Jingmen Tick Virus in Ticks from Kenya

Latitude-driven patterns and dynamics in Jingmen group viral lineages: Spatial correlation, recombination, and phylogeography

The global emergence of Jingmen group viruses (JMVs), including Jingmen tick virus (JMTV), Alongshan virus (ALSV), and Yanggou tick virus (YGTV), has significantly broadened our perspective on the potential public health risks posed by segmented flaviviruses. However, the global evolutionary and genetic epidemiology of JMVs remains unclear. In this study, we conducted a comprehensive analysis of the spatial correlation, recombination, and phylogeography of JMVs. Our phylogenetic analysis identified three latitudinal lineages: (1) a mid-high-latitude group with YGTV and ALSV, prevalent in Europe and Asia; (2) a mid-latitude group with JMTV in Romania, Turkey, Kosovo, Trinidad, and Tobago; and (3) a mid-low-latitude group with JMTV and the Sichuan tick virus in Brazil, Japan, China, Kenya, and Uganda. The strong correlation between genetic distance and latitude also supports a latitude-dependent evolutionary pattern. Notably, concordance between the phylogenies of dominant tick species and JMVs underscores the pivotal role of tick species in the evolution of JMVs. Furthermore, the detection of frequent intra-lineage recombination and global migration events underscores the ecological pressures and tick-mediated evolutionary mechanisms that propel the global dissemination of emerging segmented flaviviruses. Additionally, the complex interplay of JMV recombination and migration events of JMVs identified here, particularly the recombination between JMTV and ALSV from disparate regions and viral migration across different regions and continents, complicates their evolutionary interrelationships and heightens potential health risks. Overall, our study provides valuable insights into ecological factors and tick species-mediated evolution and transmission that shape the global spread of emerging segmented flaviviruses.

Detection of multiple novel viruses in argasid and ixodid ticks in Mexico

We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.

First detection and molecular characterization of Jingmen tick virus with a high occurrence in Rhipicephalus (Boophilus) microplus collected from livestock in Cameroon (2024)

BACKGROUND

Jingmen tick virus (JMTV) is a novel tick-borne virus detected for the first time in Rhipicephalus (Boophilus) microplus in China. To date, there is no information regarding the circulation of JMTV in ticks collected from livestock in Cameroon. As part of the surveillance for arboviral circulation, this study aimed to assess the presence of JMTV in ticks collected from livestock (cattle and sheep) in an area of the Akonolinga health district, Center Region, Cameroon.

METHODS

A cross sectional study was carried out during the dry season between 5 and 14 March 2024. Ticks were collected from cattle and sheep in six sampling sites in an area approximately 30 km long and 18 km wide along the Nyong River, in central Cameroon. Ticks were identified morphologically and molecularly. Total RNA/DNA was extracted from tick pools and screened for JMTV RNA using a segment 2 RT-qPCR system. Positive JMTV pools were sequenced for partial JMTV-Segment 1 and full genome analyses.

RESULTS

A total of 622 ticks, organized into 251 pools were collected from 155 cattle and nine sheep. They consisted of five species covering three genera: R. (B.) microplus (472; 75.9%), Amblyomma variegatum (118; 19.0%), Hyalomma truncatum (13; 2.1%), Hyalomma rufipes (2; 0.3%), and other Rhipicephalus spp. (17; 2.7%). The quantitative reverse transcription polymerase chain reaction (qRT-PCR) screening of 251 tick pools yielded 61 JMTV-positive pools, of which 58 corresponded to R. (B.) microplus. Multiple sequence analysis revealed that JMTV from the Akonolinga area shared > 95% identity with strains from Guinea, and that these strains clustered phylogenetically together.

CONCLUSIONS

We provide molecular evidence of the presence of JMTV in R. (B.) microplus and A. variegatum collected from cattle and sheep from an area not yet recognized as endemic for this virus, confirming its wide geographical distribution.

