Metagenomic Profile of the Viral Communities in Rhipicephalus spp. Ticks from Yunnan,China

Besides mosquitoes, ticks are regarded as the primary source of vector-borne infectious diseases. Indeed, a wide variety of severe infectious human diseases, including those involving viruses, are transmitted by ticks in many parts of the world. To date, there are no published reports on the use of next-generation sequencing for studying viral diversity in ticks or discovering new viruses in these arthropods from China. Here, Ion-torrent sequencing was used to investigate the presence of viruses in three Rhipicephalus spp. tick pools (NY-11, NY-13, and MM-13) collected from the Menglian district of Yunnan, China. The sequencing run resulted in 3,641,088, 3,106,733, and 3,871,851 reads in each tick pool after trimming. Reads and assembled contiguous sequences (contigs) were subject to basic local alignment search tool analysis against the GenBank database. Large numbers of reads and contigs related to known viral sequences corresponding to a broad range of viral families were identified. Some of the sequences originated from viruses that have not been described previously in ticks. Our findings will facilitate better understanding of the tick virome, and add to our current knowledge of disease-causing viruses in ticks living under natural conditions.     

Metagenomic Profiling of Viruses Associated with Rhipicephalus microplus Ticks in Yunnan Province,China

Ticks are well known as vectors of many viruses which usually do great harm to human and animal health. Yunnan Province, widely covered by flourishing vegetation and mainly relying on farming husbandry, is abundant with Rhipicephalus microplus ticks. Therefore, it is of great significance to characterize the viral profile present in R. microplus parasitizing on cattle in Yunnan Province. In this study, a total of 7387 R. microplus ticks were collected from cattle and buffalo in the northwest and southeast areas of Yunnan Province from 2015 to 2017. We investigated the virome of R.microplus using next-generation sequencing(NGS) and the prevalence of important identified viruses among tick groups by RT-PCR. It revealed the presence of diverse virus concerning chu-, rhabdo-, phlebo-, flavi-and parvo-viruses in Yunnan. These viruses consist of single-stranded, circular and segmented sense RNAs, showing a greatly diversity in genomic organization. Furthermore, continuous epidemiological survey among ticks reveals broad prevalence of three viruses(Yunnan mivirus 1, Wuhan tick vrius 1 and YN tick-associated phlebovirus 1) and two possible prevalent viruses including a flavivirus-like segmented virus(Jingmen tick virus) and a bovine hokovirus 2 in Yunnan. Serological investigation among cattle indicates that these identified viruses may be infectious to cattle and can elicit corresponding antibody. Our findings on R. microplus-associated viral community will contribute to the prevention of viral disease and tracking the viral evolution. Further analysis is needed to better elucidate the pathogenicity and natural circulation of these viruses.     

Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater

Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.     

The ecology, genetic diversity, and phylogeny of Huaiyangshan virus in China

Surveys were carried out to better understand the tick vector ecology and genetic diversity of Huaiyangshan virus (HYSV) in both regions of endemicity and regions of nonendemicity. Haemaphysalis longicornis ticks were dominant in regions of endemicity, while Rhipicephalus microplus is more abundant in regions of nonendemicity. HYSV RNA was found in human and both tick species, with greater prevalence in H. longicornis and lesser prevalence in R. microplus. Phylogenetic analyses indicate that HYSV is a novel species of the genus Phlebovirus.     

Ixodid ticks (Acari: Ixodidae) infesting humans in Tokat Province of Turkey: species diversity and seasonal activity

Ixodid ticks (Acari: Ixodidae) are the major vectors of pathogens threatening animal and human health. Tokat Province, Turkey, is a suitable habitat for extended tick activity with its moderate climate and vegetation. In the present study, we surveyed humans visiting health centers to determine the species diversity, geographical distribution, and seasonal activity of ixodid ticks infesting them. Out of 5,999 adult ticks collected from humans from April to September, 2008, 800 ticks were identified to species, while the remaining were identified to genus according to their distinct morphological characteristics. Hyalomma marginatum, Hyalomma detritum, Rhipicephalus bursa, Rhipicephalus (Boophilus) annulatus, Haemaphysalis punctata, Dermacentor marginatus, and Ixodes laguri were the most prevalent tick species among 24 ixodid tick species infesting humans in the region. One of these tick species, Hyalomma isacii was identified as a new record for the ixodid tick fauna of Turkey. Hyalomma species were the most abundant in summer, while Dermacentor and Ixodes species displayed the lowest frequency. Hyalomma aegyptium infestation was very common on humans in the province. Results indicated that a variety of ixodid tick species infest humans depending on the season in the target area. It is possible that a variety of ixodid tick species may contribute to the spread of tick‐borne diseases such as Crimean‐Congo haemorrhagic fever virus (CCHFV), which is endemic in the region.     

