Viral Metagenomics Analysis of Planktonic Viruses in East Lake,Wuhan,China

East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.

Human viral pathogens are pervasive in wastewater treatment center aerosols

Wastewater treatment center（WTC） workers may be vulnerable to diseases caused by viruses, such as the common cold, influenza and gastro-intestinal infections. Although there is a substantial body of literature characterizing the microbial community found in wastewater, only a few studies have characterized the viral component of WTC aerosols,despite the fact that most diseases affecting WTC workers are of viral origin and that some of these viruses are transmitted through the air. In this study, we evaluated in four WTCs the presence of 11 viral pathogens of particular concern in this milieu and used a metagenomic approach to characterize the total viral community in the air of one of those WTCs. The presence of viruses in aerosols in different locations of individual WTCs was evaluated and the results obtained with four commonly used air samplers were compared.We detected four of the eleven viruses tested, including human adenovirus（h Ad V）,rotavirus, hepatitis A virus（HAV） and Herpes Simplex virus type 1（HSV1）. The results of the metagenomic assay uncovered very few viral RNA sequences in WTC aerosols, however sequences from human DNA viruses were in much greater relative abundance.

Viral metagenomics reveals diverse viruses in the fecal samples of children with diarrhea

Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.

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.

Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae

Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease(CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD.Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.

Virome diversity of ticks feeding on domestic mammals in China

Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses.From 2017 to 2018,640 ticks were collected in eight different provinces in central and western China.Six species were detected,including H.longicornis,De.everestianus,Rh.microplus,Rh.turanicus,Rh.sanguineous,and Hy.asiaticum.Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform,resulting in 13.44 G(5.88×10^(7))of 250-bp-end reads,in which 2,437,941 are viral reads.We found 27 nearly complete genome sequences,including 16 genome sequences encoding entire protein-coding regions(lack of 30 or 50 end non-coding regions)and complete viral genomes,distributed in the arboviral family(Chuviridae,Rhabdoviridae,Nairoviridae,Phenuiviridae,Flaviviridae,Iflaviridae)as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans.In addition,13 virus sequences found in Chuviridae,Nairoviridae,Flaviviridae,Iflaviridae,Hepeviridae,Parvoviridae,and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera.Besides,an epidemiological survey shows a high prevalence(9.38%and 15.63%)of two viruses(Ovine Copiparvovirus and Bovine parvovirus 2)in the tick cohort.

Comparison of Viromes in Ticks from Different Domestic Animals in China

Ticks are involved in the transmission of various arboviruses and some tick-borne viruses pose significant threats to the health of humans or livestock.This study aimed to investigate the geographical distribution of tick species and tickassociated viruses in central and eastern China.Total 573 ticks from domestic animals including dogs,sheep and cattle were collected in 2017.Two genera of ticks were identified including Rhipicephalus and Haemaphysalis.Sequencing was performed on Miseq Illumina platform to characterize the tick viromes from the four different sampling locations.Following trimming,13,640 reads were obtained and annotated to 19 virus families.From these sequences,above 37.74%of the viral reads were related to the RNA viruses.Virome comparison study revealed that the tick viral diversity was considerably different in the two identified tick genera.The viral diversity of R.microplus was significantly different from that of other Rhipicephalus species.On the other hand,substantial overlap in viral species was observed between the same genera.In addition,we found no evidence that the natural host played a major role in shaping virus diversity based on the comparison of their viromes.Rather,the geographic location seems to significantly influence the viral families.Phylogenetic study indicated that the novel negative-sense RNA viruses identified in this study was closely related to Bole tick virus 1 and 3 viruses.In conclusion,the present study provides a baseline for comparing viruses detected in ticks,according to species,natural hosts,and geographic locations.

New strategy for virus discovery:viruses identified in human feces in the last decade

Emerging and re-emerging viruses continue to surface all over the world.Some of these viruses have the potential for rapid and global spread with high morbidity and mortality,such as the SARS coronavirus outbreak.It is extremely urgent and important to identify a novel virus near-instantaneously to develop an active preventive and/or control strategy.As a cultureindependent approach,viral metagenomics has been widely used to investigate highly divergent and completely new viruses in humans,animals,and even environmental samples in the past decade.A new model of Koch's postulates,named the metagenomic Koch's postulates,has provided guidance for the study of the pathogenicity of novel viruses.This review explains the viral metagenomics strategy for virus discovery and describes viruses discovered in human feces in the past 10 years using this approach.This review also addresses issues related to the metagenomic Koch's postulates and the challenges for virus discovery in the future.

Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China

Fur seal feces-associated circular DNA virus(FSfa CV)is an unclassified circular replication-associated protein(Rep)-encoding single-stranded(CRESS)DNA virus that has been detected in mammals(fur seals and pigs).The biology and epidemiology of the virus remain largely unknown.To investigate the virus diversity among pigs in Anhui Province,China,we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods.From the assembled contigs,12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfa CVs.Based on these sequences,a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing,and the virus was designated as FSfa CV-CHN(Gen Bank No.MK462122).This virus shared 91.3%and 90.9%genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfa CV-as50 and the Japanese pig strain FSfa CVJPN1,respectively.It also clustered with the two previously identified FSfa CVs in a unique branch in the phylogenetic tree based on the open reading frame 2(ORF2),Rep-coding gene,and the genome of the reference CRESS DNA viruses.Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4%(111/197)in Anhui Province.This is the first report of FSfa CVs identified in pigs in China,and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.