Figure 1.
Phylogenetic trees featuring HSV-1 strains which depict the formation of six clades based on geographic origin.
A maximum likelihood (ML) phylogenetic tree was constructed with 31 HSV-1 whole or partial genomic sequences, using HSV-2 as an outgroup. (B) An expansion of the HSV-1 specific node from the ML tree in (A). The ML tree was generated from aligned sequences using the Mega 5 package. Clade I includes European/North American strains, Clade II comprises East Asian strains and III, IV, V and VI are East African. HSV-2 was used as an outgroup. The viral isolates are colored according to country of origin and are as follows: U.S.A: light blue, U.K.: dark blue, China: red, South Korea: purple, Japan: orange, and Kenya: green.
Table 1.
Genomes and accession numbers.
Figure 2.
Phylogenetic network generated from 500, maximum likelihood bootstrap replicates.
The HSV-1 strains in the network form the same six clades as in Figure 1. Clade I includes European/North American strains, Clade II comprises East Asian strains and III, IV, V and VI are East African. HSV-2 was used as an outgroup. Splitstree 4 was used to generate the network. The viral isolates are colored according to country of origin and are as follows: U.S.A: light blue, U.K.: dark blue, China: red, South Korea: purple, Japan: orange, and Kenya: green.
Figure 3.
Consensus network constructed from 26 alignment partition consensus trees.
The genome alignment was partitioned into 5(70% confidence threshold) was constructed for each partition, and a consensus network was generated from the combined results using Splitstree 4. Clade I includes European/North American strains, Clade II comprises North American/East Asian strains and III, IV, V and VI are East African HSV-2 was used as an outgroup. The viral isolates are colored according to country of origin and are as follows: U.S.A: light blue, U.K.: dark blue, China: red, South Korea: purple, Japan: orange, and Kenya: green.
Table 2.
Estimates of viral population divergence dates with respect to human populations splits.
Figure 4.
World map featuring the geographic location of the 6 HSV-1 clades with respect to human migration.
The phylogenetic data supports the “out of Africa model” of human migration with HSV-1 traveling and diversifying with its human host. Each clade is depicted by a roman numeral inside a circle. Land migration is depicted by yellow lines and air/sea migration is shown by the pink line. The countries of origin for the strains in the current study are China (red), Japan (orange), Kenya (dark green), South Korea (purple), UK (dark blue), and USA (light blue). The map was generated using R (version 3.4.2, “maps” package).