A new lineage nomenclature to aid genomic surveillance of dengue virus

Abstract

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.

Fig 1. Current system of classifying dengue virus serotypes into distinct genotypes provides insufficient geographical resolution.

Maximum likelihood phylogenetic trees scaled by genetic distance for each DENV serotype: (A) DENV-1, (B) DENV-2, (C) DENV-3, and (D) DENV-4. Trees are colored by the current genotype classification obtained using the Genome Detective Dengue Virus Typing Tool [22,23]. Bar charts indicate the frequency of whole genomes sampled in each continent assigned to each existing genotype, and numbers at the end of each bar indicate the number of sequences in each data set. Note that every serotype has a dominant genotype across the Americas (i.e., North America, Caribbean, and South America). “Related” refers to sequences that are not reliably placed into the clade as there is considerable bootstrap support for the clade without the query as well as with the query. We note that there are no whole genomes in this data set (see Methods) which are assigned DENV-1III, only to its related genotype.

Fig 2. Description of proposed dengue virus lineage classification system using serotype 3 as an example.

Genotype-level classification has been expanded to include most previously unassigned genomes. Two additional layers of classification have been proposed, major and minor lineages, the rules of which are shown here. The nomenclature is described here in its shorthand form (e.g., DENV-3III_C.2), with each element highlighted by a dotted box. The new lineage classifications for serotypes 1, 2, and 4 are shown in S2 Fig.

Fig 3. Global distributions of the new classifications of dengue virus genotypes and major lineages.

Each serotype’s new genotype (first column) and major lineage (second column). Genetic distance trees are colored by genotype or major lineage, and bar charts show the percentage of whole genome sequences in each continent by classification level. Note that major lineages break down genotypic diversity further and provide additional resolution and a continent level. Numbers by each bar represent the number of sequences in each continent by serotype.

Fig 4. Examples of increased geographical resolution using the new classifications of dengue virus lineages.

(A) Each map shows the number of sequences in the data set in each country classified as, respectively, DENV serotype 2 genotype II, serotype 2 genotype II major lineage A, and then 2 minor lineages of A.2.1 and A.2.2. The color represents the number of genome sequences from blue to purple running from low to high. (B) Map shows the distribution of the whole of DENV-1 genotype V and all of its constituent major lineages in the Americas. Major lineage 1V_A also has sequences from India, 1V_B and 1V_E have some from France, and 1V_D and 1V_D have some from Italy, although these are not shown here in the interests of space. Color represents the number of genome sequences. Base map layer downloaded from the Global Administrative Database (https://gadm.org/download_world.html).

Fig 5. Number of dengue virus whole genome sequences mostly from Ho Chi Minh City, Vietnam, assigned to each lineage over time.

Bar graphs shown for (A) DENV-1, (B) DENV-2, (C) DENV-3, and (D) DENV-4. (E) Time series of whole genome sequences from Rio Grande do Sul, Brazil, by year. (F) Lineage assignments of whole genome sequences from the rest of Brazil in this data set (non-case study sequences from Rio Grande Do Sul have been removed).