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Genomic surveillance of the Lambda SARS‐CoV‐2 variant in a global phylogenetic context
The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in P...
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Published in: | Journal of medical virology 2022-10, Vol.94 (10), p.4689-4695 |
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creator | Mestanza, Orson Lizarraga, Wendy Padilla‐Rojas, Carlos Jimenez‐Vasquez, Víctor Hurtado, Verónica Molina, Iris S. Barcena, Luis Acedo, Steve Nuñez, Alicia Gordillo, Sara Sevilla, Nieves Medrano, Princesa Bailon, Henri Cáceres, Omar Galarza, Marco Rojas‐Serrano, Nancy Vargas‐Herrera, Natalia Lope‐Pari, Priscila Huayra, Joseph Araujo‐Castillo, Roger V. Solari, Lely |
description | The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS‐CoV‐2 wave. |
doi_str_mv | 10.1002/jmv.27889 |
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The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS‐CoV‐2 wave.</description><identifier>ISSN: 0146-6615</identifier><identifier>EISSN: 1096-9071</identifier><identifier>DOI: 10.1002/jmv.27889</identifier><identifier>PMID: 35644902</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Coronaviruses ; Epidemiology ; genomic surveillance ; Genomics ; lambda ; local outbreaks ; Mutation ; Pandemics ; Phylogenetics ; Phylogeny ; SARS‐CoV‐2 ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Spike mutations ; Surveillance ; Viral diseases ; Virology ; Viruses</subject><ispartof>Journal of medical virology, 2022-10, Vol.94 (10), p.4689-4695</ispartof><rights>2022 Wiley Periodicals LLC.</rights><rights>This article is protected by copyright. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4439-cc71db153c44b60f497bcf6ed82b2b9755ced74790424beb265eaaa586018913</citedby><cites>FETCH-LOGICAL-c4439-cc71db153c44b60f497bcf6ed82b2b9755ced74790424beb265eaaa586018913</cites><orcidid>0000-0003-0974-9096 ; 0000-0001-7268-0496 ; 0000-0002-8041-8807 ; 0000-0003-3667-6806 ; 0000-0002-0948-0114 ; 0000-0002-9940-1036 ; 0000-0002-6547-2354 ; 0000-0002-3740-1962 ; 0000-0003-2595-5674 ; 0000-0003-1529-2475 ; 0000-0002-3194-8043 ; 0000-0003-1906-7419 ; 0000-0001-7290-9254 ; 0000-0002-9593-6092 ; 0000-0001-8776-8888 ; 0000-0003-0451-604X ; 0000-0002-7439-4351 ; 0000-0002-0562-0431 ; 0000-0001-6547-6999 ; 0000-0003-4126-7038</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjmv.27889$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjmv.27889$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,315,786,790,891,27957,27958,50923,51032</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35644902$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mestanza, Orson</creatorcontrib><creatorcontrib>Lizarraga, Wendy</creatorcontrib><creatorcontrib>Padilla‐Rojas, Carlos</creatorcontrib><creatorcontrib>Jimenez‐Vasquez, Víctor</creatorcontrib><creatorcontrib>Hurtado, Verónica</creatorcontrib><creatorcontrib>Molina, Iris S.</creatorcontrib><creatorcontrib>Barcena, Luis</creatorcontrib><creatorcontrib>Acedo, Steve</creatorcontrib><creatorcontrib>Nuñez, Alicia</creatorcontrib><creatorcontrib>Gordillo, Sara</creatorcontrib><creatorcontrib>Sevilla, Nieves</creatorcontrib><creatorcontrib>Medrano, Princesa</creatorcontrib><creatorcontrib>Bailon, Henri</creatorcontrib><creatorcontrib>Cáceres, Omar</creatorcontrib><creatorcontrib>Galarza, Marco</creatorcontrib><creatorcontrib>Rojas‐Serrano, Nancy</creatorcontrib><creatorcontrib>Vargas‐Herrera, Natalia</creatorcontrib><creatorcontrib>Lope‐Pari, Priscila</creatorcontrib><creatorcontrib>Huayra, Joseph</creatorcontrib><creatorcontrib>Araujo‐Castillo, Roger V.</creatorcontrib><creatorcontrib>Solari, Lely</creatorcontrib><title>Genomic surveillance of the Lambda SARS‐CoV‐2 variant in a global phylogenetic context</title><title>Journal of medical virology</title><addtitle>J Med Virol</addtitle><description>The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS‐CoV‐2 wave.