Genome-scale phylogeny of the alphavirus genus suggests a marine origin

Abstract

The genus Alphavirus comprises a diverse group of viruses, including some that cause severe disease. Using full-length sequences of all known alphaviruses, we produced a robust and comprehensive phylogeny of the Alphavirus genus, presenting a more complete evolutionary history of these viruses compared to previous studies based on partial sequences. Our phylogeny suggests the origin of the alphaviruses occurred in the southern oceans and spread equally through the Old and New World. Since lice appear to be involved in aquatic alphavirus transmission, it is possible that we are missing a louse-borne branch of the alphaviruses. Complete genome sequencing of all members of the genus also revealed conserved residues forming the structural basis of the E1 and E2 protein dimers.

Fig 1

Phylogenetic tree produced using Bayesian methods and rooted using the midpoint. The tree includes representatives from all species of the alphaviruses, except the WEEV complex, using the full-genome alignment of both ORFs, excluding portions of the nsP3 and capsid that do not produce significant alignments due to frequent indels. Viruses sequenced for the present study are indicated in boldface. The light gray shading indicates viruses classified as New World alphaviruses, while dark gray shading indicates those classified as Old World viruses, and the open box signifies the aquatic alphaviruses. It should be noted that the Old and New World designation refers to the geographical placement of the majority of the viruses within the group, although representatives of the New World alphaviruses are found in the Old World and vice versa. Posterior probabilities are shown on major branches. The recombinant WEEV complex alphaviruses were excluded to prevent bias. (Likelihood scores for both Bayesian and ML trees were −ln L 277174.42319).

Fig 2

Phylogenetic trees produced using Bayesian methods, the trees were rooted using the midpoint. The trees include representatives from all species of the alphaviruses with the structural proteins comprising E2, 6K, and E1 proteins (the likelihood scores for the Bayesian and ML trees were −ln L 87879.75390 and −ln L 87872.05667, respectively) (A) and the nonstructural proteins excluding regions of the nsP3 (the likelihood score for both Bayesian and ML trees was −ln L 198542.90397) (B). The recombinant alphaviruses are highlighted in boldface.

Fig 3

Diagram showing a hypothetical origin of the alphaviruses. New World alphaviruses are indicated by gray arrows: arrow 1, introduction from Oceania to the New World; and arrow 2, secondary introduction to the Old World. Old World viruses are indicated by black arrows: arrow 1, introduction from Oceania to Australasia; arrow 2, secondary introduction into Southern Africa; arrow 3, tertiary introduction to Northern Africa and Eurasia; arrow 4A, secondary introduction of RRV to Australasia; and arrow 4B, secondary introduction of MAYV and UNAV to the New World.

Fig 4

Chikungunya E1-E2 heterodimer (PDB code 2XFB, chains F and G [79]) fitted into cryo-EM map of WEEV (67). (A) Three-dimensional WEEV cryo-EM map showing E1-E2 spikes on the surface of the virus. (B) A spike from the map with trimer of E1-E2 heterodimers fitted into the density. Part of the E1 is sticking out from the density owing to restricted size of the spike density cut out from the WEEV map. (C) Side view of the spike with a single E1-E2 heterodimer fitted into cryo-EM density. (D) E1-E2 structure (79) rotated by 180° relative to the orientation in panel C with the conserved residues shown in green (E1) and in cyan (E2). (E) Close-up view of a fragment of the E1-E2 heterodimer as in panel D, with some of the conserved residues labeled. See the details in the text.