The segmented flavivirus Alongshan virus reduces mitochondrial mass by degrading STAT2 to suppress the innate immune response

Alongshan virus (ALSV) is a newly discovered pathogen in the Flaviviridae family, characterized by a unique multi-segmented genome that is distantly related to the canonical flaviviruses. Understanding the pathogenic mechanism of this emerging segmented flavivirus is crucial for the development of effective intervention strategies. In this study, we demonstrate that ALSV can infect various mammalian cells and induce the expression of antiviral genes. Furthermore, ALSV is sensitive to IFN-β, but it has developed strategies to counteract the host's type I IFN response. Mechanistically, ALSV's nonstructural protein NSP1 interacts with and degrades human STAT2 through an autophagy pathway, with species-dependent effects. This degradation directly inhibits the expression of interferon-stimulated genes (ISGs). Additionally, NSP1-mediated degradation of STAT2 disrupts mitochondrial dynamics, leading to mitophagy and inhibition of mitochondrial biogenesis. This, in turn, suppresses the host's innate immune response. Interestingly, we found that inhibiting mitophagy using 3-methyladenine and enhancing mitochondrial biogenesis with the PPARγ agonist pioglitazone can reverse NSP1-mediated inhibition of ISGs, suggesting that promoting mitochondrial mass could serve as an effective antiviral strategy. Specifically, the NSP1 methyltransferase domain binds to the key sites of F175/R176 located in the coiled-coil domain of STAT2. Our findings provide valuable insights into the intricate regulatory cross talk between ALSV and the host's innate immune response, shedding light on the pathogenesis of this emerging segmented flavivirus and offering potential intervention strategies.IMPORTANCEAlongshan virus (ALSV), a segmented flavivirus belonging to the Flaviviridae family, was first identified in individuals who had been bitten by ticks in Northeastern China. ALSV infection is responsible for causing Alongshan fever, a condition characterized by various clinical symptoms, including fever, headache, skin rash, myalgia, arthralgia, depression, and coma. There is an urgent need for effective antiviral therapies. Here, we demonstrate that ALSV is susceptible to IFN-β but has developed mechanisms to counteract the host's innate immune response. Specifically, the ALSV nonstructural protein NSP1 interacts with STAT2, leading to its degradation via an autophagy pathway that exhibits species-dependent effects. Additionally, NSP1 disrupts mitochondrial dynamics and suppresses mitochondrial biogenesis, resulting in a reduction in mitochondrial mass, which ultimately contributes to the inhibition of the host's innate immune response. Interestingly, we found that inhibiting mitophagy and promoting mitochondrial biogenesis can reverse NSP1-mediated suppression of innate immune response by increasing mitochondrial mass. These findings provide valuable insights into the molecular mechanisms of ALSV pathogenesis and suggest potential therapeutic targets against ALSV infection.

Identification and characterization of Jingmen tick virus from Rhipicephalus microplus in Hunan, China

Jingmen tick virus (JMTV) is a tick-borne pathogen known to affect human beings, characterized by a segmented genome structure that defies the conventional understanding of the Flaviviridae family. In the present study, we employed metagenomic analysis to screen for tick-borne viruses in Hunan Province, China, and identified five JMTV variants with complete genomes from Rhipicephalus microplus ticks sampled from cattle. These viral strains exhibited the highest sequence similarity to JMTV isolates previously reported in Hubei Province, China. However, evidence of genomic reassortment was detected, particularly with the S2 segment showing greater similarity to the strains from Japan. Phylogenetic analysis demonstrated that JMTV strains cluster predominantly based on their geographic origin. In agreement with the homology data, the S1, S3, and S4 segments of the strains identified in this study grouped with those from Hubei Province, while the S2 segment displayed a distinct topological structure. Moreover, JMTV displayed limited replication in mammal-derived cells, but thrived in tick-derived cell lines. In addition to the commonly used R. microplus-derived BME/CTVM23 cells, we found that JMTV also proliferated robustly in both Ixodes scapularis-derived ISE6 and Ixodes ricinus-derived IRE/CTVM19 cells, offering new avenues for in vitro production of the virus. In summary, this study expands the known geographic distribution and genetic diversity of JMTV, providing valuable insights into its epidemiology and potential for in vitro cultivation.