Transporting Ocean Viromes: Invasion of the Aquatic Biosphere

Studies of marine viromes (viral metagenomes) have revealed that DNA viruses are highly diverse and exhibit biogeographic patterns. However, little is known about the diversity of RNA viruses, which are mostly composed of eukaryotic viruses, and their biogeographic patterns in the oceans. A growth in global commerce and maritime traffic may accelerate spread of diverse and non-cosmopolitan DNA viruses and potentially RNA viruses from one part of the world to another. Here, we demonstrated through metagenomic analyses that failure to comply with mid-ocean ballast water exchange regulation could result in movement of viromes including both DNA viruses and RNA viruses (including potential viral pathogens) unique to geographic and environmental niches. Furthermore, our results showed that virus richness (known and unknown viruses) in ballast water is associated with distance between ballast water exchange location and its nearest shoreline as well as length of water storage time in ballast tanks (voyage duration). However, richness of only known viruses is governed by local environmental conditions and different viral groups have different responses to environmental variation. Overall, these results identified ballast water as a factor contributing to ocean virome transport and potentially increased exposure of the aquatic bioshpere to viral invasion.     

Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012–2014

Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012–2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.     

Tick survey and detection of Crimean-Congo hemorrhagic fever virus in tick species from a non-endemic area, South Marmara region, Turkey

Crimean-Congo hemorrhagic fever (CCHF) is an increasing health concern in Turkey since 2002. There were also some recent human cases from the South Marmara region of Turkey; thus, a tick survey was performed, and possible vector tick species for the CCHF virus were determined in the region. A total of 740 adult ticks were collected from infested livestock from five locations: Çanakkale-Biga, Bursa-Orhaneli, Bursa-Keles, Bal?kesir and Bilecik. Total of 11 tick species from the genera Hyalomma, Rhipicephalus, Dermacentor, Ixodes and Haemaphysalis were identified. Rhipicephalus ticks were dominant in the region; the most frequently observed tick species was R. turanicus, (53.1 %), and only 15.4 % of the identified ticks were H. marginatum. The occurrence of H. rufipes infestation in the region fort he first time. A total of 73 pools of adult ticks were tested with both an antigen-detecting ELISA and RT real-time PCR (RT rt PCR). The presence of the CCHF virus was demonstrated in 9 (12.3 %) of the tested tick pools. Although seven of the tick pools were positive for the CCHF virus with both of the methods, one pool was positive only with RT rt PCR and the other pool was only positive with the ELISA. Positive results were obtained from ticks collected from cattle, sheep and goats from two locations, Bursa-Orhaneli and Bilecik. The CCHF virus was detected in R. turanicus (n = 3), R. bursa (n = 2), H. marginatum (n = 2) and D. marginatus (n = 2) ticks. The results of this study confirm the presence of the CCHF virus and present preliminary data on the vector tick species in the southern Marmara region of Turkey.     

Marine viruses,a genetic reservoir revealed by targeted viromics

Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52–163 estimated genotypes, was much lower than in previous virome reports. Fragment recruitment of metagenome reads to selected reference viral genomes yields high genome coverage, suggesting little amplification and sequencing bias against some genomic regions. These results underscore the value of our approach as an effective way to target and investigate specific virus groups. In particular, it will help reveal the diversity and abundance of giant viruses in marine ecosystems.     

An updated list of the ticks of Ghana and an assessment of the distribution of the ticks of Ghanaian wild mammals in different vegetation zones

Twenty one species of ticks belonging to five genera of the family Ixodidae (Order Acari, sub-order Ixodida) - Amblyomma, Haemaphysalis, Hyalomma, Ixodes and Rhipicephalus (including the sub-genus Rhipicephalus (Boophilus)) - were collected from 1260 mammals, representing 29 species, 14 families and 6 orders, in four vegetation zones in Ghana during the period 1971-1978. Four other species were collected from humans in 1977. In all, eight species appeared to be new records for Ghana: Amblyomma tholloni Neumann; Dermacentor circumguttatus Neumann; Haemaphysalis houyi Nuttall & Warburton; Ixodes loveridgei Arthur; Ixodes oldi Nuttall; Ixodes vanidicus Schultze; Rhipicephalus complanatus Neumann; Rhipicephalus cuspidatus Neumann. The updated list of tick species in Ghana given here includes 41 species of ixodid ticks and four species of argasid ticks. Most species have been found in neighbouring regions of West Africa but 56 of the 121 different combinations of ixodid tick species and host species found in the collection described here have not apparently been reported before. The new combinations recorded here bring the total number of different combinations of ixodid tick species and mammalian host species now reported in Ghana to 151. The tick species found on wild mammals in Ghana mostly differed from those reported from domestic stock by other authors. The data showed that different tick species occurred in different vegetation zones and that most species displayed a pronounced preference for certain groups of related host species. Some tick species were found in the savanna feeding mainly on large bovids and/or suids; others were found in forests feeding mainly on small bovids, large rodents or small carnivores.     

