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.     

Increased Prevalence of Anellovirus in Pediatric Patients with Fever

The Anelloviridae family consists of non-enveloped, circular, single-stranded DNA viruses. Three genera of anellovirus are known to infect humans, named TTV, TTMDV, and TTMV. Although anelloviruses were initially thought to cause non-A-G viral hepatitis, continued research has shown no definitive associations between anellovirus and human disease to date. Using high-throughput sequencing, we investigated the association between anelloviruses and fever in pediatric patients 2–36 months of age. We determined that although anelloviruses were present in a large number of specimens from both febrile and afebrile patients, they were more prevalent in the plasma and nasopharyngeal (NP) specimens of febrile patients compared to afebrile controls. Using PCR to detect each of the three species of anellovirus that infect humans, we found that anellovirus species TTV and TTMDV were more prevalent in the plasma and NP specimens of febrile patients compared to afebrile controls. This was not the case for species TTMV which was found in similar percentages of febrile and afebrile patient specimens. Analysis of patient age showed that the percentage of plasma and NP specimens containing anellovirus increased with age until patients were 19–24 months of age, after which the percentage of anellovirus positive patient specimens dropped. This trend was striking for TTV and TTMDV and very modest for TTMV in both plasma and NP specimens. Finally, as the temperature of febrile patients increased, so too did the frequency of TTV and TTMDV detection. Again, TTMV was equally present in both febrile and afebrile patient specimens. Taken together these data indicate that the human anellovirus species TTV and TTMDV are associated with fever in children, while the highly related human anellovirus TTMV has no association with fever.     

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin

It is a matter of fact that the human gut microbiome also includes a non‐bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter‐gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre‐agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co‐occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome‐host co‐evolutionary process.     

Two distinct variants of erythrocyte spectrin βIV domain

Summary Thirty-nine Turkish phenylketonuria (PKU) families were investigated for their DNA haplotypes at the phenylalanine hydroxylase (PAH) locus. There was a threefold higher incidence of consanguinity in the population studied compared with the general Turkish population. The PAH DNA haplotype 6 was found to be almost exclusively associated not only with the mutant PAH genes but also with the classic phenotype in 39% of the Turkish patients. This haplotype was of no importance in northern European populations. The two DNA haplotypes (1 and 4) that were almost equally frequent among the normal and the mutant PAH genes in northern European populations show virtually the same distribution in Turkish individuals. In all populations studied, these haplotypes are associated with different phenotypes.     

Metagenomic analysis of the viral flora of pine marten and European badger feces

A thorough understanding of the diversity of viruses in wildlife provides epidemiological baseline information about potential pathogens. Metagenomic analysis of the enteric viral flora revealed a new anellovirus and bocavirus species in pine martens and a new circovirus-like virus and geminivirus-related DNA virus in European badgers. In addition, sequences with homology to viruses from the families Paramyxo- and Picornaviridae were detected.     

North‐African house martins endure greater haemosporidian infection than their European counterparts

Afro‐Palearctic migrant species are exposed to parasites at both breeding and over‐wintering grounds. The house martin Delichon urbicum is one such migratory species facing high instances of blood parasite infection. In an attempt to determine whether breeding European house martins harbour similar blood parasite communities to populations breeding in North Africa, birds were sampled at their breeding grounds in Switzerland and Algeria. Moreover, haemosporidian prevalence and parasite communities were compared to published data sets on Spanish and Dutch breeding populations. This study furthermore wanted to establish whether co‐infection with multiple genera or lineages of parasites had negative e?ects on host body condition. Breeding house martins caught in Algeria showed a higher prevalence of avian haemosporidian parasites than did European populations. Swiss house martins showed a prevalence comparable to that of Spanish and Dutch populations. There were slight differences in the haemosporidian community between European and North‐African populations in terms of composition and abundance of each lineage. Similar to the Dutch house martins, but in contrast to the Spanish population, infection status and number of genera of parasites infecting single hosts did not in?uence Swiss house martin body condition.     

Trends in a Life Threatening Condition: Morbid Obesity in Dutch,Turkish and Moroccan Children in The Netherlands

Background

Morbid obesity can be a life threatening condition. The aim of our study is to assess the trend in morbid obesity in The Netherlands among children of Dutch origin since 1980, and among children of Turkish and Moroccan origin since 1997.

