Phylogenomic Analysis of Global Isolates of Canid Alphaherpesvirus 1

Abstract

Canid alphaherpesvirus 1 (CHV-1) is a widespread pathogen of dogs with multiple associated clinical signs. There has been limited prior investigation into the genomics and phylogeny of this virus using whole viral genome analysis. Fifteen CHV-1 isolates were collected from animals with ocular disease based in the USA. Viral DNA was extracted for Illumina MiSeq full genome sequencing from each isolate. These data were combined with genomes of previously sequenced CHV-1 isolates obtained from hosts in the UK, Australia and Brazil. Genomic, recombinational and phylogenetic analysis were performed using multiple programs. Two isolates were separated into a clade apart from the remaining isolates and accounted for the majority of genomic distance (0.09%): one was obtained in 2019 from a USA-based host (ELAL-1) and the other in 2012 from a host in Brazil (BTU-1). ELAL-1 was found to contain variants previously reported in BTU-1 but also novel variants in the V57 gene region. Multiple non-synonymous variants were found in USA-based isolates in regions associated with antiviral resistance. Evidence of recombination was detected between ELAL-1 and BTU-1. Collectively, this represents evidence of trans-boundary transmission of a novel form of CHV-1, which highlights the importance of surveillance for this pathogen in domestic dog populations.

Full Viral Genome Sequencing and Phylogenomic Analysis of Feline Herpesvirus Type 1 (FHV-1) in Cheetahs (Acinonyx jubatus)

“…Reference-based assembly was performed using Geneious Prime ver 2020.2.4 as previously described [17]. In summary, paired-end reads were trimmed using BBDuk adapter/quality trimmer ver 38.84 (right end, Kmer length = 27, maximum substitutions= 1, minimum quality = 20, minimum overlap = 20, minimum length = 20).…”

“…Viral genomes were aligned as previously described using MAFFT ver 7.450 within Geneious Prime ver 2020.2.4 [17,18]. Default parameters were used for all alignments (scoring matrix of 1PAM/k = 2, gap penalty of 1.53 and offset value of 0.123).…”

“…Analysis of variants was performed as previously described using the Geneious variant finder within Geneious Prime ver 2020.2.4 [17,18]. Each sequenced isolate was compared to the reference genome (C-27) to identify variants.…”

“…All phylogenetic and recombinational analyses were performed as previously described, with some modifications as follows [17]. An alignment including all available FHV-1 genomes and the CHV-1 outgroup was analyzed (1000 bootstrap replicates) using ModelFinder [19] via IQ-Tree 2 ver 1.6.12 [20], which described the best-fit model (TVM + F + R7).…”

“…Ten diagnostic samples from cheetahs infected with FHV-1 and one FHV-1 MLV (Purevax Feline 3, Merial, Inc., Athens, GA, USA) were used to create viral isolates which were then sequenced using Illumina MiSeq. Fifty-two previously sequenced FHV-1 isolates [15,16], two additional commercially available MLV [16], and one CHV-1 outgroup [17] were included in the analyses. Both male and female cheetahs are represented in this group, with a median age of 6.5 years (9 months-11 years).…”