A new lineage nomenclature to aid genomic surveillance of dengue virus.
Hill V., Cleemput S., Pereira JS., Gifford RJ., Fonseca V., Tegally H., Brito AF., Ribeiro G., de Souza VC., Brcko IC., Ribeiro IS., De Lima ITT., Slavov SN., Sampaio SC., Elias MC., Tran VT., Kien DTH., Huynh T., Yacoub S., Dieng I., Salvato R., Wallau GL., Gregianini TS., Godinho FMS., Vogels CBF., Breban MI., Leguia M., Jagtap S., Roy R., Hapuarachchi C., Mwanyika G., Giovanetti M., Alcantara LCJ., Faria NR., Carrington CVF., Hanley KA., Holmes EC., Dumon W., Lima ARJ., Oliveira TD., Grubaugh ND.
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 assignment tools 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.