Study extends known range of recently identified Hendra virus variant

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A coloured transmission electron micrograph of the Hendra virus.
A coloured transmission electron micrograph of the Hendra virus. Photo: The Electron Microscopy Unit of the Australian Animal Health Laboratory, part of the CSIRO science agency CC BY 3.0 via Wikimedia Commons

Two species of Australian fruit bats excrete a recently discovered variant of the Hendra virus in their urine and are likely competent reservoir hosts, researchers report.

The Hendra virus, first isolated in 1994, is a dangerous Australian pathogen carried by fruit bats, usually referred to as flying foxes.

Spillover events from bats to horses have been detected 63 times. Seven people have been infected through the body fluids of infected horses, with four of them dying.

In October last year, a novel variant, genotype 2, resulted in the death of a horse in New South Wales, further south than Hendra had previously been detected in horses.

It was detected only because diagnostic tests had been recently updated after the retrospective discovery of the genotype 2 variant in a horse that showed signs of the disease in 2015, but tested negative through routine screening at that time.

The variant showed 84% pairwise nucleotide identity genomewide to the more common genotype 1 form, and 99% similarity with partial sequences recovered from tissue samples from a grey-headed flying fox (Pteropus poliocephalus).

Bats submitted for other diagnostic work were opportunistically screened using the new test that covers genotype 2, resulting in additional positive detections in tissue collected from P. poliocephalus in 2019–2021 and a little red flying fox (P. scapulatus) in 2015.

Although the original variant has been detected in tissues from all four flying fox species in continental Australia, its excretion has been confirmed only in the black flying fox (P. alecto) and the spectacled flying fox (P. conspicillatus), suggesting these species are the sources of transmission to horses.

Alison Peel and her fellow researchers, in a dispatch published in the journal Emerging Infectious diseases, used the new test to screen stored flying fox urine samples collected in recent years in a bid to learn more about the circulation of the new variant.

In all, they screened 4539 pooled urine samples collected on plastic from 129 under-roost sampling sessions and 1674 urine samples collected from individual bats over 39 catching sessions across a four-year period from late 2016.

Eight pooled urine samples and two samples from individual flying foxes tested positive for the genotype 2 variant. Positive samples were from Sunnybank in Queensland and Clunes, Lismore, Dorroughby, Maclean, and Nambucca Heads in New South Wales.

They detected the new variant in samples collected across all seasons. In pooled samples, genotype 2 was only detected where genotype 1 was also detected.

Individual flying foxes that tested positive included a P. poliocephalus juvenile female captured in Maclean, New South Wales, and a P. alecto adult male captured in Clunes, New South Wales.

The genotype 2 variant was found in pooled samples from mixed-species roosts containing P. alecto and P. poliocephalus flying foxes. They identified DNA from P. alecto flying foxes in 6 of the 8 positive under-roost samples and from P. poliocephalus flying foxes in 2 of the 8 samples.

The evidence indicates that P. alecto and P. poliocephalus flying foxes excrete the later variant in their urine and both are likely competent reservoir hosts, they said.

The researchers did not screen urine samples from P. conspicillatus or P. scapulatus flying foxes, so the potential of those species to excrete the new variant in their urine remains unconfirmed.

The authors said the significantly lower prevalence of genotype 2 compared to genotype 1 could indicate lower prevalence in the sampled population. “Alternatively, repeated freeze-thaw cycles in our samples or the bias toward collecting P. alecto urine in our sampling design might have led to lower detection.

They noted that the genotype 2 variant was previously detected in tissue samples from South Australia (3 positives from 4 samples), Victoria (7/64), and Western Australia (1/2).

Their findings extend the known range of genotype 2 to southeastern Queensland and mid to north-coast New South Wales – areas close to the two known cases of spillover of the later variant in horses.

“Our findings support expanding the expected geographic risk area for Hendra virus spillover to include the distribution of P. poliocephalus flying foxes.”

They said screening flying fox urine samples from a broader geographic range, including regions where P. alecto flying foxes are absent, should lead to a better understanding of the relative prevalence of the Hendra virus variants.

Given that data on the true diversity of Hendra virus and related viruses in flying fox populations remain incomplete, further viral surveillance in reservoir and spillover hosts might identify further variants, they said.

“Developing a panel of diagnostic tools to detect a more comprehensive range of the viruses capable of spillover would substantially advance our ability to forecast spillover risk, manage biosecurity, and provide guidance to horse owners, veterinarians, and other stakeholders.”

The research team comprised Peel, Claude Kwe Yinda, Edward Annand, Adrienne Dale, Peggy Eby, John-Sebastian Eden, Devin Jones, Maureen Kessler, Tamika Lunn, Tim Pearson, Jonathan Schulz, Ina Smith, Vincent Munster, Raina K. Plowright, and the Bat One Health Group, affiliated with various institutions.

Peel AJ, Yinda C, Annand EJ, Dale AS, Eby P, Eden J, et al. Novel Hendra Virus Variant Circulating in Black Flying Foxes and Grey-Headed Flying Foxes, Australia. Emerg Infect Dis. 2022;28(5):1043-1047. https://doi.org/10.3201/eid2805.212338

The study, published under a Creative Commons License, can be read here

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