</description><subject>Coronaviruses</subject><subject>Epidemiology</subject><subject>genomic surveillance</subject><subject>Genomics</subject><subject>lambda</subject><subject>local outbreaks</subject><subject>Mutation</subject><subject>Pandemics</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>SARS‐CoV‐2</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Spike mutations</subject><subject>Surveillance</subject><subject>Viral diseases</subject><subject>Virology</subject><subject>Viruses</subject><issn>0146-6615</issn><issn>1096-9071</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNp1kcFu1DAQhi0EokvhwAsgS1zoIa3tOHZ8QapWtIAWIdGqBy6W7Ux2vUrsbZws7I1H4Bl5ErxsqQCJi0fWfPo0Mz9Czyk5pYSws3W_PWWyrtUDNKNEiUIRSR-iGaFcFELQ6gg9SWlNCKkVY4_RUVkJzhVhM_T5EkLsvcNpGrbgu84EBzi2eFwBXpjeNgZfnX-6-vHt-zze5JfhrRm8CSP2ARu87KI1Hd6sdl1cQoAxq1wMI3wdn6JHrekSPLurx-j64s31_G2x-Hj5bn6-KBznpSqck7SxtCrz1wrSciWtawU0NbPMKllVDhrJpSKccQuWiQqMMVUtCK0VLY_R64N2M9keGgdhHEynN4PvzbDT0Xj9dyf4lV7GrVYlzzcrs-DVnWCItxOkUfc-OdifAuKUNBOSlVRSIjL68h90Hach5O00k4RJWTGxp04OlBtiSgO098NQoveB6RyY_hVYZl_8Of09-TuhDJwdgC--g93_Tfr9h5uD8ieyw6HB</recordid><startdate>202210</startdate><enddate>202210</enddate><creator>Mestanza, Orson</creator><creator>Lizarraga, Wendy</creator><creator>Padilla‐Rojas, Carlos</creator><creator>Jimenez‐Vasquez, Víctor</creator><creator>Hurtado, Verónica</creator><creator>Molina, Iris S.</creator><creator>Barcena, Luis</creator><creator>Acedo, Steve</creator><creator>Nuñez, Alicia</creator><creator>Gordillo, Sara</creator><creator>Sevilla, Nieves</creator><creator>Medrano, Princesa</creator><creator>Bailon, Henri</creator><creator>Cáceres, Omar</creator><creator>Galarza, Marco</creator><creator>Rojas‐Serrano, Nancy</creator><creator>Vargas‐Herrera, Natalia</creator><creator>Lope‐Pari, Priscila</creator><creator>Huayra, Joseph</creator><creator>Araujo‐Castillo, Roger V.</creator><creator>Solari, Lely</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7TK</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0974-9096</orcidid><orcidid>https://orcid.org/0000-0001-7268-0496</orcidid><orcidid>https://orcid.org/0000-0002-8041-8807</orcidid><orcidid>https://orcid.org/0000-0003-3667-6806</orcidid><orcidid>https://orcid.org/0000-0002-0948-0114</orcidid><orcidid>https://orcid.org/0000-0002-9940-1036</orcidid><orcidid>https://orcid.org/0000-0002-6547-2354</orcidid><orcidid>https://orcid.org/0000-0002-3740-1962</orcidid><orcidid>https://orcid.org/0000-0003-2595-5674</orcidid><orcidid>https://orcid.org/0000-0003-1529-2475</orcidid><orcidid>https://orcid.org/0000-0002-3194-8043</orcidid><orcidid>https://orcid.org/0000-0003-1906-7419</orcidid><orcidid>https://orcid.org/0000-0001-7290-9254</orcidid><orcidid>https://orcid.org/0000-0002-9593-6092</orcidid><orcidid>https://orcid.org/0000-0001-8776-8888</orcidid><orcidid>https://orcid.org/0000-0003-0451-604X</orcidid><orcidid>https://orcid.org/0000-0002-7439-4351</orcidid><orcidid>https://orcid.org/0000-0002-0562-0431</orcidid><orcidid>https://orcid.org/0000-0001-6547-6999</orcidid><orcidid>https://orcid.org/0000-0003-4126-7038</orcidid></search><sort><creationdate>202210</creationdate><title>Genomic surveillance of the Lambda SARS‐CoV‐2 variant in a global phylogenetic context</title><author>Mestanza, Orson ; 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The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. 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subjects | Coronaviruses Epidemiology genomic surveillance Genomics lambda local outbreaks Mutation Pandemics Phylogenetics Phylogeny SARS‐CoV‐2 Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Spike mutations Surveillance Viral diseases Virology Viruses |
title | Genomic surveillance of the Lambda SARS‐CoV‐2 variant in a global phylogenetic context |
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