Detection and prevalence of a novel Bandavirus related to Guertu virus in Amblyomma gemma ticks and human populations in Isiolo County, Kenya

INTRODUCTION

Emerging tick-borne viruses of medical and veterinary importance are increasingly being reported globally. This resurgence emphasizes the need for sustained surveillance to provide insights into tick-borne viral diversity and associated potential public health risks. We report on a virus tentatively designated Kinna virus (KIV) in the family Phenuiviridae and genus Bandavirus. The virus was isolated from a pool of Amblyomma gemma ticks from Kinna in Isiolo County, Kenya. High throughput sequencing of the virus isolate revealed close relatedness to the Guertu virus. The virus genome is consistent with the described genomes of other members of the genus Bandavirus, with nucleotides lengths of 6403, 3332 and 1752 in the Large (L), Medium (M) and Small (S) segments respectively. Phylogenetic analysis showed that the virus clustered with Guertu virus although it formed a distinct and well supported branch. The RdRp amino acid sequence had a 93.3% identity to that of Guertu virus, an indication that the virus is possibly novel. Neutralizing antibodies were detected in 125 (38.6%, 95% CI 33.3-44.1%) of the human sera from the communities in this region. In vivo experiments showed that the virus was lethal to mice with death occurring 6-9 days post-infection. The virus infected mammalian cells (Vero cells) but had reduced infectivity in the mosquito cell line (C636) tested.

CONCLUSION

Isolation of this novel virus with the potential to cause disease in human and animal populations necessitates the need to evaluate its public health significance and contribution to disease burden in the affected regions. This also points to the need for continuous monitoring of vector and human populations in high-risk ecosystems to update pathogen diversity.

Serologic evidence of human exposure to the severe fever with thrombocytopenia syndrome virus and associated viruses in Kenya

BACKGROUND

Although the diverse communities of tick-borne viruses (TBVs) have recently been proposed, the threat of infection and exposure to TBVs among humans across Kenya has been poorly understood.

OBJECTIVE

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne viral agent associated with the epidemic of severe fever with thrombocytopenia syndrome (SFTS) disease in East Asian countries. This study investigated the seroprevalence of SFTSV among humans in Kenya.

METHODS

Serum samples were collected from 459 healthy people in Kenya and tested for anti-SFTSV antibodies, which were further confirmed by immunofluorescence assays. Micro neutralization assays were performed to identify neutralising antibodies against SFTSV and SFTSV-related viruses.

RESULTS

A high seroprevalence (162/459, 35.3%) of SFTSV was found in the samples from nine of the ten surveyed counties in Kenya, with higher rates in the eastern plateau forelands, semiarid and arid areas, and coastal areas than in the area aside Rift valley. The seropositive rate was slightly higher in women than in men and was significantly higher in the 55-64 age group. Neutralising activity against SFTSV was detected in four samples, resulting in a rate of 0.9%. No cross-neutralising activity against the SFTSV-related Guertu virus and Heartland virus was detected in the anti-SFTSV positive serum samples.

CONCLUSION

The results provide serologic evidence of human exposure to SFTSV in Kenya and extend our understanding of SFTSV prevalence from Asia to Africa. The findings suggest an increasing threat of exposure to emerging TBVs and the need to investigate tick viromes in Kenya.

Tick-Borne Diseases in Sub-Saharan Africa: A Systematic Review of Pathogens, Research Focus, and Implications for Public Health

Sub-Saharan Africa, with its hot and humid climate, is a conducive zone for tick proliferation. These vectors pose a major challenge to both animal and human health in the region. However, despite the relevance of emerging diseases and evidence of tick-borne disease emergence, very few studies have been dedicated to investigating zoonotic pathogens transmitted by ticks in this area. To raise awareness of the risks of tick-borne zoonotic diseases in sub-Saharan Africa, and to define a direction for future research, this systematic review considers the trends of research on tick-borne bacteria, parasites, and viruses from 2012 to 2023, aiming to highlight the circulation of these pathogens in ticks, cattle, sheep, goats, and humans. For this purpose, three international databases were screened to select 159 papers fitting designed inclusion criteria and used for qualitative analyses. Analysis of these studies revealed a high diversity of tick-borne pathogens in sub-Saharan Africa, with a total of 37 bacterial species, 27 parasite species, and 14 viruses identified. Among these, 27% were zoonotic pathogens, yet only 11 studies investigated their presence in humans. Furthermore, there is growing interest in the investigation of bacteria and parasites in both ticks and ruminants. However, research into viruses is limited and has only received notable interest from 2021 onwards. While studies on the detection of bacteria, including those of medical interest, have focused on ticks, little consideration has been given to these vectors in studies of parasites circulation. Regarding the limited focus on zoonotic pathogens transmitted by ticks, particularly in humans, despite documented cases of emerging zoonoses and the notable 27% proportion reported, further efforts should be made to fill these gaps. Future studies should prioritize the investigation of zoonotic pathogens, especially viruses, which represent the primary emerging threats, by adopting a One Health approach. This will enhance the understanding of their circulation and impact on both human and animal health. In addition, more attention should be given to the risk factors/drivers associated to their emergence as well as the perception of the population at risk of infection from these zoonotic pathogens.