Methods and Findings

Cross-sectional height and weight data of children of Dutch, Turkish and Moroccan origin aged 2–18 years were selected from three national Dutch Growth Studies performed in 1980, 1997 and 2009 (n = 54,814). Extended international (IOTF) cut-offs in childhood were used to define morbid obesity (obesity class II and III combined). The morbidity index for overweight was calculated as the prevalence of morbid obesity divided by the prevalence of overweight. Our study showed that the prevalence of morbid obesity in children of Dutch origin was 0.59% in boys and 0.53% in girls in 2009. Significant upward trends occurred since 1980 and 1997. The prevalence was three to four fold higher in Turkish children compared to Dutch children. The Turkish children also had an upward trend since 1997, but this was only statistically significant in boys. The prevalence of morbid obesity in Moroccan children was two to three fold higher than in Dutch children, but it remained almost stable between 1997 and 2009. The Dutch and Turkish children showed an upward trend in morbidity index for overweight since respectively 1980 and 1997, while the Moroccan children showed a downward trend since 1997. In 2009, children of low educated parents had the highest prevalence rates of morbid obesity; 1.06% in Dutch, 2.11% in Turkish and 1.41% in Moroccan children.

Conclusions and Significance

An upward trend of morbid obesity in Dutch and Turkish children in The Netherlands occurred. Monitoring and reducing the prevalence of childhood morbid obesity is of high importance for these children, health care and the community.     

Comparative prevalence of plasma human herpesvirus 8 DNA in sexual contact and intravenous injection routes of HIV transmission

Detection of plasma human herpesvirus (HHV)-8 DNA correlates with antibodies to lytic HHV-8 antigens, being predictive of Kaposi's sarcoma in HIV-infected patients. We show that the prevalence of plasma HHV-8 DNA was 10.6% for HIV infection through sexual contact and 7.1% for HIV infection through intravenous injection. In addition, the prevalence of plasma HHV-8 DNA was significantly associated with male gender (9.4%) and HIV viral load below 1000 copies mL(-1) (12.1%), but not age or CD4 cell count in HIV-infected patients. The study suggested that detection of plasma HHV-8 DNA could be important for monitoring replicating HHV-8 in HIV-infected patients, and may have use as a marker for the diagnosis of HHV-8 infection in blood-borne transmission.     

Neutralizing and IgG Antibodies against Simian Virus 40 in Healthy Pregnant Women in Italy

Objective

Polyomavirus simian virus 40 (SV40) sequences have been detected in various human specimens and SV40 antibodies have been found in human sera from both healthy individuals and cancer patients. This study analyzed serum samples from healthy pregnant women as well as cord blood samples to determine the prevalence of SV40 antibodies in pregnancy.

Methods

Serum samples were collected at the time of delivery from two groups of pregnant women as well as cord bloods from one group. The women were born between 1967 and 1993. Samples were assayed by two different serological methods, one group by neutralization of viral infectivity and the other by indirect ELISA employing specific SV40 mimotopes as antigens. Viral DNA assays by real-time polymerase chain reaction were carried out on blood samples.

Results

Neutralization and ELISA tests indicated that the pregnant women were SV40 antibody-positive with overall prevalences of 10.6% (13/123) and 12.7% (14/110), respectively. SV40 neutralizing antibodies were detected in a low number of cord blood samples. Antibody titers were generally low. No viral DNA was detected in either maternal or cord bloods.

Conclusions

SV40-specific serum antibodies were detected in pregnant women at the time of delivery and in cord bloods. There was no evidence of transplacental transmission of SV40. These data indicate that SV40 is circulating at a low prevalence in the northern Italian population long after the use of contaminated vaccines.     

Maternal serum alpha-fetoprotein screening for neural tube defects

Summary The basis of maternal serum alpha-fetoprotein (AFP)-screening for neural tube defects is discussed. A report is given of a large scale screening study in the Federal Republic of Germany combining the experiences in Giessen and Hannover on over 50,000 pregnant women, about evently distributed among both centers. Published and known forthcoming data from other low incidence populations, particularly of European countries, are reviewed briefly. The conclusion is reached that general screening could effectively be instituted and in the final result should also be cost-beneficial.     

