the first year of the local epidemic. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in the country. Lineages B.1.1.222 and B.1.1.519 showed comparable dynamics, represented by clades likely originating in Mexico and persisting for over a year. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. We further explored viral movements across the country, applied within the largest clades identified (belonging to lineage B.1.617.2). Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

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Section: Introductionmentioning

confidence: 99%

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Castelán-Sánchez

Delaye

Inward

et al. 2022

Preprint

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“…Both 3SEQ, as well as RDP5 using the default settings, were unable to detect recombination events on these three lineage sequences. Parent sequences of XB were previously reported to be B.1.631 and B.1.634 (15). Of the three recombinant lineages that emerged before the omicron wave, XA is recombinant of the alpha variant sub-lineage (Q4) 1].…”

Section: The Majority Of Sars-cov-2 Recombinant Lineages Emerged Thro...mentioning

confidence: 99%

“…Recombination events in the SARS-CoV-2 genome during COVID-19 pandemic have been examined before in specific contexts (15,20,(23)(24)(25). The first recombinant lineage reported, named XA appeared first in the UK and continued to circulate for a limited time (20).…”

Section: Introductionmentioning

confidence: 99%

Enhanced Recombination Among SARS-CoV-2 Omicron Variants Contributes to Viral Immune Escape

Shiraz

Tripathi

2022

Preprint

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SARS-CoV-2 virus evolution occurs as a result of antigenic drift and shift. Although antigenic drift has been extensively studied, antigenic shift, which for SARS-CoV-2 occurs through genetic recombination, has been examined scarcely. To gain a better understanding of the emergence and prevalence of recombinant SARS-CoV-2 lineages through time and space, we analyzed SARS-CoV-2 genome sequences from public databases. Our study revealed an extraordinary increase in the emergence of SARS-CoV-2 recombinant lineages during the Omicron wave, particularly in Northern America and Europe. This phenomenon was independent of sequencing density or genetic diversity of circulating SARS-CoV-2 strains. In SARS-CoV-2 genomes, recombination breakpoints were found to be more concentrated in the 3- UTR followed by ORF1a. Additionally, we noted enrichment of certain amino acids in the spike protein of recombinant lineages, which have been reported to confer immune escape from neutralizing antibodies, increase ACE2 receptor binding, and enhance viral transmission in some cases. Overall, we report an important and timely observation of accelerated recombination in the currently circulating Omicron variants and explore their potential contribution to viral fitness, particularly immune escape.

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“…La recombinación es un proceso habitual en la evolución de los coronavirus. Si bien no se ha podido determinar su implicación directa e inmediata en la aparición del SARS-CoV-2, la documentación de su presencia en etapas evolutivas anteriores (Boni et al, 2020) y en la actualidad (Gutierrez et al, 2021;Jackson et al, 2021) hacen que no sea una mera conjetura invocar su papel en el origen de este virus. La obtención de la primera secuencia genómica del SARS-CoV-2 en enero de 2020 permitió un análisis inmediato de su relación con otros coronavirus ya secuenciados hasta ese momento.…”

Section: Palabras Claveunclassified

Genética y evolución en la pandemia de COVID-19

Cadenas¹

2021

ambiociencias

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La pandemia ocasionada por el coronavirus SARS-CoV-2 ha alterado la vida, la economía, las relaciones sociales y personales en nuestro planeta y, desgraciadamente, ha producido más de 5 millones de muertes (datos a noviembre de 2021). Por otra parte, ha puesto de manifiesto el papel esencial que tiene la investigación biomédica y lo dependiente que es nuestra sociedad de muchos trabajos científicos que solían pasar inadvertidos. Además de mostrar el poder que se deriva de la acción coordinada y cooperativa de grupos de investigación, la pandemia también ha puesto un foco en disciplinas que, en gran medida, han sido ignoradas hasta el momento. La aparición de variantes de preocupación e interés y su relación con los incrementos en la incidencia de las infecciones en diferentes olas o la posibilidad de que representen escapes vacunales ha llevado a la OMS a establecer la vigilancia genómica como una de las herramientas fundamentales para conocer y controlar la expansión del virus. En este artículo, vamos a analizar algunos aspectos fundamentales de la evolución y genética de las poblaciones delvirus y cómo nos pueden ayudar a interpretar adecuadamente los datos derivados de los análisis de secuencias completas del genoma viral, método ideal pararealizar dicha vigilancia.

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Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Cited by 32 publications

References 52 publications

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Enhanced Recombination Among SARS-CoV-2 Omicron Variants Contributes to Viral Immune Escape

Genética y evolución en la pandemia de COVID-19

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