Exposure to Arboviruses in Cattle: Seroprevalence of Rift Valley Fever, Bluetongue, and Epizootic Hemorrhagic Disease Viruses and Risk Factors in Baringo County, Kenya

Rift Valley fever virus (RVFV) causes disease outbreaks in livestock and humans; however, its inter-epidemic circulation is poorly understood, similar to other arboviruses affecting cattle such as bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV). Serum samples were collected in Baringo County, Kenya from 400 cattle, accompanied by a risk factor questionnaire. Serological tests were then conducted to determine the exposure of cattle to RVFV, BTV, and EHDV. RVFV, BTV, and EHDV IgG seroprevalence rates were 15.5%, 91.5%, and 91%, respectively. Seropositivity for RVFV, BTV, and EHDV was significantly higher in adult cattle, as well as in females for RVFV. Cattle with herd owners aged between 30-39 years were less likely to be seropositive for RVFV compared to those with owners over the age of 60 years. High seroprevalence of BTV and EHDV in cattle indicates significant exposure and the subclinical circulation of these viruses, presenting a risk of outbreaks to sheep and naïve cattle. Moreover, the detection of RVFV-seropositive young cattle born after the last reported outbreak suggests inter-epidemic circulation of the virus. Overall, monitoring these arboviruses in cattle is crucial in understanding their distribution and seroprevalence during inter-epidemic periods.

Identification and phylogenetic analysis of Jingmen tick virus in Jiangxi Province, China

Jingmen tick virus (JMTV) is a newly identified segmented flavivirus that has been recognized in multiple hosts, such as humans, buffalos, bats, rodents, mosquitos and ticks. Various clinical cases and studies manifested that JMTV is a true arbovirus with wide host spectrum and showed potential threats toward public health. JMTV has been reported in multiple countries in Asia, Europe, Africa, and America. Moreover, wild boars serve as an important intermediary between humans and the wild ecological system. In China, it has been reported in nine provinces, while the prevalence and the distribution of JMTV in most regions including Jiangxi Province are still unknown. Thus, to profile the distribution of JMTV in Jiangxi Province, an epidemiological investigation was carried out from 2020 to 2022. In current study, 66 ticks were collected from 17 wild boars in Jiangxi Province. The results showed that 12 out of 66 ticks were JMTV positive, indicating JMTV is prevalent in ticks and boars in Jiangxi Province. The genome sequences of JMTV strain WY01 were sequenced to profile viral evolution of JMTV in China. Phylogenetic analysis divided JMTV strains into two genotypes, Group I and Group II. WY01 belongs to Group II and it shares the closest evolutionary relationship with the Japan strains rather than the strains from neighboring provinces in China suggesting that JMTV might have complex transmission routes. Overall, current study, for the first time, reported that JMTV is prevalent in Jiangxi Province and provided additional information concerning JMTV distribution and evolution in China.

First detection of Jingmen tick virus in Corsica, France and development of a real time detection system for multiple tick-associated jingmenviruses

Jingmen tick virus (JMTV) is a recently discovered segmented RNA virus, closely related to flaviviruses. It was identified for the first time in 2014, in China and subsequently in Brazil. Following this discovery, JMTV-related sequences have been identified in arthropods, vertebrates (including humans), plants, fungus and environmental samples from Asia, America, Africa, Europe and Oceania. Several studies suggest an association between these segmented flavi-like viruses, termed jingmenviruses, and febrile illness in humans. The development of rapid diagnostic assays for these viruses is therefore crucial to be prepared for a potential epidemic, for the early detection of these viruses via vector surveillance or hospital diagnosis. In this study, we designed a RT-qPCR assay to detect tick-associated jingmenviruses, validated it and tested its range and limit of detection with six tick-associated jingmenviruses using in vitro transcripts. Then we screened ticks collected in Corsica (France) from different livestock species, in order to determine the distribution of these viruses on the island. In total, 6,269 ticks from eight species were collected from 763 cattle, 538 horses, 106 sheep and 218 wild boars and grouped in 1,715 pools. We report the first detection of JMTV in Corsica, in Rhipicephalus bursa, Hyalomma marginatum and R. sanguineus ticks collected from cattle and sheep. The highest prevalence was found in the Rhipicephalus genus. The complete genome of a Corsican JMTV was obtained from a pool of Rhipicephalus bursa ticks and shares between 94.7% and 95.1% nucleotide identity with a JMTV sequence corresponding to a human patient in Kosovo and groups phylogenetically with European JMTV strains. These results show that a Mediterranean island such as Corsica could act as a sentinel zone for future epidemics.

