Abstract
We identified and isolated a novel Hendra virus (HeV) variant not detected by routine testing from a horse in Queensland, Australia, that died from acute illness with signs consistent with HeV infection. Using whole-genome sequencing and phylogenetic analysis, we determined the variant had ≈83% nt identity with prototypic HeV. In silico and in vitro comparisons of the receptor-binding protein with prototypic HeV support that the human monoclonal antibody m102.4 used for postexposure prophylaxis and current equine vaccine will be effective against this variant. An updated quantitative PCR developed for routine surveillance resulted in subsequent case detection. Genetic sequence consistency with virus detected in grey-headed flying foxes suggests the variant circulates at least among this species. Studies are needed to determine infection kinetics, pathogenicity, reservoir-species associations, viral-host coevolution, and spillover dynamics for this virus. Surveillance and biosecurity practices should be updated to acknowledge HeV spillover risk across all regions frequented by flying foxes.
Highlights
We identified and isolated a novel Hendra virus (HeV) variant not detected by routine testing from a horse in Queensland, Australia, that died from acute illness with signs consistent with HeV infection
Passive surveillance using suspected disease testing is affected by a strong regional bias for areas where HeV has previously been detected and where domestic horse populations overlap with black flying foxes (BFF) distribution ranges, from eastern coastal Queensland to northern New South Wales [25]
Testing for HeV is less commonly performed on horses with similar disease manifestations farther south in Australia because of a perception that spillover infection is less likely to occur in regions without BFF [26]
Summary
Study Cohort A biobank of diagnostic specimens collected in Queensland during 2015–2018 was developed from horses that underwent quantitative reverse transcription PCR (RT-PCR) testing but were negative for HeV [28]. We plated samples (EDTA blood, serum, nasal swab, rectal swab) from cases assigned priority category 1 or 2 status, considered as having the highest likelihood of infectious cause, for serologic screening and high-throughput nucleic acid extraction using the MagMAX mirVANA and CORE pathogen kits (ThermoFisher, https://www.thermofisher.com). Identification of Novel HeV-var Given the high assigned likelihood of a zoonotic infectious cause (Appendix Table), we screened both the EDTA blood and pooled swab samples using panparamyxovirus RT-PCR [36]. This identified the partial polymerase sequence of a novel paramyxovirus, most closely related to HeV (≈89% nt identity). No other viruses were present in either sample, and other microbial reads assembled were from common microflora, including Staphylococcus aureus and Aeromonas, Veillonella, Pseudarthrobacter, Streptococcus, Acinetobacter, and Psychrobacter spp
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