@article{fdi:010095541,
  title = {{B}lood donors as sentinels for genomic surveillance of {W}est {N}ile virus in {G}ermany using a sensitive amplicon-based sequencing approach},
  author = {{T}oth, {G}. {E}. and {P}etersen, {M}. and {C}hevenet, {F}ran{\c{c}}ois and {S}ikora, {M}. and {T}omazatos, {A}. and {B}ialonski, {A}. and {H}orváth, {B}. and {B}aum, {H}. and {S}iriyasatien, {P}. and {H}eitmann, {A}. and {J}ansen, {S}. and {O}ffergeld, {R}. and {L}achmann, {R}. and {S}chmidt, {M}. and {S}chmidt-{C}hanasit, {J}. and {C}adar, {D}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {W}est {N}ile virus ({WNV}) has emerged as a public health concern in {G}ermany since its first detection in 2018, with evidence of expanding geographic spread. {G}enomic surveillance is critical for tracking viral evolution, identifying introductions, and monitoring local transmission. {H}owever, genome recovery from low-viremia samples such as those obtained through blood donor screening remains technically challenging. {A}im: {T}o develop and validate a sensitive amplicon-based sequencing protocol optimized for {WNV} lineage 2 and apply it to low-titer samples to support genomic surveillance in {G}ermany. {M}ethods: {A} novel primer scheme was designed for {WNV} lineage 2 and applied to 43 nucleic acid testing ({NAT})-positive blood donor samples collected between 2020 and 2024. {A}mplicon-based sequencing performance was benchmarked against metagenomic next-generation sequencing (m{NGS}). {R}ecovered genomes were subjected to phylogenomic analysis to assess viral diversity and transmission dynamics. {R}esults: {T}he amplicon protocol enabled genome recovery (>70% coverage) from samples with viral loads as low as similar to 10(1) {RNA} copies/mu {L}, outperforming metagenomic {NGS} (m{NGS}). {O}f the 43 samples, 30 yielded complete or near-complete genomes. {S}ix distinct {WNV} subclades (2{A}-2{F}), including {G}erman strains, were identified, indicating multiple introductions into {G}ermany from {C}entral {E}urope. {S}ubclade 2{F} emerged as the dominant and widely distributed group. {B}erlin, {B}randenburg, {S}axony, and {S}axony-{A}nhalt were identified as persistent transmission hubs. {C}onclusion: {T}his study highlights blood donors as valuable sentinels for {WNV} genomic surveillance. {T}he validated amplicon-based sequencing approach enables sensitive, scalable genome recovery from low-viremia samples, and when integrated with routine blood donor screening, provides a robust framework for early detection, transmission dynamics, and public health preparedness.},
  keywords = {{W}est {N}ile virus ; {A}mplicon sequencing ; {M}etagenomics ; {G}enomic surveillance ; {P}hylogeography ; {V}irus evolution ; {B}lood donor surveillance ; {G}ermany ; {ALLEMAGNE}},
  booktitle = {},
  journal = {{J}ournal of {I}nfection},
  volume = {91},
  numero = {5},
  pages = {106647 [12 ]},
  ISSN = {0163-4453},
  year = {2025},
  DOI = {10.1016/j.jinf.2025.106647},
  URL = {https://www.documentation.ird.fr/hor/fdi:010095541},
}