Diversity of species and geographic distribution of tick-borne viruses in China

Introduction

Tick-borne pathogens especially viruses are continuously appearing worldwide, which have caused severe public health threats. Understanding the species, distribution and epidemiological trends of tick-borne viruses (TBVs) is essential for disease surveillance and control.

Methods

In this study, the data on TBVs and the distribution of ticks in China were collected from databases and literature. The geographic distribution of TBVs in China was mapped based on geographic locations of viruses where they were prevalent or they were detected in vector ticks. TBVs sequences were collected from The National Center for Biotechnology Information and used to structure the phylogenetic tree.

Results

Eighteen TBVs from eight genera of five families were prevalent in China. Five genera of ticks played an important role in the transmission of TBVs in China. According to phylogenetic analysis, some new viral genotypes, such as the Dabieshan tick virus (DTV) strain detected in Liaoning Province and the JMTV strain detected in Heilongjiang Province existed in China.

Discussion

TBVs were widely distributed but the specific ranges of viruses from different families still varied in China. Seven TBVs belonging to the genus Orthonairovirus of the family Nairoviridae such as Nairobi sheep disease virus (NSDV) clustered in the Xinjiang Uygur Autonomous Region (XUAR) and northeastern areas of China. All viruses of the family Phenuiviridae except Severe fever with thrombocytopenia syndrome virus (SFTSV) were novel viruses that appeared in the last few years, such as Guertu virus (GTV) and Tacheng tick virus 2 (TcTV-2). They were mainly distributed in the central plains of China. Jingmen tick virus (JMTV) was distributed in at least fourteen provinces and had been detected in more than ten species of tick such as Rhipicephalus microplus and Haemaphysalis longicornis, which had the widest distribution and the largest number of vector ticks among all TBVs. Parainfluenza virus 5 (PIV5) and Lymphatic choriomeningitis virus (LCMV) were two potential TBVs in Northeast China that could cause serious diseases in humans or animals. Ixodes persulcatus carried the highest number of TBVs, followed by Dermacentor nuttalli and H. longicornis. They could carry as many as ten TBVs. Three strains of Tick-borne encephalitis (TBEV) from Inner Mongolia Province clustered with ones from Russia, Japan and Heilongjiang Province, respectively. Several SFTSV strains from Zhejiang Province clustered with strains from Korea and Japan. Specific surveillance of dominant TBVs should be established in different areas in China.

Genomics evolution of Jingmen viruses associated with ticks and vertebrates

Jingmen virus (JMV) associated with ticks and vertebrates have been found to be related to human disease. We obtained the genome of a Jingmen tick virus (JMTV) strain from Rhipicephalus microplus in Guizhou province and compared the genomes of seven JMV species associated with ticks and vertebrates to understand the evolutionary relationships. The topology of the phylogenetic tree of segment 1 and segment 3 is similar, and segment 2 and segment 4 formed two different topologies, with the main differences being between Alongshan virus (ALSV), Takachi virus, Yanggou tick virus and Pteropus lylei jingmen virus (PLJV), and the possibility of genetic reassortment among these viruses. Moreover, we detected recombination within JMTV and between PLJV and ALSV. The genetic reassortment and recombination that occurs during cross-species transmission of these JMV associated with ticks and vertebrates not only complicates their evolutionary relationships, but also raises the risk of these viruses to humans.

