Dataset Information

Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.

ABSTRACT: We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflecting superspreading dynamics from mid-February during the carnival season, distinct viral strains were circulating in Düsseldorf in March, reflecting the city's international links. Limited detection of Heinsberg strains in the Düsseldorf area despite geographical proximity may reflect efficient containment and contact-tracing efforts.

SUBMITTER: Walker A

PROVIDER: S-EPMC7336109 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.

Walker Andreas A Houwaart Torsten T Wienemann Tobias T Vasconcelos Malte Kohns MK Strelow Daniel D Senff Tina T Hülse Lisanna L Adams Ortwin O Andree Marcel M Hauka Sandra S Feldt Torsten T Jensen Björn-Erik BE Keitel Verena V Kindgen-Milles Detlef D Timm Jörg J Pfeffer Klaus K Dilthey Alexander T AT

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 20200601 22

We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflecting superspreading dynamics from mid-February during the carnival season, distinct viral strains were circulating in Düsseldorf in March, reflecting the city's international links. Limited detection of Heinsberg strains in the Düsseldorf area despite geographical ...[more]

PMID: 32524946

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Project description:Background:Due to the risk of spreading epizootic diseases through rodents, pest control is mandatory in pig farming in European countries. However, there is limited research focused on rodent control practices, usage of anticoagulant rodenticides, and the acceptance of Pest Control Operators (PCOs) in pig farming in Germany. Therefore, the present study aims to investigate current control practices in pig holdings and to analyze the potential of a financial support on the implementation of professional pest control. Results:Data were collected from monitoring records of PCOs and personal interviews with farmers and PCOs. 33 of 47 farmers, who were offered the possibility to outsource rodent control to PCOs supported by financial contribution of the North Rhine-Westphalian Animal Disease Fund (TSK) for a period of 2 years, joined the project.Despite the widespread opinion that the professional would not be beneficial - the authors figured out that farmers could financially benefit in time saved and by improved rodent control measures from the work of the PCOs. Costs of pest control measures per operation on average did not differ significantly between costs incurred by employment of PCOs (1.310 € per year) and calculated costs that arise by farmers themselves (1.217 € per year).All PCOs used Difenacoum and Brodifacoum against pest infestations. In doing so, the infestation with rodents was reduced and most of the participating farmers assessed the project as successful and employ the PCOs permanently. However, mapping the farm locations to resistance areas of the Rodenticide Resistance Action Committee (RRAC) shows that Brodifacoum was frequently used in areas which are marked as areas that are at low risk or rather have no risk for resistance. The environmental risks, however, are increased in these areas. Conclusion:The instrument of temporal start-up financing professional pest control allows ensuring the continuous engagement of PCOs after the project period. This could possibly lead to long-term effects on the individual farm hygiene and on disease prevention. Nevertheless, important research questions with regard to the application of anticoagulant rodenticides of farmers and PCOs in livestock farming and with regard to risk mitigation measures were generated, meriting further investigation.

Project description:BackgroundThe Dutch province of Limburg borders the German district of Heinsberg, which had a large cluster of COVID-19 cases linked to local carnival activities before any cases were reported in the Netherlands. However, Heinsberg was not included as an area reporting local or community transmission per the national case definition at the time. In early March, two residents from a long-term care facility (LTCF) in Sittard, a Dutch town located in close vicinity to the district of Heinsberg, tested positive for COVID-19. In this study we aimed to determine whether cross-border introduction of the virus took place by analysing the LTCF outbreak in Sittard, both epidemiologically and microbiologically.MethodsSurveys and semi-structured oral interviews were conducted with all present LTCF residents by health care workers during regular points of care for information on new or unusual signs and symptoms of disease. Both throat and nasopharyngeal swabs were taken from residents suspect of COVID-19, based on regional criteria, for the detection of SARS-CoV-2 by Real-time Polymerase Chain Reaction. Additionally, whole genome sequencing was performed using a SARS-CoV-2 specific amplicon-based Nanopore sequencing approach. Moreover, twelve random residents were sampled for possible asymptomatic infections.ResultsOut of 99 residents, 46 got tested for COVID-19. Out of the 46 tested residents, nineteen (41%) tested positive for COVID-19, including 3 asymptomatic residents. CT-values for asymptomatic residents seemed higher compared to symptomatic residents. Eleven samples were sequenced, along with three random samples from COVID-19 patients hospitalized in the regional hospital at the time of the LTCF outbreak. All samples were linked to COVID-19 cases from the cross-border region of Heinsberg, Germany.ConclusionsSequencing combined with epidemiological data was able to virtually prove cross-border transmission at the start of the Dutch COVID-19 epidemic. Our results highlight the need for cross-border collaboration and adjustment of national policy to emerging region-specific needs along borders in order to establish coordinated implementation of infection control measures to limit the spread of COVID-19.

Dataset Information

Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.

Publications

Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.

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