Tick-Borne Viruses

Ticks are important vectors for the transmission of pathogens including viruses. The viruses carried by ticks also known as tick-borne viruses (TBVs), contain a large group of viruses with diverse genetic properties and are concluded in two orders, nine families, and at least 12 genera. Some members of the TBVs are notorious agents causing severe diseases with high mortality rates in humans and livestock, while some others may pose risks to public health that are still unclear to us. Herein, we review the current knowledge of TBVs with emphases on the history of virus isolation and identification, tick vectors, and potential pathogenicity to humans and animals, including assigned species as well as the recently discovered and unassigned species. All these will promote our understanding of the diversity of TBVs, and will facilitate the further investigation of TBVs in association with both ticks and vertebrate hosts.     

The fecal viral flora of wild rodents

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.     

贵州省四种蝙蝠携带病毒组

翼手目(Chiroptera)动物已被确认是人畜共患病毒的重要自然宿主。贵州省翼手目物种多样性资源丰富,包括了2亚目7科19属65种,但在其携带病毒方面的研究仍然不全面。本文基于病毒宏基因组学和s RNA病毒检测,对贵州省广泛分布的大蹄蝠(Hipposideriderosarmiger)、三叶蹄蝠(Aselliscus wheeleri)、贵州菊头蝠(Rhinolophus rex)和皮氏菊头蝠(R. pearsoni)携带的病毒进行注释及鉴定。通过分析得到所携带病毒的种类;并比较了贵州省与云南省和广西省3个地区翼手目携带病毒在种类上的差异。结果显示,在4种蝙蝠中检测出脊椎动物病毒、昆虫病毒、植物病毒、细菌病毒4大类,共计53科111属170余种病毒,其中具有公共卫生学意义病毒9科10属46种,如:人疱疹病毒1型病毒(Human herpesvirus 1)、戊型肝炎病毒(Hepatitis E virus)、人乳头瘤病毒16型(Human papillomavirustype16)等相关的病毒。贵州省与云南省和广西省3个地区的蝙蝠所携带病毒种类比较发现,只有腺病毒科(Adenovir...     

Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region,China

BackgroundMosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently.MethodsMosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes.ResultsA total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes.ConclusionViral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.     

Metagenomic Analysis of Viral Communities in (Hado)Pelagic Sediments

In this study, we analyzed viral metagenomes (viromes) in the sedimentary habitats of three geographically and geologically distinct (hado)pelagic environments in the northwest Pacific; the Izu-Ogasawara Trench (water depth = 9,760 m) (OG), the Challenger Deep in the Mariana Trench (10,325 m) (MA), and the forearc basin off the Shimokita Peninsula (1,181 m) (SH). Virus abundance ranged from 10⁶ to 10¹¹ viruses/cm³ of sediments (down to 30 cm below the seafloor [cmbsf]). We recovered viral DNA assemblages (viromes) from the (hado)pelagic sediment samples and obtained a total of 37,458, 39,882, and 70,882 sequence reads by 454 GS FLX Titanium pyrosequencing from the virome libraries of the OG, MA, and SH (hado)pelagic sediments, respectively. Only 24−30% of the sequence reads from each virome library exhibited significant similarities to the sequences deposited in the public nr protein database (E-value <10⁻³ in BLAST). Among the sequences identified as potential viral genes based on the BLAST search, 95−99% of the sequence reads in each library were related to genes from single-stranded DNA (ssDNA) viral families, including Microviridae, Circoviridae, and Geminiviridae. A relatively high abundance of sequences related to the genetic markers (major capsid protein [VP1] and replication protein [Rep]) of two ssDNA viral groups were also detected in these libraries, thereby revealing a high genotypic diversity of their viruses (833 genotypes for VP1 and 2,551 genotypes for Rep). A majority of the viral genes predicted from each library were classified into three ssDNA viral protein categories: Rep, VP1, and minor capsid protein. The deep-sea sedimentary viromes were distinct from the viromes obtained from the oceanic and fresh waters and marine eukaryotes, and thus, deep-sea sediments harbor novel viromes, including previously unidentified ssDNA viruses.     

