Genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020-2022
Background: Genome surveillance is used to understand the origin, transmission and evolution of the SARS-CoV-2, but global and even national surveillance approaches do not provide the resolve needed to respond rapidly and accurately enough directly on site by public health authorities. Aim: The purpose of this study was the investigation of the molecular epidemiology of circulating SARS-CoV-2 virus lineages between November 2020 and March 2022 of the German federal state of Mecklenburg-Western Pomerania (M-V). Methods: A total of 4750 samples were obtained from all counties in M-V and sequenced using Illumina and Nanopore technologies. Overall, 3,493 (73.5%) sequences fulfilled quality criteria for different phylogenetic analyses including time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/median clustering. Results: We identified 116 different Pangolin virus lineages which could be classified to 16 Nextstrain clades. The most sequenced virus lineages belonged to B.1.1.7, AY.122, AY.43, BA.1, B.1.617.2, BA.1.1, AY.9.2, AY.4, P.1 and AY.126 representing 67.99 % of all sequences. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial time delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant only in the western counties of M-V. Finally, a k-mean/median clustering (KMC) elucidated a successively introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. Conclusion: The COVID-19 pandemic in M-V was ultimately shaped by a combination of several introductions of SARS-CoV-2, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. In general, pathogen surveillance is feasible at a state or regional level, which will certainly lead to a higher surveillance resolution tailored for responsible public health authorities on site.