Using HSV-1 Genome Phylogenetics to Track Past Human Migrations

<div><p>We compared 31 complete and nearly complete globally derived HSV-1 genomic sequences using HSV-2 HG52 as an outgroup to investigate their phylogenetic relationships and look for evidence of recombination. The sequences were retrieved from NCBI and were then aligned using Clustal W. The generation of a maximum likelihood tree resulted in a six clade structure that corresponded with the timing and routes of past human migration. The East African derived viruses contained the greatest amount of genetic diversity and formed four of the six clades. The East Asian and European/North American derived viruses formed separate clades. HSV-1 strains E07, E22 and E03 were highly divergent and may each represent an individual clade. Possible recombination was analyzed by partitioning the alignment into 5 kb segments, performing individual phylogenetic analysis on each partition and generating a.phylogenetic network from the results. However most evidence for recombination spread at the base of the tree suggesting that recombination did not significantly disrupt the clade structure. Examination of previous estimates of HSV-1 mutation rates in conjunction with the phylogenetic data presented here, suggests that the substitution rate for HSV-1 is approximately 1.38×10⁻⁷ subs/site/year. In conclusion, this study expands the previously described HSV-1 three clade phylogenetic structures to a minimum of six and shows that the clade structure also mirrors global human migrations. Given that HSV-1 has co-evolved with its host, sequencing HSV-1 isolated from various populations could serve as a surrogate biomarker to study human population structure and migration patterns.</p></div

Estimates of viral population divergence dates with respect to human populations splits.

<p>Estimates of viral population divergence dates with respect to human populations splits.</p

Phylogenetic network generated from 500, maximum likelihood bootstrap replicates.

<p>The HSV-1 strains in the network form the same six clades as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076267#pone-0076267-g001" target="_blank">Figure 1</a>. 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.</p

Consensus network constructed from 26 alignment partition consensus trees.

<p>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.</p

Phylogenetic trees featuring HSV-1 strains which depict the formation of six clades based on geographic origin.

<p>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.</p

Genomes and accession numbers.

<p>Genomes and accession numbers.</p

Protein-protein interaction network of high scoring vQTLmap identified virulence proteins.

<p>A key is provided near the bottom of the Fig. The size of the nodes corresponds to the number of interactions. The network was produced by literature search using the GADGET tool, and the display was generated using Cytoscape 3.2.0.</p

Map of high scoring nonsynonymous vQTLmap detected SNP/INDELs and statistical analysis of ocular disease trends.

<p>(A) HSV-1 genomic map of genes containing high scoring vQTLmap identified features (pink). (B) Mapping of nonsynonymous highly scoring features identified by vQTLmap analysis to their corresponding proteins. Functional domains and motifs have also been mapped in each protein if applicable with the key at the bottom of the Fig. The trends of ocular disease associated with vQTLmap identified SNPs are found to the right of the maps. The parental strain OD4 was designated as the baseline with the disease trend associated with the CJ994 SNP variation to the right of each protein map. The average of the sum of the MPDS scores associated with OD4 and CJ994 have also been included. Mann-Whitney rank sum tests were performed on the MPDS scores of the recombinants containing OD4 versus CJ994 variants, with the resulting <i>p</i>-values shown at the end of each row.</p

Functional groups of viral genes identified by vQTLmap.

<p>Functional groups of viral genes identified by vQTLmap.</p

Evaluation of learned vQTLmap models mapping 40 OD4-CJ994 recombinant genotypes to ocular phenotypes.

<p>(A) The results of cross-validated predictions for blepharitis and stromal keratitis using learned Lasso, Random Forest, and Ridge regression models. The red circles indicate the R² values for models learned from the actual data, whereas the blue box plots show the R² values for models learned from 1,000 permuted datasets. The vertical blue dotted lines indicate the R² values for the non-learned baseline. (B) Association between 491 loci and the two phenotypes as determined by the Ridge regression models. The horizontal axis represents coordinates in the HSV-1 strain 17 reference genome, and the vertical axis represents the change in the mean squared error (MSE) of predicted phenotypes when the values for a given locus are permuted. The horizontal blue lines indicate the thresholds for associations to be considered significant.</p