Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3

Abstract

We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012–2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level. The phylogenetic and network analyses performed support a temporal evolution from the first Australian recombinant virus sequence from November 2013 to March/April 2014, onto the 2015 outbreak. The 2015 outbreak samples fall into two separate clusters with a possible common ancestor between March/April 2014 and September 2015, with each cluster further evolving in the period from September to November/December 2015.

Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study

“…Across the study, PeV-A3 was detected infrequently until the 2013-2014 spring/summer when it predominated. This coincided with the outbreak of PeV-A3-associated sepsis in Australian infants [5,19], and aligns with the predicted timing of a genomic recombination event leading to a more virulent phenotype [28]. Nevertheless, in our cohort PeV-A3 was not associated with severe symptoms, even when detected during the outbreak period or within the high-risk first 3 months of life.…”

“…Although completion rates were excellent for such a demanding study, not all diaries and swabs were returned. Finally, the 2 genotyping regions used in this study are highly conserved within the genome and may not reflect the true genetic diversity shown by the PeV-A3 recombinant variant associated with sepsis [28]. The sharp increase in ORChID PeV-A3 cases observed during the first PeV-A3 outbreak [19] suggests this recombinant variant was circulating within the community.…”

“…Phylogenetic analysis confirmed the genotyping results and revealed the high diversity of multiple PeV genotypes co-circulating in the cohort (Figure 2 and Supplementary Figure 2). Among PeV-A3 detected in the cohort, samples collected during the same period from different children formed unique clusters in the VP3/1 region, including alignment with local strains from hospitalized infants with sepsis during the 2013-2014 outbreak (Supplementary Figure 3) [28,29].…”

“…The overall PeV incidence rate was 144 (95%CI, 128-161) episodes per 100 child-years. Incidence rates for the 3 major types (PeV-A types 1, 3, and 6) were 64 (95% CI, 54-75), 24 (95% CI, [19][20][21][22][23][24][25][26][27][28][29][30][31][32], and 27 (95% CI, 21-35) episodes per 100 childyears, respectively. After the first 3 months of life, the incidence of new PeV infections rose steadily until age 8 months before plateauing and then gradually declining in the second year ( Supplementary Figure 4).…”

Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds

“…Absence of evidence of recombination was confirmed using the Genetic Algorithm Recombination Detection (GARD) method 40 of the HyPhy package hosted on the DataMonkey webserver 41 . Codon specific selection pressure was analysed using the single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL) and random effects likelihood (REL) methods available on the DataMonkey server as previously described 42 . All analyses were performed on the optimum model as determined by the model selection algorithm of the server, and using Neighbour-Joining phylogenetic trees.…”