Abstract
The novel and emerging severe fever with thrombocytopenia syndrome virus (SFTSV) has spread throughout East Asia since discovery of the virus in 2009. This tick-borne negative-sense RNA virus has a human case fatality rate as high as 30% in endemic regions. Haemaphysalis longicornis, an Ixodid tick species, is considered a major vector of SFTSV. This tick was unintentionally introduced to New Zealand over a century ago, where it now thrives as an invasive species and can be found throughout the North and South Islands. The risk now lies with the fact that New Zealand has an effective vector for a deadly virus spreading in Southeast Asia. In this study, 454 ticks were collected from different animal species across New Zealand to characterise the associated virome and microbiome, while also searching for the potential introduction of SFTSV, or closely related tick-borne phleboviruses (TBPV). A series of molecular methods, including polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) as well as Sanger and deep sequencing methods were used to determine the species of ticks used in this study. Virus isolation was attempted by inoculating Vero cells with tick homogenate. A one-step qRT-PCR assay was established to detect SFTSV and/or TBPV from RNA extracted from the ticks. Deep sequencing (MiSeq, Illumina) was used to characterise the ticks virome and microbiome. Bioinformatics was performed using mostly IDseq, but also quantitative insights into microbial ecology (QIIME2) and Trinity. The ticks used in this study were found to be H. longicornis if they were collected from a land-based animal and Ixodes species if collected from penguins. Replication-competent viruses were not isolated from these ticks. Moreover, the phlebovirus specific qRT-PCR did not detect SFTSV and/or TBPV. Interestingly, both bioinformatics pipelines (IDseq and Trinity) identified sequences associated with three phleboviruses: Blacklegged phlebovirus 3, Norway phlebovirus and Beniji phlebovirus. More viral sequences were detected in ticks collected from penguins, compared to ticks collected from other animals. Finally, a difference in microbial community structure was detected between adult ticks and larvae, as well as fed and unfed ticks, with unfed larvae being the most rich group. In ticks collected from land-based animals, Proteobacteria was the most abundant phyla and Rickettsiella the most abundant bacterial genus. In summary, a comprehensive metagenomics analysis of the virome and microbiome of ticks circulating in New Zealand was conducted. Although SFTSV was not detected in this country, a series of phleboviruses were identified in ticks collected from the Otago Peninsula, highlighting the need to continue surveillance for potential emergent viruses in New Zealand. This work suggests directions for future work in terms of both analytical approach and directions of enquiry, specifically the role of New Zealand visiting seabirds in introducing and exporting SFTSV.