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A new lineage nomenclature to aid genomic surveillance of dengue virus.

Verity HillSara CleemputJames Siqueira PereiraRobert J GiffordVagner FonsecaHouriiyah TegallyAnderson F BritoGabriela RibeiroVinicius Carius de SouzaIsabela Carvalho BrckoIgor Santana RibeiroIago Trezena Tavares De LimaSvetoslav Nanev SlavovSandra Coccuzzo SampaioMaria Carolina EliasVi Thuy TranDuong Thi Hue KienTuyen HuynhSophie YacoubIdrissa DiengRichard SalvatoGabriel Luz WallauTatiana S GregianiniFernanda M S GodinhoChantal B F VogelsMallery I BrebanMariana LeguiaSuraj JagtapRahul RoyChanditha HapuarachchiGaspary MwanyikaMarta GiovanettiLuiz C J AlcantaraNuno R FariaChristine V F CarringtonKathryn A HanleyEdward C HolmesWim DumonAlex Ranieri Jerônimo LimaTulio de OliveiraNathan D Grubaugh
Published in: PLoS biology (2024)
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we propose adding 2 sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national, and subnational discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.
Keyphrases
  • dengue virus
  • zika virus
  • aedes aegypti
  • public health
  • machine learning
  • copy number
  • deep learning
  • healthcare
  • sars cov
  • dna methylation
  • climate change
  • artificial intelligence
  • social media
  • infectious diseases