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SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany
OBJECTIVES: Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters in Hamburg, Germany. METHODS: Metagenomic RNA-sequencing and amplicon-sequencing...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524521/ https://www.ncbi.nlm.nih.gov/pubmed/33007476 http://dx.doi.org/10.1016/j.cmi.2020.09.034 |
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author | Pfefferle, Susanne Günther, Thomas Kobbe, Robin Czech-Sioli, Manja Nörz, Dominic Santer, René Oh, Jun Kluge, Stefan Oestereich, Lisa Peldschus, Kersten Indenbirken, Daniela Huang, Jiabin Grundhoff, Adam Aepfelbacher, Martin Knobloch, Johannes K. Lütgehetmann, Marc Fischer, Nicole |
author_facet | Pfefferle, Susanne Günther, Thomas Kobbe, Robin Czech-Sioli, Manja Nörz, Dominic Santer, René Oh, Jun Kluge, Stefan Oestereich, Lisa Peldschus, Kersten Indenbirken, Daniela Huang, Jiabin Grundhoff, Adam Aepfelbacher, Martin Knobloch, Johannes K. Lütgehetmann, Marc Fischer, Nicole |
author_sort | Pfefferle, Susanne |
collection | PubMed |
description | OBJECTIVES: Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters in Hamburg, Germany. METHODS: Metagenomic RNA-sequencing and amplicon-sequencing and subsequent variant calling in 25 respiratory samples from SARS-CoV-2 infected patients involved in the earliest infection clusters in Hamburg. RESULTS: Amplikon sequencing and cluster analyses of these SARS-CoV-2 sequences allowed the identification of the first infection cluster and five non-related infection clusters occurring at the beginning of the viral entry of SARS-CoV-2 in the Hamburg metropolitan region. Viral genomics together with epidemiological analyses revealed that the index patient acquired the infection in northern Italy and transmitted it to two out of 134 contacts. Single nucleotide polymorphisms clearly distinguished the virus variants of the index and other clusters and allowed us to track in which sequences worldwide these mutations were first described. Minor variant analyses identified the transmission of intra-host variants in the index cluster and household clusters. CONCLUSIONS: SARS-CoV-2 variant tracing allows the identification of infection clusters and the follow up of infection chains occurring in the population. Furthermore, the follow up of minor viral variants in infection clusters can provide further resolution on transmission events indistinguishable at a consensus sequence level. |
format | Online Article Text |
id | pubmed-7524521 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75245212020-09-30 SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany Pfefferle, Susanne Günther, Thomas Kobbe, Robin Czech-Sioli, Manja Nörz, Dominic Santer, René Oh, Jun Kluge, Stefan Oestereich, Lisa Peldschus, Kersten Indenbirken, Daniela Huang, Jiabin Grundhoff, Adam Aepfelbacher, Martin Knobloch, Johannes K. Lütgehetmann, Marc Fischer, Nicole Clin Microbiol Infect Research Note OBJECTIVES: Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters in Hamburg, Germany. METHODS: Metagenomic RNA-sequencing and amplicon-sequencing and subsequent variant calling in 25 respiratory samples from SARS-CoV-2 infected patients involved in the earliest infection clusters in Hamburg. RESULTS: Amplikon sequencing and cluster analyses of these SARS-CoV-2 sequences allowed the identification of the first infection cluster and five non-related infection clusters occurring at the beginning of the viral entry of SARS-CoV-2 in the Hamburg metropolitan region. Viral genomics together with epidemiological analyses revealed that the index patient acquired the infection in northern Italy and transmitted it to two out of 134 contacts. Single nucleotide polymorphisms clearly distinguished the virus variants of the index and other clusters and allowed us to track in which sequences worldwide these mutations were first described. Minor variant analyses identified the transmission of intra-host variants in the index cluster and household clusters. CONCLUSIONS: SARS-CoV-2 variant tracing allows the identification of infection clusters and the follow up of infection chains occurring in the population. Furthermore, the follow up of minor viral variants in infection clusters can provide further resolution on transmission events indistinguishable at a consensus sequence level. European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. 2021-01 2020-09-29 /pmc/articles/PMC7524521/ /pubmed/33007476 http://dx.doi.org/10.1016/j.cmi.2020.09.034 Text en © 2020 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Research Note Pfefferle, Susanne Günther, Thomas Kobbe, Robin Czech-Sioli, Manja Nörz, Dominic Santer, René Oh, Jun Kluge, Stefan Oestereich, Lisa Peldschus, Kersten Indenbirken, Daniela Huang, Jiabin Grundhoff, Adam Aepfelbacher, Martin Knobloch, Johannes K. Lütgehetmann, Marc Fischer, Nicole SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany |
title | SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany |
title_full | SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany |
title_fullStr | SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany |
title_full_unstemmed | SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany |
title_short | SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany |
title_sort | sars coronavirus-2 variant tracing within the first coronavirus disease 19 clusters in northern germany |
topic | Research Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524521/ https://www.ncbi.nlm.nih.gov/pubmed/33007476 http://dx.doi.org/10.1016/j.cmi.2020.09.034 |
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