Prevalence of antibody to human herpesvirus 6 in women and children

The antibody prevalence to human herpesvirus 6 (HHV-6) was compared between pregnant women and control women of similar ages in Thailand. No significant difference was detected in the antibody positive rate and antibody titers between both groups. The antibody titers in sera collected from pregnant women at 1st and 3rd trimester remained unchanged. Next, the antibody prevalence in infants were examined and the positive rate decreased until 3 months and started to increase from 6 months after birth. The present results suggest that the reactivation of HHV-6 might not occur during pregnancy and this virus infects infants postnatally.     

Viral infections in free-living populations of the European wildcat

While the importance of viral infections is well studied in domestic cats, only limited information is available on their occurence and prevalence in the European wildcat (Felis silvestris silvestris). The aim of this study was to determine the prevalence of antibodies to feline coronavirus (FCoV), calicivirus (FCV), herpesvirus (FHV), parvovirus (FPV), immunodeficiency virus (FIV), leukemia virus (FeLV), and FeLV antigenemia in 51 European wildcat sera. Samples were collected between 1996 and 1997 from wildcat populations in France, Switzerland, and Germany. Antibodies to FCoV were detected in two cats (4%) and FCoV RNA was detected in feces of one of these two cats. Antibodies to FCV, FHV and FPV were found at relatively low frequencies of 16%, 4%, and 2%, respectively. Antibodies to FIV were not detected. Although antigen and antibodies to FeLV were detected in 49%, and 75%, respectively, no evidence of FeLV-associated pathology was found. From the low prevalence of FCoV, FCV, FHV and FPV infections and from the fact that the European wildcats live solitarily, it was concluded that these viral infections do not spread readily within a population. Therefore, it may be assumed that release into the wild of European wildcats bred in captivity would not bring about a high risk of introducing of these viral infections to the free-ranging wildcats. As an exception, wildcats should be tested for absence of FIV infection before release if they were at risk to acquire this infection from domestic cats.     

Human papillomavirus infection in Brazilian women with normal cervical cytology

We examined the prevalence of human papillomavirus (HPV) infection in a sample of Brazilian women presenting normal cervical cytology. Possible interactions between patient characteristics and HPV infection were analyzed in order to provide background data to improve cervical cancer screening and prophylaxis. Cervical samples of 399 women, received for routine evaluation in the Health Department of Ouro Preto, MG, Brazil, were subjected to HPV-DNA testing by PCR with MY09/11 primers. HPV-positive specimens were typed by RFLP. A structured epidemiological questionnaire was administered to each woman. HPV prevalence among these cytologically normal women was 11%. Twelve viral types were detected, the most common being HPV-16, -6, -61, -83, and -66. HPV was more prevalent in younger women; high-risk viral types were detected in 61% of the infected women and 27% of the infected women had multiple HPV infections. Significant associations of HPV infection were found with age, literacy, residence, marital status, lifetime number of sexual partners, and parity. We detected a great diversity of HPV types in women with normal cytology. This kind of information about local populations is useful for HPV prevention and vaccination strategies.     

Hepatitis E virus infection in selected Brazilian populations

A retrospective study on the prevalence of hepatitis E virus (HEV) infection was conducted in selected populations in Rio de Janeiro, Brazil. A total of 1,115 subjects were tested including 146 patients with acute Non-A Non-B Non-C (NANBNC) viral hepatitis, 65 hemodialysis patients, 93 blood donors, 102 intravenous drug users (IVDUs), 304 pregnant women, 145 individuals living in the rural area and 260 individuals living in the urban area. In order to characterize a favorable epidemiological set for enterically transmitted infection in the studied populations we also evaluated the prevalence of anti-HAV IgG (hepatitis A virus) antibodies. Specific antibodies to HEV (anti-HEV IgG) were detected by a commercial EIA and specific antibodies to HAV (anti-HAV IgG) were detected using a competitive "in house" EIA. We found a high prevalence of anti-HAV IgG in these populations, that could indicate some risk for infections transmitted via the fecal-oral route. The anti-HEV IgG prevalence among the different groups were: 2.1% in patients with acute NANBNC viral hepatitis, 6.2% in hemodialysis patients, 4.3% in blood donors, 11.8% in IVDUs, 1% in pregnant women, and 2.1% in individuals form the rural area. Among individuals living in the urban area we did not find a single positive serum sample. Our results demonstrated the presence of anti-HEV IgG in almost all studied populations; however, further studies are necessary to establish the real situation of HEV epidemiology in Rio de Janeiro, Brazil.     