Jingmen tick virus: an emerging arbovirus with a global threat

Jingmen tick virus (JMTV), belonging to the Flaviviridae family, is a novel segmented RNA virus identified in 2014 in the Jingmen region of Hubei Province, China. Up to now, JMTV has been detected in a variety of countries or regions in Asia, Europe, Africa, and the Americas, involving a wide range of arthropods and mammals, and even humans. The JMTV genome is composed of four linear RNA segments, two of which are derived from flaviviruses, while the other two segments are unique to JMTV and has no matching virus. Currently, JMTV has been shown to have a pathogenic effect on humans. Humans who had been infected would develop viremia and variable degrees of clinical symptoms. However, the pathogenic mechanism of JMTV has not been elucidated yet. Therefore, it is crucial to strengthen the epidemiological surveillance and laboratory studies of JMTV.

Transmission Dynamics of Crimean-Congo Haemorrhagic Fever Virus (CCHFV): Evidence of Circulation in Humans, Livestock, and Rodents in Diverse Ecologies in Kenya

Crimean-Congo haemorrhagic fever virus (CCHFV) is the causative agent of CCHF, a fatal viral haemorrhagic fever disease in humans. The maintenance of CCHFV in the ecosystem remains poorly understood. Certain tick species are considered as vectors and reservoirs of the virus. Diverse animals are suspected as amplifiers, with only scarce knowledge regarding rodents in virus epidemiology. In this study, serum samples from febrile patients, asymptomatic livestock (cattle, donkeys, sheep, and goats), and peridomestic rodents from Baringo (Marigat) and Kajiado (Nguruman) counties within the Kenyan Rift Valley were screened for acute CCHFV infection by RT-PCR and for CCHFV exposure by ELISA. RT-PCR was performed on all livestock samples in pools (5-7/pool by species and site) and in humans and rodents individually. CCHFV seropositivity was significantly higher in livestock (11.9%, 113/951) compared to rodents (6.5%, 6/93) and humans (5.9%, 29/493) (p = 0.001). Among the livestock, seropositivity was the highest in donkeys (31.4%, 16/51), followed by cattle (14.1%, 44/310), sheep (9.8%, 29/295) and goats (8.1%, 24/295). The presence of IgM antibodies against CCHFV was found in febrile patients suggesting acute or recent infection. CCHFV RNA was detected in four pooled sera samples from sheep (1.4%, 4/280) and four rodent tissues (0.83%, 4/480) showing up to 99% pairwise nucleotide identities among each other. Phylogenetic analyses of partial S segment sequences generated from these samples revealed a close relationship of 96-98% nucleotide identity to strains in the CCHFV Africa 3 lineage. The findings of this study suggest active unnoticed circulation of CCHFV in the study area and the involvement of livestock, rodents, and humans in the circulation of CCHFV in Kenya. The detection of CCHF viral RNA and antibodies against CCHFV in rodents suggests that they may participate in the viral transmission cycle.

Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond

The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses.

Analyses of Mosquito Species Composition, Blood-Feeding Habits and Infection with Insect-Specific Flaviviruses in Two Arid, Pastoralist-Dominated Counties in Kenya

Insect-specific flaviviruses (ISFs), although not known to be pathogenic to humans and animals, can modulate the transmission of arboviruses by mosquitoes. In this study, we screened 6665 host-seeking, gravid and blood-fed mosquitoes for infection with flaviviruses and assessed the vertebrate hosts of the blood-fed mosquitoes sampled in Baringo and Kajiado counties; both dryland ecosystem counties in the Kenyan Rift Valley. Sequence fragments of two ISFs were detected. Cuacua virus (CuCuV) was found in three blood-fed Mansonia (Ma.) africana. The genome was sequenced by next-generation sequencing (NGS), confirming 95.8% nucleotide sequence identity to CuCuV detected in Mansonia sp. in Mozambique. Sequence fragments of a potential novel ISF showing nucleotide identity of 72% to Aedes flavivirus virus were detected in individual blood-fed Aedes aegypti, Anopheles gambiae s.l., Ma. africana and Culex (Cx.) univittatus, all having fed on human blood. Blood-meal analysis revealed that the collected mosquitoes fed on diverse hosts, primarily humans and livestock, with a minor representation of wild mammals, amphibians and birds. The potential impact of the detected ISFs on arbovirus transmission requires further research.

Identification of novel Jingmen tick virus from parasitic ticks fed on a giant panda and goats in Sichuan Province, southwestern China

Introduction

Tick-borne viruses (TBVs) pose a significant risk to the health of humans and other vertebrates. A class of multisegmented flavi-like viruses, Jingmen tick virus (JMTV) was first discovered in Rhipicephalus microplus ticks collected from Jingmen of Hubei Province, China in 2010. JMTV has been confirmed to have a relatively wide distribution in vectors and hosts and is associated with human diseases.

