Detection of severe fever with thrombocytopenia syndrome virus and other viruses in cats via unbiased next-generation sequencing

We used unbiased next-generation sequencing (NGS) to detect unknown viruses in cats. Serum or plasma samples were obtained from clinically ill cats with suspected acute viral infections. Nucleic acid was extracted from serum or plasma samples to construct a complementary DNA library for NGS. Comprehensive nucleotide sequencing analyses enabled detection of the genomes of various viruses, including the severe fever with thrombocytopenia syndrome virus, feline immunodeficiency virus, feline morbillivirus, parvovirus, and Torque teno felis virus. Our findings indicate that comprehensive nucleotide analyses of serum or plasma samples can be used to detect infections with unknown viruses in cats.     

Characterization of microbiota diversity of engorged ticks collected from dogs in China

BackgroundTicks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs.ObjectivesTo date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China.MethodsA total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3–V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied.ResultsAfter pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs.ConclusionsThe findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.     

Viral-derived DNA invasion and individual variation in an Indonesian population of large flying fox Pteropus vampyrus

Here, we performed next-generation sequencing (NGS) on six large flying foxes (Pteropus vampyrus) collected in Indonesia. Seventy-five virus species in the liver tissue of each specimen were listed. Viral homologous sequences in the bat genome were identified from the listed viruses. This finding provides collateral evidence of viral endogenization into the host genome. We found that two of the six specimens bore partial sequences that were homologous to the plant pathogens Geminiviridae and Luteoviridae. These sequences were absent in the P. vampyrus chromosomal sequences. Hence, plant viral homologous sequences were localized to the hepatocytes as extrachromosomal DNA fragments. Therefore, this suggests that the bat is a potential carrier or vector of plant viruses. The present investigation on wild animals offered novel perspectives on viral invasion, variation, and host interaction.     

Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories

The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.     

Viral infections shared between water buffaloes and small ruminants in Switzerland

Importation of exotic animals that may harbor infectious agents poses risks for native species with potentially severe impacts on animal health and animal production. Although the Asian water buffalo (Bubalus bubalis) population in Europe is steadily increasing, its susceptibility to viral infections and its role for interspecies transmission is largely unknown. To identify viral infections that are shared between exotic water buffaloes and native small ruminants, we collected blood samples from 3 Swiss farms on which water buffaloes were kept either without, or together with, sheep or goats. These samples were analyzed by next-generation sequencing (NGS) as well as by selected conventional tests, including PCR, ELISA, and in some cases a virus neutralization test. By NGS, a novel virus of the genus Gemykrogvirus (GyKV; Genomoviridae) was first detected in the buffaloes on one farm, and subsequently confirmed by PCR, and was also detected in the co-housed sheep. In contrast, this virus was not detected in buffaloes on the farms without sheep. Moreover, conventional methods identified a number of viral infections that were not shared between the exotic and the native animals, and provided evidence for potential roles of water buffaloes in the epidemiology of ruminant pestiviruses, especially bovine viral diarrhea virus, bluetongue virus, and possibly bovine alphaherpesvirus 2. Our results clearly indicate that water buffaloes are susceptible to interspecies viral transmission and may act as intermediate hosts, or even as reservoirs, for these viruses.     

Detection of Borrelia garinii, Borrelia tanukii and Borrelia sp. closely related to Borrelia valaisiana in Ixodes ticks removed from dogs and cats in Japan

Ticks removed from 1136 dogs and 134 cats all over Japan were examined for Borrelia infection by PCR and sequencing. The 5S-23S rDNA intergenic spacer of Borrelia was detected from two Ixodes persulcatus ticks from two dogs and two unidentified Ixodes spp. from another two dogs in Hokkaido, and two Ixodes granulatus ticks from two cats in Okinawa. Additional 2 I. granulatus from the same cats also showed positive. Sequence analysis of the PCR products revealed that the one from Hokkaido was similar to B. garinii, the three from Hokkaido to B. tanukii, and the four from Okinawa to a novel Borrelia sp. closely related to B. valaisiana. The data was confirmed by analysis of the flagellin gene sequence. Infected ticks carried by companion animals can be introduced into the human environment.     

Genetic typing of bovine viral diarrhoea virus: most Slovenian isolates are of genotypes 1d and 1f

A selection of 43 bovine viral diarrhoea viruses isolated from mainly persistently infected cattle on 23 Slovenian farms between 1997 and 2001 were characterised genetically. Viral RNA was extracted from infected cell cultures, reverse transcribed and amplified by PCR with primers targeting the 5'-UTR and the N(pro) gene, followed by direct sequencing of purified PCR products obtained for both genomic regions. The N(pro) sequences provided the best genetic resolution, and gave also higher statistical support for phylogenetic classification of the viruses. Thirty-eight of the Slovenian isolates were of genetic subtypes 1d and 1f, four were 1b, and one subtype 1g. No BVDV type 2 viruses were found. This genetic prevalence matched those previously reported for neighbouring countries, as opposed to findings reported for more distant European countries, e.g. France, Spain and the UK. From eight cattle herds several virus isolates were analysed; with one exception all isolates from each herd were of the same genetic group. Extended sequencing of the N(pro) and part of the C gene of virus isolates with identical 5'-UTR sequences allowed differentiation between isolates obtained at different times from one herd.     

