Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City. Wertheim, J. O, Wang, J. C, Leelawong, M., Martin, D. P, Havens, J. L, Chowdhury, M. A, Pekar, J., Amin, H., Arroyo, A., Awandare, G. A, Chow, H. Y., Gonzalez, E., Luoma, E., Morang'a, C. M, Nekrutenko, A., Shank, S. D, Quashie, P. K, Rakeman, J. L, Ruiz, V., Torian, L. V, Vasylyeva, T. I, Pond, S. L. K., & Hughes, S. medRxiv, Cold Spring Harbor Laboratory Press, jan, 2022.
Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City [link]Paper  doi  abstract   bibtex   
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts revealed that Alpha variant alleles comprised between 70-80% of the genomes, whereas the Epsilon variant alleles comprised between 20-30% of the sample. Further investigation revealed the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity. ### Competing Interest Statement J.O.W. and S.L.K.P has received funding from the CDC (ongoing) via contracts or agreements to their institution unrelated to this research. All other authors declare no competing interests. ### Funding Statement J.O.W. acknowledges funding from the National Institutes of Health (AI135992 and AI136056). D.P.M was funded by the Wellcome Trust (222574/Z/21/Z). PKQ is funded by a Crick African Network Fellowship. T.I.V. is funded by a Branco Weiss Fellowship. S.L.K.P and A.N were supported in part by a grant from the National Institutes of Health (AI134384). This work was supported (in part) by the Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases Cooperative Agreement (Grant Number: ELC DETECT (6NU50CK000517-01-07) funded by the Centers for Disease Control and Prevention (CDC). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC or the Department of Health and Human Services. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IRB of UC San Diego waived gave ethical approval of this work as human subjects except. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The data analyzed as part of this project were obtained from the GISAID database and through a Data Use Agreement between NYC DOHMH and the University of California San Diego. We gratefully acknowledge the authors from the originating laboratories and the submitting laboratories, who generated and shared via GISAID the viral genomic sequence data on which this research is based. A complete list acknowledging the authors who submitted the data analyzed in this study can be found in Data S1. Trimmed, host-depleted viral sequencing data and cloned sequence fragments have been submitted to NCBI (accession numbers pending).
@article{Wertheim2022a,
abstract = {Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts revealed that Alpha variant alleles comprised between 70-80{\%} of the genomes, whereas the Epsilon variant alleles comprised between 20-30{\%} of the sample. Further investigation revealed the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity. {\#}{\#}{\#} Competing Interest Statement J.O.W. and S.L.K.P has received funding from the CDC (ongoing) via contracts or agreements to their institution unrelated to this research. All other authors declare no competing interests. {\#}{\#}{\#} Funding Statement J.O.W. acknowledges funding from the National Institutes of Health (AI135992 and AI136056). D.P.M was funded by the Wellcome Trust (222574/Z/21/Z). PKQ is funded by a Crick African Network Fellowship. T.I.V. is funded by a Branco Weiss Fellowship. S.L.K.P and A.N were supported in part by a grant from the National Institutes of Health (AI134384). This work was supported (in part) by the Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases Cooperative Agreement (Grant Number: ELC DETECT (6NU50CK000517-01-07) funded by the Centers for Disease Control and Prevention (CDC). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC or the Department of Health and Human Services. {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IRB of UC San Diego waived gave ethical approval of this work as human subjects except. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The data analyzed as part of this project were obtained from the GISAID database and through a Data Use Agreement between NYC DOHMH and the University of California San Diego. We gratefully acknowledge the authors from the originating laboratories and the submitting laboratories, who generated and shared via GISAID the viral genomic sequence data on which this research is based. A complete list acknowledging the authors who submitted the data analyzed in this study can be found in Data S1. Trimmed, host-depleted viral sequencing data and cloned sequence fragments have been submitted to NCBI (accession numbers pending).},
author = {Wertheim, Joel O and Wang, Jade C and Leelawong, Mindy and Martin, Darren P and Havens, Jennifer L and Chowdhury, Moinuddin A and Pekar, Jonathan and Amin, Helly and Arroyo, Anthony and Awandare, Gordon A and Chow, Hoi Yan and Gonzalez, Edimarlyn and Luoma, Elizabeth and Morang'a, Collins M and Nekrutenko, Anton and Shank, Stephen D and Quashie, Peter K and Rakeman, Jennifer L and Ruiz, Victoria and Torian, Lucia V and Vasylyeva, Tetyana I and Pond, Sergei L. Kosakovsky and Hughes, Scott},
doi = {10.1101/2022.01.18.22269300},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wertheim et al. - 2022 - Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New(2).pdf:pdf},
journal = {medRxiv},
keywords = {OA,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,genomics{\_}fund{\_}ack,original},
month = {jan},
pages = {2022.01.18.22269300},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City}},
url = {https://www.medrxiv.org/content/10.1101/2022.01.18.22269300v1 https://www.medrxiv.org/content/10.1101/2022.01.18.22269300v1.abstract},
year = {2022}
}
Downloads: 0
About
Documentation
Keywords
Search
Users
Terms and Conditions of Use
Privacy Policy
Sitemap
© BibBase.org 2021