Refine
Document Type
- Article (25)
Language
- English (25)
Has Fulltext
- yes (25)
Is part of the Bibliography
- no (25)
Keywords
- - (15)
- Germany (4)
- MRSA (4)
- antimicrobial resistance (3)
- coagulase-negative staphylococci (3)
- infection prevention (3)
- susceptibility testing (3)
- <i>Staphylococcus aureus</i> (2)
- ESBL (2)
- North Rhine–Westphalia (2)
Institute
- Friedrich-Loeffler-Institut für Medizinische Mikrobiologie (18)
- Institut für Community Medicine (1)
- Institut für Hygiene und Umweltmedizin (1)
- Institut für Immunologie u. Transfusionsmedizin - Abteilung Immunologie (1)
- Institut für Med. Biochemie u. Molekularbiologie (1)
- Institut für Mikrobiologie - Abteilung für Genetik & Biochemie (1)
- Klinik und Poliklinik für Mund-, Kiefer- und Gesichtschirurgie/Plastische Operationen (1)
Publisher
- MDPI (18)
- Frontiers Media S.A. (4)
- American Society for Microbiology (ASM) (1)
- Springer Nature (1)
- Taylor & Francis (1)
Global and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the German federal state of Mecklenburg-Western Pomerania (M-V) was formed to investigate the regional molecular epidemiology of circulating SARS-CoV-2 lineages between 11/2020 and 03/2022. More than 4750 samples from all M-V counties were sequenced using Illumina and Nanopore technologies. Overall, 3493 (73.5%) sequences fulfilled quality criteria for time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/ median clustering (KMC). We identified 116 different Pangolin virus lineages that can be assigned to 16 Nextstrain clades. The ten most frequently detected 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. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant limited to western M-V counties. Finally, KMC elucidated a successive introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. The COVID-19 pandemic in M-V was shaped by a combination of several SARS-CoV-2 introductions, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. Complementing global and national surveillance, regional surveillance adds value by providing a higher level of surveillance resolution tailored to local health authorities.