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SARS-CoV-2 variant tracing within the first COVID-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.
Afiliación
  • Pfefferle S; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  • Günther T; Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany.
  • Kobbe R; (b) I. Medical Clinic and Polyclinic, Section Infectious Diseases, University Medical Center Eppendorf, Hamburg, Germany.
  • Czech-Sioli M; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  • Nörz D; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  • Santer R; (b) I. Medical Clinic and Polyclinic, Section Infectious Diseases, University Medical Center Eppendorf, Hamburg, Germany.
  • Oh J; (b) I. Medical Clinic and Polyclinic, Section Infectious Diseases, University Medical Center Eppendorf, Hamburg, Germany.
  • Kluge S; Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  • Oestereich L; Bernhard Nocht Institute, Leibniz Institute for Tropical Medicine, Hamburg, Germany.
  • Peldschus K; Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  • Indenbirken D; Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany.
  • Huang J; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  • Grundhoff A; Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany.
  • Aepfelbacher M; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Electronic address: m.aepfelbacher@uke.de.
  • Knobloch JK; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Electronic address: j.knobloch@uke.de.
  • Lütgehetmann M; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Electronic address: mluetgehetmann@uke.de.
  • Fischer N; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Electronic address: nfischer@uke.de.
Artículo en Inglés | MEDLINE | ID: mdl-33007476
ABSTRACT

OBJECTIVES:

Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first SARS-CoV-2 infection clusters in Hamburg, Germany.

METHODS:

Metagenomic RNA- 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 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 cluster can provide further resolution on transmission events indistinguishable on consensus sequence level.
Texto completo: Disponible Colección: Bases de datos internacionales Base de datos: MEDLINE Idioma: Inglés Asunto de la revista: Enfermedades Transmisibles / Microbiologia Año: 2020 Tipo del documento: Artículo País de afiliación: Alemania

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Texto completo: Disponible Colección: Bases de datos internacionales Base de datos: MEDLINE Idioma: Inglés Asunto de la revista: Enfermedades Transmisibles / Microbiologia Año: 2020 Tipo del documento: Artículo País de afiliación: Alemania