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@ARTICLE{Bundschuh:288580,
      author       = {C. Bundschuh and N. Weidner and J. Klein and T. Rausch and
                      N. Azevedo and A. Telzerow and J.-P. Mallm$^*$ and H. Kim
                      and S. Steiger$^*$ and I. Seufert$^*$ and K. Börner and K.
                      Bauer$^*$ and D. Hübschmann$^*$ and K. L. Jost and S.
                      Parthé and P. Schnitzler and M. Boutros$^*$ and K.
                      Rippe$^*$ and B. Müller and R. Bartenschlager$^*$ and H.-G.
                      Kräusslich and V. Benes},
      title        = {{E}volution of {SARS}-{C}o{V}-2 in the
                      {R}hine-{N}eckar/{H}eidelberg {R}egion 01/2021 - 07/2023.},
      journal      = {Infection, genetics and evolution},
      volume       = {119},
      issn         = {1567-1348},
      address      = {Amsterdam [u.a.]},
      publisher    = {Elsevier Science},
      reportid     = {DKFZ-2024-00426},
      pages        = {105577},
      year         = {2024},
      note         = {2024 Apr;119:105577},
      abstract     = {In January 2021, the monitoring of circulating variants of
                      SARS-CoV-2 was initiated in Germany under the Corona
                      Surveillance Act, which was discontinued after July 2023.
                      This initiative aimed to enhance pandemic containment, as
                      specific amino acid changes, particularly in the spike
                      protein, were associated with increased transmission and
                      reduced vaccine efficacy. Our group conducted whole genome
                      sequencing using the ARTIC protocol (currently V4) on
                      Illumina's NextSeq 500 platform (and, starting in May 2023,
                      on the MiSeq DX platform) for SARS-CoV-2 positive specimen
                      from patients at Heidelberg University Hospital, associated
                      hospitals, and the public health office in the
                      Rhine-Neckar/Heidelberg region. In total, we sequenced
                      26,795 SARS-CoV-2-positive samples between January 2021 and
                      July 2023. Valid sequences, meeting the requirements for
                      upload to the German electronic sequencing data hub (DESH)
                      operated by the Robert Koch Institute (RKI), were determined
                      for 24,852 samples, and the lineage/clade could be
                      identified for 25,912 samples. The year 2021 witnessed
                      significant dynamics in the circulating variants in the
                      Rhine-Neckar/Heidelberg region, including A.27.RN, followed
                      by the emergence of B.1.1.7 (Alpha), subsequently displaced
                      by B.1.617.2 (Delta), and the initial occurrences of
                      B.1.1.529 (Omicron). By January 2022, B.1.1.529 had
                      superseded B.1.617.2, dominating with over $90\%.$ The years
                      2022 and 2023 were then characterized by the dominance of
                      B.1.1.529 and its sublineages, particularly BA.5 and BA.2,
                      and more recently, the emergence of recombinant variants
                      like XBB.1.5. Since the global dominance of B.1.617.2, the
                      identified variant distribution in our local study, apart
                      from a time delay in the spread of new variants, can be
                      considered largely representative of the global
                      distribution. om a time delay in the spread of new variants,
                      can be considered largely representative of the global
                      distribution.},
      keywords     = {ARTIC protocol (Other) / Bioinformatics (Other) /
                      Heidelberg/Rhine Neckar region (Other) / SARS-CoV-2 (Other)
                      / Whole genome sequencing (Other)},
      cin          = {W192 / B066 / A010 / B110 / F170 / D430},
      ddc          = {570},
      cid          = {I:(DE-He78)W192-20160331 / I:(DE-He78)B066-20160331 /
                      I:(DE-He78)A010-20160331 / I:(DE-He78)B110-20160331 /
                      I:(DE-He78)F170-20160331 / I:(DE-He78)D430-20160331},
      pnm          = {314 - Immunologie und Krebs (POF4-314)},
      pid          = {G:(DE-HGF)POF4-314},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38403035},
      doi          = {10.1016/j.meegid.2024.105577},
      url          = {https://inrepo02.dkfz.de/record/288580},
}