Viromes of Haemaphysalis longicornis reveal different viral abundance and diversity in free and engorged ticks

Haemaphysalis longicornis ticks,commonly found in East Asia,can transmit various pathogenic viruses,includingthe severe fever with thrombocytopenia syndrome virus(SFTSV)that has caused febrile diseases among humansin Hubei Province.However,understanding of the viromes of H.longicornis was limited,and the prevalence ofviruses among H.longicornis ticks in Hubei was not well clarified.This study investigates the viromes of bothengorged(fed)and free(unfed)H.longicornis ticks across three mountainous regions in Hubei Province from 2019to 2020.RNA-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging tounclassified viruses and seven RNA viral families,namely Chuviridae,Nairoviridae,Orthomyxoviridae,Parvoviridae,Phenuiviridae,Rhabdoviridae,and Totiviridae.Viral abundance and diversity in these ticks were analysed,andphylogenetic characteristics of the Henan tick virus(HNTV),Dabieshan tick virus(DBSTV),Okutama tick virus(OKTV),and Jingmen tick virus(JMTV)were elucidated based on their full genomic sequences.Prevalenceanalysis demonstrated that DBSTV was the most common virus found in individual H.longicornis ticks(12.59%),followed by HNTV(0.35%),whereas JMTV and OKTV were not detected.These results improve our understanding of H.longicornis tick viromes in central China and highlight the role of tick feeding status and geographyin shaping the viral community.The findings of new viral strains and their potential impact on public health raisethe need to strengthen surveillance efforts for comprehensively assessing their spillover potentials.

Genetic diversity of RNA viruses infecting invertebrate pests of rice

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop fields.However,information on viruses infecting invertebrate pests of crops is limited.In this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields.We identified 296 new RNA viruses and 13 known RNA viruses.These viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and genera.Of the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of mycoviruses.We detected known rice viruses in novel invertebrate hosts at high abundances.Furthermore,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species.Fortyfive potential insect pathogenic RNA viruses were detected in invertebrate species.Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity.Cross-species transmission of RNA viruses was detected between invertebrate hosts.Newly identified viral genomes showed extensive variation for invertebrate viral families or genera.Together,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea

The deep-sea brines of the Red Sea include some of the most extreme and unique envi- ronments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine-seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine-seawater interfaces were diverse and generally dominated by Candovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface： the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, represent- ing one of the first steps for ongoing and future sampling efforts and studies.

A new pattern-based method for identifying recent HIV-1 infections from the viral env sequence

The long asymptomatic stage of HIV infection poses a great challenge in identifying recent HIV infections. This is a bottleneck for monitoring HIV epidemic trends and evaluating the effectiveness of national AIDS control programs. Several serological methods were used to address this issue with some success. Because of high false-positive rates in patients with advanced infection or in ART treatment, UNAIDS still hesitates to recommend their use in routine surveillance. We developed a new pattern-based method for measuring intra-patient viral genetic diversity for determination of recent infections and estimation of population incidence. This method is verified by using several datasets (424 subtype B and 77 CRF07_BC samples) with clearly identified HIV-1 infection times. Pattern-based diversities of recent infections are significantly lower than that of chronic ones. With larger window periods varying from 200 to 350 days, a higher accuracy (90% 95%) not affected by advanced disease nor ART treatment could be obtained. The pattern-based genetic method is supplementary to the existing serology-based assays, both of which could be suitable for use in low and high epidemic regions, respectively.

Characterization of tick viromes collected from dogs in China

In this study,we explored the viral diversity and community structures of the ticks collected from dogs and detected possible tick-borne viruses(TBVs)using metagenomic analysis.Additionally,full-length sequences and the structural,phylogenetic andmolecular features of the possible TBVs were characterized using bioinformatics tools.The sequence run produced 12,254,268 reads and 6,667,259 unique reads from the tick pools.Further analysis of the viral reads revealed that 92.73%were similar to ssRNA viruses,and 90.5%of the total viral sequences belonged to Non-classified viral families.Of the 29 classified viral families,most virome sequenceswere homologouswith vertebrate viruses from Circoviridae,plant viruses from Virgaviridae,phages fromMicroviridae,insect viruses from Baculoviridae,and giant viruses from Mimiviridae.In the process of assembly of reads,large contigs representing four virus families were identified,including Phenuiviridae,Chuviridae,Parvoviridae and Non-classified families.Some sequences of Non-classified family shared a highly divergent amino acid sequence identities from existing virus sequences.The importance of these newly identified virus contigs to public and veterinary health needs additional researches.Because of the lack of the acquired viral reads from these families,we only demonstrated the complete sequences of Circoviridae in detail.The complete canine circovirus(CaCV)-NC21 genome detected from police dogs was 2,063 bp long with a GC content of 53.6%.Our results suggested that tick viromes collected fromdogs contained diverse sequences with a broad range of animal,insect,plant,and phage viruses,which may reflect the ecological characteristics of the dogs and their ticks.Furthermore,our study revealed the existence of the partial contigs belonging to the four virus families in ticks.More researches are needed to verify their importance to public and veterinary health.As well,our detection of CaCv-NC21 demonstrated that ticks can harbor and potentially transmit canine circoviruses.