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Molecular epidemiology of SARS-CoV-2: a regional to global perspective


Kühnert,  Denise
tide, Max Planck Institute for the Science of Human History, Max Planck Society;

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Brandt, C., Spott, R., Hölzer, M., Kühnert, D., Fuchs, S., Lohde, M., et al. (2021). Molecular epidemiology of SARS-CoV-2: a regional to global perspective. medRxiv, 2021.01.25.21250447. doi:10.1101/2021.01.25.21250447.

Cite as: https://hdl.handle.net/21.11116/0000-0007-DCE8-C
Background After a year of the global SARS-CoV-2 pandemic, a highly dynamic genetic diversity is surfacing. Among nearly 1000 reported virus lineages, dominant lineages such as B.1.1.7 or B.1.351 attract media attention with questions regarding vaccine efficiency and transmission potential. In response to the pandemic, the Jena University Hospital began sequencing SARS-CoV-2 samples in Thuringia in early 2020.Methods Viral RNA was sequenced in tiled amplicons using Nanopore sequencing. Subsequently, bioinformatic workflows were used to process the generated data. As a genomic background, 9,642 representative SARS-CoV-2 genomes (1,917 of German origin) were extracted from more than 300.000 genomes.Results In a comprehensive bioinformatics analysis, we have set Thuringian isolates in the German, European and global context. In Thuringia, a largely rural German region without an international airport and a population density below the German average, we discovered many of the common “EU lineages”. German samples are scattered across eight major clades, and Thuringian samples occupy four of them.Conclusion The rapid emergence and spread of novel variants are of great concern as these lineages could transmit more efficiently, evade current vaccine efforts or undermine diagnostic test accuracy. To anticipate and mitigate these threats, a continuous molecular surveillance is essential.Key messagesBioinformatics analysis of 1,917, 4,251, and 3,474 SARS-CoV-2 genomes from Germany, the EU (except Germany), and non-EU, respectively, subsampled from more than 300,000 public genomes and placed in the context of Thuringian sequencesConstant antigenic drift for SARS-CoV-2 and no clear pattern or clustering is visible in Thuringia based on the current number of samplesCurrently over 100 described lineages are identified in Germany and only a subset (9) are detected in Thuringia so far, most likely due to genetic undersamplingFrom a national perspective, it is likely that high-frequency lineages, which are currently spreading throughout Europe, will eventually also reach ThuringiaSystematic and dense molecular surveillance via whole-genome sequencing is needed to detect concerning new lineages early, limit spread and adjust vaccines if necessaryCompeting Interest StatementThe authors have declared no competing interest.Funding StatementThe work is funded by the German Ministry of Education and Research (BMBF), grant number 01KX2021, and the Thuringian Region Government, grant number TZUZI82094.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:not applicableAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI 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).YesI 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.YesAll data is available on GISAID.