Methods

Parasitic and host-seeking ticks were collected in Wolong Nature Reserve, Sichuan Province. Total RNA was extracted and then enriched the viral RNA. The DNA library was constructed and then were sequenced with MGI High-throughput Sequencing Set (PE150). After the adaptor sequences,low-quality bases and host genome were removed, resulting reads classified as a virus were subsequently de novo assembled into contigs, which were then compared to the NT database. Those annotated under the kingdom virus were initially identified as potential virus-associated sequences. Phylogenetic and Reassortment analysis of sequences were performed using MEGA and SimPlot software, respectively.

Results and discussion

Two host-seeking ticks and 17 ticks that fed on giant pandas and goats were collected. Through high-throughput sequencing, whole virus genomes were attained from four tick samples (PC-13, PC-16, PC-18, and PC-19) that shared 88.7-96.3% similarity with known JMTV. Phylogenetic tree showed that it was a novel JMTV-like virus, referred to as Sichuan tick virus, which also had the signals of reassortment with other JMTV strains, suggesting a cross-species transmission and co-infection of segmented flavi-like viruses among multiple tick hosts.

Conclusion

We discovered and confirmed one new Jingmen tick virus, Sichuan tick virus. Further investigation is required to determine the pathogenicity of Sichuan tick virus to humans and animals, as well as its epidemiological characteristics in nature.

Conserved Sequences in the 5' and 3' Untranslated Regions of Jingmenvirus Group Representatives

The Jingmenvirus group (JVG), with members such as Jingmen tick virus (JMTV), Alongshan virus (ALSV), Yanggou tick virus (YGTV), and Takachi virus (TAKV), is drawing attention due to evidence of it causing disease in humans and its unique genome architecture. In the current work, complete untranslated regions (UTRs) of four strains of ALSV and eight strains of YGTV were obtained. An analysis of these sequences, as well as JVG sequences from GenBank, uncovered several regions within viral UTRs that were highly conserved for all the segments and viruses. Bioinformatics predictions suggested that the UTRs of all the segments of YGTV, ALSV, and JMTV could form similar RNA structures. The most notable feature of these structures was a stable stem-loop with one (5' UTR) or two (3' UTR) AAGU tetraloops on the end of a hairpin.

Detection and Characterization of Alongshan Virus in Ticks and Tick Saliva from Lower Saxony, Germany with Serological Evidence for Viral Transmission to Game and Domestic Animals

The newly discovered group of Jingmenviruses has been shown to infect a wide range of hosts and has been associated with febrile illness in humans. During a survey for Jingmenviruses in ticks from Lower Saxony, Germany, Alongshan virus (ALSV) was identified in Ixodes spp. ticks. Additional virus screenings revealed the presence of ALSV in the bodies and saliva of ticks collected at several locations in Lower Saxony. Vector competence studies that included Ixodes ricinus and Dermacentor reticulatus validated the replication of ALSV within those tick species. In vitro feeding experiments with ALSV-injected Ixodes ricinus demonstrated effective viral transmission during blood feeding. To evaluate the potential viral transmission during a natural blood meal, sera from wild game and domestic animals were investigated. One serum sample from a red deer was found to be positive for ALSV RNA, while serological screenings in game and domestic animals revealed the presence of ALSV-specific antibodies at different locations in Lower Saxony. Overall, those results demonstrate the broad distribution of ALSV in ticks in Lower Saxony and hypothesize frequent exposure to animals based on serological investigations. Hence, its potential risk to human and animal health requires further investigation.