Virologic investigations of free-living European bison (Bison bonasus) from the Bialowieza Primeval Forest,Poland

We conducted virologic investigations on postmortem specimens from 261 free-living European bison (Bison bonasus) from the Bialowieza Primeval Forest, Poland collected between 1990 and 2000. Fifty-four of 94 males had balanoposthitis; none of the 167 female bison examined had reproductive tract lesions. Peripheral blood, swabs, and various tissues were analyzed for bovine viruses as well as for viral DNA by bovine herpesvirus 1 (BoHV-1) and bovine herpesvirus 4 (BoHV-4) specific polymerase chain reaction (PCR) technique. An infectious bovine rhinotracheitis like BoHV-1 strain was isolated from the spleen of a female bison calf and additionally was detected by nested PCR from splenic tissue. None of the bison had significant antibody titers against BoHV-1, bovine herpesvirus 2, BoHV-4, caprine herpesvirus 1, cervid herpesvirus 1, or bovine viral diarrhea (BVD) virus-1. However, low antibody titers in two animals indicate that this European bison population has been exposed to BVD virus or BVD-like viruses and BoHV-2.     

Molecular cloning and physical mapping of the tupaia herpesvirus genome.

Purified virion DNA of about 200 kilobase pairs of tupaia herpesvirus strain 2 was cleaved with EcoRI or HindIII restriction endonuclease. Restriction fragments representing the complete viral genome including both termini were inserted into the EcoRI, HindIII, and EcoRI-HindIII sites of the bacterial plasmid pAT153. Restriction maps for the restriction endonucleases EcoRI and HindIII were constructed with data derived from Southern blot hybridizations of individual viral DNA fragments or cloned DNA fragments which were hybridized to either viral genome fragments or recombinant plasmids. The analysis revealed that the tupaia herpesvirus genome consists of a long unique sequence of 200 kilobase pairs and that inverted repeat DNA sequences of greater than 40 base pairs do not occur, in agreement with previous electron microscopic data. No DNA sequence homology was detectable between the tupaia herpesvirus DNA and the genome of murine cytomegalovirus, which was reported to have a similar structure. In addition, seven individual isolates of tupaia herpesvirus were characterized. The isolates can be grouped into five strains by their DNA cleavage patterns.     

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.     

Viral metagenome analysis to guide human pathogen monitoring in environmental samples

Aims: The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome. Methods and Results: In silico bioinformatic experiments were used to select an optimum annotation strategy for discovering human viruses in virome data sets and applied to annotate a class B biosolid virome. Results from the in silico study indicated that <1% errors in virus identification could be achieved when nucleotide‐based search programs (BLASTn or tBLASTx), viral genome only databases and sequence reads >200 nt were considered. Within the 51 925 annotated sequences, 94 DNA and 19 RNA sequences were identified as human viruses. Virus diversity included environmentally transmitted agents such as parechovirus, coronavirus, adenovirus and aichi virus, as well as viruses associated with chronic human infections such as human herpes and hepatitis C viruses. Conclusions: This study provided a bioinformatic approach for identifying pathogens in a virome data set and demonstrated the human virus diversity in a relevant environmental sample. Significance and Impact of the Study: As the costs of next‐generation sequencing decrease, the pathogen diversity described by virus metagenomes will provide an unbiased guide for subsequent cell culture and quantitative pathogen analyses and ensures that highly enriched and relevant pathogens are not neglected in exposure and risk assessments.     

Prevalence of hepatitis C virus antibody among healthy blood donors and non-A, non-B hepatitis patients in Thailand

With the antigen expressed in yeast from a cDNA clone encoding a non-structural region of newly discovered hepatitic C virus (HCV) genome, the prevalence of HCV antibody in people in Thailand was investigated. Antibody was detected in 2.6% of healthy blood donors and in 2.8% of healthy pregnant women. These prevalence rates were higher than those reported previously from Japan, USA and European countries. Among community-acquired, sporadic cases of acute and chronic non-A, non-B hepatitis, however, only 5.7% and 15.4% were shown to possess the antibody, respectively. Among hepatocellular carcinoma patients who were negative for hepatitis B surface antigen in the sera, 11.1% had antibody to HCV. These seroepidemiological data suggest that HCV plays an important role as an etiological agent in Thailand; however, other agents must also be involved in etiologic agents of viral hepatitis and chronic liver disease.