Investigating the cause of a 2021 winter wave of COVID-19 in a border region in Eastern Germany: a mixed-methods study, August to November 2021.

In winter 2020 and 2021 many countries worldwide experienced a COVID-19 pandemic wave which led to severe burdens on healthcare systems and huge economic losses. Yet, it remains unclear how the winter waves started and many debates are ongoing about actions necessary to prevent future winter waves. In this study we deciphered the dynamic course of a winter wave in 2021 in Saxony, a state in Eastern Germany neighboring Czech Republic and Poland. The information we achieved might help future pandemic prevention. The dynamic course of the 2021 winter wave in Saxony was investigated through integration of multiple virus genomic epidemiology approaches and functional evaluations of locally circulating variants. Through international collaborations, we performed genomic epidemiology analysis on a weekly base with samples from Saxony and also from one neighbor region in the Czech Republic. Phylogeny analyses were used to track transmission chains, monitor virus genetic changes and identify emerging variants. Phylodynamic approaches have been applied to track the dynamic changes of transmission clusters. For identified local variants of interest, active viruses were isolated and functional evaluations were performed. Genomic epidemiology studies revealed multiple long-lasting community transmission clusters acting as the major driving forces for the winter wave 2021. Analysis of the dynamic courses of two representative long-lasting community transmission clusters indicated similar dynamic changes. In the first 6-8 weeks, the relevant variant was mainly circulating in a small region among young and middle-aged people; after eight weeks, the ratio of people aged above 60 years in the infected population markedly increased, and the virus got more widely spread to distant regions. On the other hand, the transmission cluster caused by a locally occurring variant showed a different transmission pattern. It got geographically widely distributed within six weeks, with many people aged above 60 years being infected since the beginning of the cluster, indicating a higher risk for escalating healthcare burdens. This variant displayed a relative growth advantage compared to co-circulating Delta sub-lineages. Functional analyses revealed a replication advantage, but no advantage in immune evasion ability. This study indicated that long-lasting community transmission clusters starting between August and October caused by imported variants as well as locally occurring variants all contributed to the development of the 2021 winter wave in Saxony. In particular, the cluster derived from a locally occurring variant with certain growth advantage might have stressed local healthcare systems. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Parts of this study were supported by a grant from the German Ministry of Health (BMG) to A.D. (project LueSeMut) as well as by a grant from the State Parliament of the Free State of Saxony to A.D. B.Y. is in part supported by a funding from German Research Foundation (DFG YI175/1-1). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of TU Dresden waived ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I 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). Yes I 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. Yes All data produced in the present work are contained in the manuscript.