Phlebovirus diversity in ticks from livestock in arid ecologies in Kenya

Phleboviruses are emerging pathogens of public health importance. However, their association with ticks is poorly described, particularly in Africa. Here, adult ticks infesting cattle, goats and sheep were collected in two dryland pastoralist ecosystems of Kenya (Baringo and Kajiado counties) and were screened for infection with phleboviruses. Ticks mainly belonged to the species Rhipicephalus appendiculatus, Hyalomma impeltatum, and Hyalomma rufipes. A fragment of the RNA-dependent RNA polymerase (RdRp) gene was identified in thirty of 671 tick pools, of which twenty-nine were from livestock sampled in Baringo county. Phylogenetic analyses revealed that twenty-five sequences were falling in three clades within the group of tick-associated phleboviruses. The sequences of the three clades showed nucleotide distances 8%, 19% and 22%, respectively, to previously known viruses suggesting that these sequence fragments may belong to three distinct viruses. Viruses of the group of tick-associated phleboviruses have been found in several countries and continents but so far have not been associated with disease in humans or animals. In addition, five sequences were found to group with the sandfly-associated phleboviruses Bogoria virus, Perkerra virus and Ntepes virus recently detected in the same region. Further studies are needed to investigate the transmission and maintenance cycles of these viruses, as well as to assess their potential to infect vertebrates.

Distribution and Characterisation of Tick-Borne Flavi-, Flavi-like, and Phenuiviruses in the Chelyabinsk Region of Russia

In this work, we presented data from a two-year study of flavi-, flavi-like, and phenuiviruses circulation in the population of ixodid ticks in the Chelyabinsk region. We isolated three tick-borne encephalitis virus (TBEV) strains from I. persulcatus, which was not detected in the ticks of the genus Dermacentor. The virus prevalence ranged from 0.66% to 2.28%. The Yanggou tick virus (YGTV) is widespread in steppe and forest-steppe zones and is mainly associated with ticks of the genus Dermacentor. We isolated 26 strains from D. reticulatus, D. marginatus, and I. persulcatus ticks in the HAE/CTVM8 tick cell line. The virus prevalence ranged from 1.58% to 4.18% in D. reticulatus, ranged from 0.78% to 3.93% in D. marginatus, and was 0.66% in I. persulcatus. There was combined focus of TBEV and YGTV in the territory of the Chelyabinsk region. The Alongshan virus (ALSV) was found to be associated with I. persulcatus ticks and is spread in forest zone. We detected 12 amplicons and isolated 7 strains of ALSV in tick cells. The virus prevalence ranged from 1.13% to 6.00%. The phlebovirus Gomselga and unclassified phenuivirus Stavropol were associated with I. persulcatus and D. reticulatus ticks, respectively. Virus prevalence of the unclassified phenuivirus Stavropol in the Chelyabinsk region is lower than that in neighbouring regions.

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

Metagenomic Investigation of Ticks From Kenyan Wildlife Reveals Diverse Microbial Pathogens and New Country Pathogen Records

Focusing on the utility of ticks as xenosurveillance sentinels to expose circulating pathogens in Kenyan drylands, host-feeding ticks collected from wild ungulates [buffaloes, elephants, giraffes, hartebeest, impala, rhinoceros (black and white), zebras (Grévy’s and plains)], carnivores (leopards, lions, spotted hyenas, wild dogs), as well as regular domestic and Boran cattle were screened for pathogens using metagenomics. A total of 75 host-feeding ticks [Rhipicephalus (97.3%) and Amblyomma (2.7%)] collected from 15 vertebrate taxa were sequenced in 46 pools. Fifty-six pathogenic bacterial species were detected in 35 pools analyzed for pathogens and relative abundances of major phyla. The most frequently observed species was Escherichia coli (62.8%), followed by Proteus mirabilis (48.5%) and Coxiella burnetii (45.7%). Francisella tularemia and Jingmen tick virus (JMTV) were detected in 14.2 and 13% of the pools, respectively, in ticks collected from wild animals and cattle. This is one of the first reports of JMTV in Kenya, and phylogenetic reconstruction revealed significant divergence from previously known isolates and related viruses. Eight fungal species with human pathogenicity were detected in 5 pools (10.8%). The vector-borne filarial pathogens (Brugia malayi, Dirofilaria immitis, Loa loa), protozoa (Plasmodium spp., Trypanosoma cruzi), and environmental and water-/food-borne pathogens (Entamoeba histolytica, Encephalitozoon intestinalis, Naegleria fowleri, Schistosoma spp., Toxoplasma gondii, and Trichinella spiralis) were detected. Documented viruses included human mastadenovirus C, Epstein-Barr virus and bovine herpesvirus 5, Trinbago virus, and Guarapuava tymovirus-like virus 1. Our findings confirmed that host-feeding ticks are an efficient sentinel for xenosurveillance and demonstrate clear potential for wildlife-livestock-human pathogen transfer in the Kenyan landscape.