Monthly dynamics of ticks (Acari: Ixodida) infesting N'Dama cattle in the Republic of Guinea

The occurrence of ixodid ticks on N'Dama cattle was studied in the Republic of Guinea between June 1994 and May 1995. Monthly tick collections were performed on 80 animals from 14 villages located in Dabola, Kouroussa and Dinguiraye prefectures. A total of 19,804 ticks was collected and classified using standard taxonomic keys. The following tick species were identified: Amblyomma variegatum, Hyalomma marginatum rufipes, Hyalomma trunctum, Hyalomma nitidum, Rhipicephalus lunulatus, Rhipicephalus muhsamae, Rhipicephalus senegalensis, Rhipicephalus sulcatus, Rhipicephalus turanicus, Boophilus annulatus, Boophilus geigyi. Boophilus spp. were the most numerous adult ticks (57.1%), Am. variegatum adults constituted 27.4%, while 12.4% were Rhipicephalus spp. and 2.5% Hyalomma spp. Rhipicephalus turanicus and Hyalomma nitidum were recorded for the first time in the country. Am. variegatum and Boophilus spp. were present throughout the year, whereas Am. variegatum adults showed a peak during the rainy season between April and September. Immature stages collected belonged exclusively to the genera Amblyomma and Boophilus. Am. variegatum larvae and nymphs showed a peak during the dry season (October-March); no significant variation between seasons was observed for Boophilus immatures. A significantly higher infestation of cattle by Rhipicephalus spp. was found in Dabola and Kouroussa prefectures, located in the southern part of the study area, with similar climatic, vegetation and rainfall characteristics. Possible options for the control of ticks in the study area are briefly discussed.     

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures

Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favouring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded seven complete or near-complete double-stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments.     

Morphological identification of ticks (Acari: Ixodidae) infesting donkeys (Equus asinus) in Maputo Province,Mozambique

Donkeys (Equus asinus) are rustic animals, but in Africa’s poorest regions, they can present multiple health problems, including tick infestation. The study’s objective was to determine the species composition of ticks that infest donkeys in Maputo Province (Mozambique). Ticks were collected in five conveniently selected southern districts of Maputo Province (Moamba, Matutuíne, Marracuene, Boane, and Matola) and were identified to species level using a stereoscopic microscope with the aid of dichotomous identification keys. In total, 500 ticks were collected from all 88 selected donkeys. Three genera of ticks were identified, namely Rhipicephalus (97.2%; 486/500), Amblyomma (2.2%; 11/500), and Hyalomma (0.6%; 3/500). Seven species were identified, of which Rhipicephalus evertsi evertsi with 50.4% (252/500) was the most prevalent, followed by Rhipicephalus appendiculatus (27.4%; 137/500), Rhipicephalus turanicus (11.6; 10/500), Rhipicephalus (boophilus) microplus (6.8; 20/500), Amblyomma hebraeum (2.2%; 11/500), Rhipicephalus sanguineus (1%; 5/500) and Hyalomma truncatum (0.6%; 3/500). Rhipicephalus evertsi evertsi occurred in all locations, whereas Hyalomma truncatum occurred only in the Boane district. Males were the most prevalent (67.2%; 336/500). The study revealed that donkeys in Maputo Province were infested with seven tick species of which R. evertsi evertsi was the main species.

     

Ticks infesting domestic animals in Italy: current acarological studies carried out in Sardinia and Basilicata regions

The note reviews published and unpublished data on acaralogical studies carried out by different parasitologists' groups in Sardinia and Basilicata regions. In Sardinia 72 collecting sites were investigated and a total of 4,086 ticks were collected from hosts (cattle, sheep, goats and pigs) and from soil. So far 2,413 ticks belonging to six genera have been identified: Rhipicephalus (67.2%), Haemaphysalis (24.1%), Hyalomma (2.7%), Boophilus (0.7%), Dermacentor (4.9%), Ixodes (0.3%). Host-associated ticks were collected from 50 out of 200 selected farms in Basilicata. About 4,000 tick specimens were collected and 1,794 ticks have been identified (of which 1,215 were adults, 6 larvae and 573 nymphs). The following genera were identified: Ixodes (20%), Rhipicephalus (27%), Hyalomma (31%), Haemaphysalis (18%), Dermacentor (6%). The seasonal distribution of the species identified in the two regions studies is discussed from a geographical and climatic point of view.     

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity

Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro‐food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant‐infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.