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Figure 3. Summary of RABV sequencing by country, including the sequencing platform, type of sequence generated, location of
sequencing and analyses undertaken. The colour intensity increases with the number of publications per country; note the different
colour scale by regions; (A) Americas, (B) Africa, (C) Asia. Only twenty nine publications generated WGS (from 4 countries) and nine
conducted phylogeographic analyses. Three publications present data from across multiple countries, with two of these increasing both
the number of countries with WGS and phylogeographic analyses [51,52] . An enlarged version of this figure is available as Supplementary
Figure 1. RABV: Rabies virus; WGS: Whole Genome Sequencing.

circulation of Cosmopolitan AF1a and AF1b subclades (Cameroon, Chad, Ghana, Mozambique, Kenya and
Uganda) [13,96,98-101] . All of the four major clades found in Asia were seen co-circulating within and between
provinces in China [72-75,102-105] . In Southeast Asian countries, only the Asian clade was seen, except in Vietnam
where the Cosmopolitan clade was also reported . More differentiated subclades were reported from
[80]
archipelagic Southeast Asian countries such as Indonesia (Asian SEA1b) [106-108] , the Philippines (SEA4), Sri
Lanka (Indian-Sub) [82,83] , and Taiwan (SEA5) [109-111] , with geographically-associated names used. As
geographic resolution increased, naming systems became more ad hoc. For example, a study from the
Philippines identified nine lineages (GrL1-9) within Group L of SEA4 subclade, named because of
circulation within Luzon Island .
[112]
Many studies used nomenclature only meaningful to that study or research group. For example, sequences
from China were variously referred to as groups I-IV [113,114] , and lineages A-F [73,115] . The same nomenclature
could represent different diversity across studies. For example, group I referred to SEA1b sequences in one
[81]
study , but SEA2a in another . Another study defined “Indian” lineages I & II , which were re-
[113]
[114]
classified by RABV-GLUE [Arctic NA (i.e., no minor clade assigned), Arctic AL1a, Asian SEA1a, Indian-
sub] revealing much broader diversity and geographic distribution than user-defined terminology implied.
In Latin America, most studies (n = 29) grouped RABVs into lineages named by geographical location or
species involved, without following a common nomenclature.

Host species
Studies reported RABVs from a broad range of domestic and wildlife hosts and humans. Sequences from
domestic animals included dogs, cats, cows, goats, sheep, pigs, camels and horses. RABVs were found in
wild carnivores such as foxes, jackals, hyenas, mongoose, African wild dogs, wolves, ferret badgers, and