Monitoring Silent Spillovers Before Emergence: A Pilot Study at the Tick/Human Interface in Thailand

Abstract

Emerging zoonoses caused by previously unknown agents are one of the most important challenges for human health because of their inherent inability to be predictable, conversely to emergences caused by previously known agents that could be targeted by routine surveillance programs. Emerging zoonotic infections either originate from increasing contacts between wildlife and human populations, or from the geographical expansion of hematophagous arthropods that act as vectors, this latter being more capable to impact large-scale human populations. While characterizing the viral communities from candidate vectors in high-risk geographical areas is a necessary initial step, the need to identify which viruses are able to spill over and those restricted to their hosts has recently emerged. We hypothesized that currently unknown tick-borne arboviruses could silently circulate in specific biotopes where mammals are highly exposed to tick bites, and implemented a strategy that combined high-throughput sequencing with broad-range serological techniques to both identify novel arboviruses and tick-specific viruses in a ticks/mammals interface in Thailand. The virome of Thai ticks belonging to the Rhipicephalus, Amblyomma, Dermacentor, Hyalomma, and Haemaphysalis genera identified numerous viruses, among which several viruses could be candidates for future emergence as regards to their phylogenetic relatedness with known tick-borne arboviruses. Luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Orthomyxoviridae, Phenuiviridae, Flaviviridae, Rhabdoviridae, and Chuviridae families was used to screen human and cattle Thai populations highly exposed to tick bites. Although no positive serum was detected for any of the six viruses selected, suggesting that these viruses are not infecting these vertebrates, or at very low prevalence (upper estimate 0.017% and 0.047% in humans and cattle, respectively), the virome of Thai ticks presents an extremely rich viral diversity, among which novel tick-borne arboviruses are probably hidden and could pose a public health concern if they emerge. The strategy developed in this pilot study, starting from the inventory of viral communities of hematophagous arthropods to end by the identification of viruses able (or likely unable) to infect vertebrates, is the first step in the prediction of putative new emergences and could easily be transposed to other reservoirs/vectors/susceptible hosts interfaces.

Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus

“…The search for antibodies against SARS-CoV-2 was carried out on the 79 sera of the two cohorts using a Luciferase Immuno-Precipitation System (LIPS) assay as described (1), using two antigens: ( i ) the S1 domain of the SARS-CoV-2 Spike S protein and (ii) the C-terminal part (residues 233-419) of the SARS-CoV-2 N nucleoprotein. Viral antigens were produced in HEK-293F cells transfected with plasmids expressing the gene for Nanoluc fused to the C-terminus of the viral protein.…”

Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes

“…Raw reads were processed with an in-house bioinformatics pipeline as previously described [31]. Summarizing, it comprised quality check and trimming based on AlienTrimmer package [32] (Phred quality score cutoff = 80, min % of correctly called nt = 20) followed by read normalization using BBnorm program (https://jgi.doe.gov/data-and-tools/bbtools) (cut-off parameter of 100).…”

RNA Viruses of Amblyomma variegatum and Rhipicephalus microplus and Cattle Susceptibility in the French Antilles

“…Raw reads were processed with an in-house bioinformatics pipeline, as previously described [15]. Briefly, raw reads were trimmed, assembled into contigs which were together with remaining singletons translated into proteins (https://figshare.com/articles/translateReads_py/7588592).…”

“…Taxonomic assignments of sequences was performed by an initial BlastP similarity search against the protein Reference Viral database (RVDB [37]), followed for all viral hit by a BlastP against the whole protein NCBI/nr database (release 10/25/2018). The quantification of abundance of each viral taxon was obtained by summing the length (in amino acids) of all sequences associated with this taxon, and weighted by the k-mer coverage of all contigs associated with a given taxon [15].…”

“…Phylogenetic reconstructions of Bunyavirales and Mononegavirales/Jingchuvirales evolution were performed on the conserved non-structural RNA-dependent RNA polymerase gene (RdRP), as previously described [15]. Briefly, complete open reading frames (ORFs) were aligned with Multiple Alignment using Fast Fourier Transform (MAFFT) aligner under the L-INS-I parameter [38].…”