Genome Sequence Analysis of First Ross River Virus Isolate from Papua New Guinea Indicates Long-Term, Local Evolution

Abstract

Ross River virus (RRV) is the most medically significant mosquito-borne virus of Australia, in terms of human morbidity. RRV cases, characterised by febrile illness and potentially persistent arthralgia, have been reported from all Australian states and territories. RRV was the cause of a large-scale epidemic of multiple Pacific Island countries and territories (PICTs) from 1979 to 1980, involving at least 50,000 cases. Historical evidence of RRV seropositivity beyond Australia, in populations of Papua New Guinea (PNG), Indonesia and the Solomon Islands, has been documented. We describe the genomic characterisation and timescale analysis of the first isolate of RRV to be sampled from PNG to date. Our analysis indicates that RRV has evolved locally within PNG, independent of Australian lineages, over an approximate 40 year period. The mean time to most recent common ancestor (tMRCA) of the unique PNG clade coincides with the initiation of the PICTs epidemic in mid-1979. This may indicate that an ancestral variant of the PNG clade was seeded into the region during the epidemic, a period of high RRV transmission. Further epidemiological and molecular-based surveillance is required in PNG to better understand the molecular epidemiology of RRV in the general Australasian region.

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and metatranscriptomics

“…All belonged to the G4 genotype, G4B lineage. As described by Michie et al (2021), all strains collected in Australia since 1996 belong to G4 genotype, indicating that it is the contemporary and dominant genotype in circulation in the country. The last Australian detection of G4A occurred in 2016 (VIC and QLD) and all recently sampled strains, including sequences from QLD (2016–2018), VIC (2016–2017), WA (2008– 2013), and this study (2021–2022), were classified as G4B.…”

“…The virus sequences originated from Papua New Guinea (PNG), the Pacific Island Countries and Territories (PICTs) and different states of Australia, including New South Wales (NSW), Queensland (QLD), South Australia (SA), Victoria (VIC) and Western Australia (WA) ( Figure S3 ). A maximum likelihood (ML) phylogeny was re-constructed showing that the sequences obtained in this study belonged to the G4 genotype, which encompasses all contemporary (1994-2022) RRV isolates (Michie et al, 2021). Our samples belonged to the G4B lineage, which includes mosquito-derived strains from QLD, VIC and WA, and human-derived strains from QLD and WA ( Figure S4 ).…”

“…All belonged to the G4 genotype, G4B lineage. As described by Michie et al (2021), all strains collected in Australia since 1996 belong to G4…”

“…This includes seasonally screening mosquitoes for specific arboviruses that are nationally notifiable, using virus isolation and/or qRT-PCR techniques (Knope et al, 2019). Sequencing is not a routine part of the surveillance, so , despite the wide distribution and clinical significance of several arboviruses, whole genome sequences have only been recorded in a few studies (Michie et al, 2023(Michie et al, , 2021(Michie et al, , 2020. Although NGS is widely available in developed countries (Pronyk et al, 2023), genomic surveillance networks for zoonotic pathogens other than SARS-CoV-2 are still in their early stages.…”

Prevalence of Barmah Forest Virus, Chikungunya Virus and Ross River Virus Antibodies among Papua New Guinea Military Personnel before 2019

“…Arbovirus infections are a major public health concern in this country. Reports of RRV in PNG date back to the 1970–1990s, with research conducted by Australian scientists revealing that RRV is prevalent throughout the country [ 16 , 17 , 18 ]. The first outbreak of CHIKV in PNG was reported in June 2012 [ 19 ].…”