Evidence of Bartonella sp. in questing adult and nymphal Ixodes ricinus ticks from France and co-infection with Borrelia burgdorferi sensu lato and Babesia sp

Ticks are known vectors for a wide range of pathogenic microorganisms. Their role in the transmission of some others is so far only suspected. Ticks can transmit multiple pathogens, however, little is known about the co-existence of these pathogens within questing ticks. We looked for the presence of DNA from three micro-organisms, Bartonella sp., Borrelia burgdorferi sensu lato and Babesia sp. which are known or suspected tick-borne pathogens, using a cohort of 92 questing Ixodes ricinus ticks collected from pastures in northern France. DNA was extracted from each individual tick and the presence of the three pathogens was investigated using Polymerase Chain Reaction (PCR) amplification. Nine among 92 samples (9.8%) demonstrated PCR products using Bartonella specific primers, 3 among 92 (3.3%) using Borrelia burgdorferi sensu lato specific primers and 19 among 92 (20.6%) using Babesia specific primers. Seven among 92 samples (7.6%) were PCR positive for at least two of the pathogens and one sample was positive for all three. Adult ticks (12/18; 67%) showed significantly higher infection rates compared to nymphs (11/74; 15%) for all three pathogens (P < 0.001). This study is the demonstration of the simultaneous presence of Bartonella sp., Borrelia burgdorferi sensu lato and Babesia sp. in questing Ixodes ricinus ticks.     

Recent progress in molecular biology of Crimean-Congo hemorrhagic fever

Crimean–Congo hemorrhagic fever (CCHF) is a severe hemorrhagic fever in humans with a case fatality rate of up to 50%. A causative agent of CCHF is CCHF virus, which is a tick-borne virus in the family Bunyaviridae, genus Nairovirus. The virus is transmitted to humans through infected tick bites, squashed ticks or from direct contact with viremic animals or humans. Outbreaks of CCHF have been documented in Africa, the Middle East, Eastern Europe and Western Asia where the vector and/or reservoir ticks of Hyalomma spp. are distributed. Recent advances in molecular and biochemical analyses of CCHF virus revealed that the virus encodes larger proteins compared to other genus of Bunyavirus and the processing of viral proteins are complicated. Recent studies also showed that the CCHF viruses are relatively divergent in its genome sequence and the viruses are grouped in seven different clades. In general, these phylogenetic analyses based on sequences of S-RNA and L-RNA segment of CCHF viruses indicate that the seven clades correlate with their geographical location. The phylogenetic topology based on M-RNA segment sequences of CCHF viruses is different from those based on S-RNA and L-RNA segments. These analyses indicate that M-RNA segment reassortment events occur more frequently than those in S- and L-RNA segments.     

多重PCR结合基因芯片技术检测5种猪繁殖障碍性病毒病方法的研究

为建立运用多重PCR和基因芯片技术同时检测5种猪繁殖障碍性病毒病的方法。本研究根据GenBank中登录的猪瘟病毒(CSFV)、猪细小病毒(PPV)、猪繁殖与呼吸综合征病毒(PRRSV)、猪日本乙型脑炎病毒(JEV)及猪圆环病毒2型(PCV2)的基因序列设计特异性引物与探针,制备相应的寡核苷酸芯片,检测了5种猪繁殖障碍性疾病病毒的标准毒株,并对16份临床样品进行检测。通过多重PCR扩增出带有荧光标记的5种病毒的特异性基因片段,并与固定有特异性探针的基因芯片杂交。结果显示,本研究建立的多重PCR结合基因芯片检测方法特异性强、稳定性好,灵敏度可达10~2拷贝/μL。16份临床样品检测结果显示阳性率达87.5%(14/16)。以上结果表明该方法特异性好、灵敏度高,可高效检测以上5种病毒,为其临床诊断及流行病学调查提供了有效的检测方法。     

反刍动物瘤胃噬菌体的宏基因组学研究方法及进展

病毒(virus)存在于各种动物胃肠道中,反刍动物瘤胃也不例外.瘤胃是一个复杂且多样的微生态系统,包括细菌、真菌、原虫、古生菌和病毒等多种微生物.目前,多组学技术和生物信息学分析手段被广泛用于瘤胃细菌群落的研究.有研究表明,饲粮、环境及宿主基因型会对瘤胃细菌多样性和菌群结构产生影响;瘤胃细菌也会反过来影响宿主机体代谢、...     

5种脑炎人兽共患病病毒多重RT-PCR检测方法的建立

为建立同时检测流行性乙型脑炎病毒(JEV)、森林脑炎病毒(TBEV)、东方马脑炎病毒(EEEV)、西方马脑炎病毒(WEEV)和基孔肯雅病毒(CHIKV)5种人兽共患脑炎病病毒的多重RT-PCR方法,本研究根据GenBank登录的相关病毒基因序列设计特异引物,通过优化引物组合及PCR反应条件,建立可同时检测5种病毒的方法,扩增片段长度分别为411 bp(JEV)、945 bp(TBEV)、193 bp(EEEV)、545 bp(WEEV)和769 bp(CHIKV);该方法具有良好的特异性,对病毒核酸最低检测拷贝数分别为7.1×103、3.6×103、2.2×103、5.6×103和5.1×103.该方法具有特异性强、灵敏度高、操作简便等优点,为以上5种人兽共患脑炎病病毒提供快速检测手段.     

Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses

Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5–28.4- and 10.1–208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.     

Diversity among bovine pestiviruses

Bovine viral diarrhoea virus (BVDV) isolates are characterized by an important genetic, antigenic and pathogenic diversity. The emergence of new hypervirulent BVDV strains in North America has provided clear evidence of pathogenic differences between BVDV strains. The origin of BVDV diversity is related to high mutation rate occurring in RNA viruses but the consequences of mutations obviously depend on the genes which are involved. Mutations in genes encoding for structural proteins of immunological importance may have practical implications.Knowledge of BVDV diversity is important for understanding the wide variety of pathogenesis of diseases caused by the virus, for monitoring the epidemiology of the different types and for the design of optimum laboratory tests and vaccines.This review focuses on the origin and consequences of BVDV diversity with regard to pathogenesis, biotypes, and antigenic and genetic variations.     

蜱的生物防治研究进展

蜱是放牧家畜体表常见的一类外寄生虫,并可作为许多疾病的传播媒介,给人类健康和动物生产带来极大的威胁。在自然界中,多种病毒、细菌、真菌和线虫可寄生于蜱体并对其产生致病性,某些寄生蜂和禽类等可充当蜱的捕食者或天敌,它们在蜱的防控中均担当着重要角色。文章将以蜱的病原和天敌为重点,对蜱的生物防治研究进展进行介绍。     

Randomly primed,strand-switching,MinION-based sequencing for the detection and characterization of cultured RNA viruses

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.     

蜱的化学和免疫学防治研究进展

蜱既是常见的吸血外寄生虫,又是人和动物许多重要疾病的传播媒介。大量的蜱叮咬宿主动物可导致宿主消瘦、贫血,同时也使动物皮革的质量降低。作为传播媒介,蜱由于可传播原虫、立克次体、支原体、衣原体、螺旋体、细菌和病毒等,在世界范围带来了很大的经济损失。有很多蜱的防治策略,但均存在不足之处,目前主要以化学和免疫学防治为主。利用化学防治较为普遍,但由于使用不当已造成了蜱的耐药性和环境污染。蜱的免疫学防治主要是开发抗蜱疫苗,接种商品化的抗蜱疫苗被证实是一种可行的防治策略,因此疫苗将在未来对蜱的防治中起举足轻重的作用。     

Effect of a prior exposure to a low pathogenic avian influenza virus in the outcome of a heterosubtypic low pathogenic avian influenza infection in mallards (Anas platyrhynchos)

Wild birds, particularly Anseriformes and Charadriiformes, are considered the natural reservoir of low pathogenic avian influenza (LPAI) viruses. The high prevalence and subtype diversity of avian influenza viruses at premigrational staging areas provide the perfect opportunity for multiple exposures to different LPAI virus subtypes. Natural consecutive and concurrent infections of sentinel ducks with different LPAI virus subtypes have been reported. The protective immune response from different LPAI virus infections is not understood nor is the effect of such repeated exposures. This study experimentally evaluated the effect of a prior exposure to a LPAI virus on the outcome of a heterosubtypic LPAI virus infection in mallards (Anas platyrhynchos). The results of this investigation suggest that recent prior exposure to a LPAI virus may affect the outcome of a subsequent heterosubtypic LPAI infection in mallards by reducing the duration of cloacal and oropharyngeal viral shedding as well as the viral load excreted via the cloaca. Wild mallards are likely exposed to multiple subtypes of LPAI virus during the periods of peak viral circulation, and the results of this study suggest that the duration of viral shedding in subsequent exposures might be reduced.     

Biology of ticks

Ticks are an ancient group of obligate bloodsucking ectoparasites that has evolved over millions of years. Two general types of ticks are evident today: argasid or soft ticks, and ixodid or hard ticks. Each lineage exhibits distinct patterns of host coevolution and preference. However, about 10% of the approximately 850 species are of medical importance because of their indiscriminate host selection and catholic feeding behavior. As a result, a number of diseases have begun to emerge in the temperate zones, including Lyme borreliosis and several others putatively associated with ticks. Ticks may serve as both pathogens and disease vectors. Because of the unique physiology of the salivary glands and the contents in tick saliva of toxins, feeding alone may cause disease. Ticks also transmit a number of different types of pathogens (viruses, rickettsiae, spirochetes and bacteria, fungi, protozoa, filarial nematodes) and even exceed mosquitoes in this regard. Abatement and control of ticks emphasizes a broad approach because of the differing types of habitats in which pest species may be found. The use of repellents and acaricides as well as cultural and management practices are of primary importance. Other approaches (ivermectin) may be beneficial; with the advent of molecular genetics and its usefulness in immunology, the development of tick vaccines for common pest species appears promising.