Large-scale SARS-CoV-2 sequencing indicates prior community circulation of the viral strain associated with Germany's largest meat processing plant.

A SARS-CoV-2 outbreak at a meat processing plant (MPP) in the German district of Gütersloh accounted for 18% of Germany's SARS-CoV-2 cases in June 2020 and was subject of intense public interest, including the speculation that the outbreak strain may have been imported by foreign MPP workers. We sequenced the SARS-CoV-2 genomes of 1,438 SARS-CoV-2 samples collected from Gütersloh MPP workers for serial diagnostic testing and screening purposes ("outbreak samples"; approximate case coverage 68%) and of 157 samples collected from Gütersloh-area cases for routine diagnostic purposes ("community samples"). Greater than 98% of outbreak samples carried the outbreak-associated strain, defined by eight mutations and lineage B.1.329, confirming the overall clonality of the outbreak and showing that potential secondary introductions of other viral lineages had an at most limited role. Of fifteen viral sub-lineages detected in early outbreak-associated samples sequenced by another study, only one showed substantial persistence into the peak outbreak period, suggesting that transmission dynamics within the MPP were influenced by bottlenecks and superspreading-like patterns. While the detection of B.1.329 in community samples peaked during the outbreak, it was found to be present in community samples between March and September 2020, with the first exact matches to the outbreak strain appearing in April 2020. We found no epidemiological connections between early B.1.329-carrying community cases and the MPP, and a GISAID search for B.1.329 did not identify any samples collected outside of Germany. The outbreak strain was therefore likely circulating within the community before the outbreak and there was no indication of importation by MPP workers. Our study demonstrates how large-scale viral genome sequencing can contribute to the investigation of outbreaks and inform public discourse.