Novel Hendra Virus Variant Circulating in Black Flying Foxes and Grey-Headed Flying Foxes, Australia

Abstract

H endra virus (HeV; genus Henipavirus, family Paramyxoviridae) is a well-characterised zoonotic pathogen endemic to Pteropus spp. bats (flying foxes) in Australia. Spillover from bats to horses has been detected 65 times; 4 of 7 persons infected from horses have died (1). Quantitative reverse-transcription PCR (qRT-PCR) (2) is a tool used for surveillance and priority disease investigation in bats and horses (3,4). The high specificity of assays limits detection to a narrow range of genotypic diversity, meaning that divergent variants might remain undetected (3).In October 2021, spillover of a novel variant, HeV genotype 2 (HeV-g2), resulted in the death of a horse in New South Wales (NSW), Australia, farther south than HeV had previously been detected in horses (5). This spillover was detected only because diagnostic assays had been recently updated after retrospective discovery of HeV-g2 in a horse that exhibited signs of HeV disease in 2015 but tested negative through routine screening at that time (3). Discovery of HeV-g2 in this horse arose using broad panparamyxovirus PCRs (6), followed by next-generation sequencing and virus isolation. The variant showed 84% pairwise nucleotide identity genomewide to prototype HeV (HeV-g1), and 99% similarity with partial sequences recovered from tissue samples from a grey-headed flying fox, P. poliocephalus (7). Bats submitted for lyssavirus diagnostics were opportunistically screened using an updated quantitative PCR specific for HeV-g2, which resulted in additional positive detections in tissue collected from P. poliocephalus in 2019-2021 and a little red flying fox (P. scapulatus) in 2015 (7).Although HeV-g1 has been detected in tissues from all 4 flying fox species in continental Australia, excretion of the virus has been confirmed only in the black flying fox (P. alecto) and the spectacled flying fox (P. conspicillatus), suggesting these species are sources of transmission to horses (8,9). Sequence mismatches between HeV-g1 and HeV-g2 mean that PCR assays used in previous surveillance of reservoir hosts would not have detected the novel HeV-g2. To address this gap, we used a new qRT-PCR (3) to screen banked flying fox urine samples collected over a large extent of space and time.

Interferon-induced protein with tetratricopeptide repeats 5 of black fruit bat (Pteropus alecto) displays a broad inhibition of RNA viruses

“…IFIT5 gene of the Australian Black flying fox ( P.alecto ) was chosen for analysis as it remains one of the few whole-bat genomes that have been sequenced and annotated ( 52 ). Furthermore, P.alecto are the natural reservoir for several pathogenic viruses, including henipaviruses, deeming them an appropriate representative species that warrants investigation ( 53 – 55 ). In order to explore bat IFIT5, we first employed a bioinformatic approach to compare the P.alecto IFIT5 gene (paIFIT5) with other animals, assessing their gene synteny, sequence conservation and phylogenetic relationship.…”

Periodic shifts in viral load increase risk of spillover from bats

“…Collectively, this suggests that prolonged low-intensity shedding of Hendra virus outside of winter months – captured only with the conventional threshold – may reflect prolonged shedding of non-infectious RNA, or viral loads that are insufficient or unlikely to overcome dose barriers to spillover infection. More broadly, this association may impact relative spillover risk of Hendra virus variants, given the low prevalence and low viral loads of Hendra virus genotype-2 in wild flying fox populations, relative to genotype-1 (Peel et al, 2022)…”

The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins

“…Since 2011, it has been administered as a postexposure therapy on a compassionate basis for high-risk HeV cases in humans and has recently completed phase I clinical trials in Australia (36). The m102.4 antibody is also effective against a new HeV variant (37) that has been found circulating in fruit bats and horses in Australia (38)(39)(40). Generation of neutralization escape mutations is possible by virus passaging in the presence of low concentrations of antibody (41,42).…”