INTRODUCTION: To test whether parechovirus and anellovirus, frequent enteric viruses, were associated with subsequent celiac disease (CD). We hypothesized that children who later developed CD would have increased frequency of parechovirus infections before transglutaminase 2 (TG2) antibody development. Anellovirus testing was exploratory, as a potential marker of immune status. METHODS: Matched case-control design nested within a longitudinal birth cohort (the MIDIA study) of children at genetic risk of CD (carrying the human leukocyte antigen genotype DR4-DQ8/DR3-DQ2, recruited throughout Norway during 2001-2007). We retrospectively tested blood samples taken at age 3, 6, 9, and 12 months, and then annually, to determine when TG2 antibodies developed. Of 220 genetically at-risk children tested, 25 were diagnosed with CD (cases; ESPGHAN 2012 criteria) and matched for follow-up time, birthdate, and county of residence with 2 randomly selected children free from CD (controls) from the cohort. Viruses were quantified in monthly stool samples (collected from 3 through 35 months of age) using real-time polymerase chain reaction methods. RESULTS: Parechovirus was detected in 222 of 2,005 stool samples (11.1%) and was more frequent in samples from cases before developing TG2 antibodies (adjusted odds ratio 1.67, 95% confidence interval 1.14-2.45, P = 0.01). The odds ratio was higher when a sample was positive for both parechovirus and enterovirus (adjusted odds ratio 4.73, 95% confidence interval 1.26-17.67, P = 0.02). Anellovirus was detected in 1,540 of 1,829 samples (84.2%), but did not differ significantly between case and control subjects. DISCUSSION: Early-life parechovirus infections were associated with development of CD in genetically at-risk children.

• MeSH
• autoimunita * MeSH
• autoprotilátky krev   MeSH
• celiakie diagnóza   imunologie   virologie   MeSH
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• následné studie MeSH
• Parechovirus imunologie   MeSH
• pikornavirové infekce diagnóza   imunologie   virologie   MeSH
• předškolní dítě MeSH
• protilátky virové imunologie   MeSH
• rizikové faktory MeSH
• studie případů a kontrol MeSH
• věkové faktory MeSH
• Check Tag
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

OBJECTIVES: Direct genotyping of adenovirus or enterovirus from clinical material using polymerase chain reaction (PCR) followed by Sanger sequencing is often difficult due to the presence of multiple virus types in a sample, or due to varying efficacy of PCR amplifying the capsid gene on the background of foreign nucleic acids. Here we present a simple protocol for virus genotyping using massive parallel amplicon sequencing. METHODS: The protocol utilized a set of 16 tailed degenerate primers flanking the seventh hypervariable region of the adenovirus hexon gene and 9 tailed degenerate primers targeted to the proximal portion of the enterovirus VP1 gene. Subsequent addition of dual indices enabled simultaneous sequencing of 384 different samples on an Illumina MiSeq instrument. Downstream bioinformatic analysis was based on remapping to a set of references representative of the presently known repertoire of virus types. RESULTS: After validation with known virus types, the sequencing method was applied on 301 adenovirus-positive samples and 350 enterovirus-positive samples from a longitudinally collected series of stools from 83 children aged 3 to 36 months. We detected 7 different adenovirus types and 27 different enterovirus types. There were 37 (6.2%) samples containing more than one genotype of the same viral genus. At least one dual infection was experienced by 23 of 83 (28%) of the children observed over the 3 years' observation period. CONCLUSIONS: Amplicon sequencing with a multiplex set of degenerate primers seems to be a rapid and reliable technical solution for genotyping of large collections of samples where simultaneous infections with multiple strains can be expected.

• MeSH
• Adenoviridae klasifikace   genetika   izolace a purifikace   MeSH
• adenovirové infekce virologie   MeSH
• DNA primery genetika   MeSH
• enterovirové infekce virologie   MeSH
• Enterovirus klasifikace   genetika   izolace a purifikace   MeSH
• genotyp * MeSH
• genotypizační techniky metody   MeSH
• kojenec MeSH
• lidé MeSH
• longitudinální studie MeSH
• předškolní dítě MeSH
• sekvenční analýza DNA metody   MeSH
• výpočetní biologie MeSH
• zvířata MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Norsko MeSH

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

• MeSH
• Bacteroidetes klasifikace   genetika   virologie   MeSH
• bakteriofágy klasifikace   genetika   MeSH
• DNA virů genetika   MeSH
• feces virologie   MeSH
• fylogeneze MeSH
• fylogeografie MeSH
• genetická variace MeSH
• koevoluce * MeSH
• lidé MeSH
• primáti virologie   MeSH
• střevní mikroflóra * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

OBJECTIVE: To determine whether infection with human enterovirus or adenovirus, both common intestinal viruses, predicts development of coeliac disease. DESIGN: Case-control study nested within Norwegian birth cohort recruited between 2001 and 2007 and followed to September 2016. SETTING: Norwegian population. PARTICIPANTS: Children carrying the HLA genotype DR4-DQ8/DR3-DQ2 conferring increased risk of coeliac disease. EXPOSURES: Enterovirus and adenovirus detected using real time polymerase chain reaction in monthly stool samples from age 3 to 36 months. MAIN OUTCOME MEASURE: Coeliac disease diagnosed according to standard criteria. Coeliac disease antibodies were tested in blood samples taken at age 3, 6, 9, and 12 months and then annually. Adjusted odds ratios from mixed effects logistic regression model were used to assess the relation between viral infections before development of coeliac disease antibodies and coeliac disease. RESULTS: Among 220 children, and after a mean of 9.9 (SD 1.6) years, 25 children were diagnosed as having coeliac disease after screening and were matched to two controls each. Enterovirus was found in 370 (17%) of 2135 samples and was significantly more frequent in samples collected before development of coeliac disease antibodies in cases than in controls (adjusted odds ratio 1.49, 95% confidence interval 1.07 to 2.06; P=0.02). The association was restricted to infections after introduction of gluten. High quantity samples (>100 000 copies/μL) (adjusted odds ratio 2.11, 1.24 to 3.60; P=0.01) and long lasting infections (>2 months) (2.16, 1.16 to 4.04; P=0.02) gave higher risk estimates. Both the commonly detected enterovirus species Enterovirus A and Enterovirus B were significantly associated with coeliac disease. The association was not found for infections during or after development of coeliac disease antibodies. Adenovirus was not associated with coeliac disease. CONCLUSIONS: In this longitudinal study, a higher frequency of enterovirus, but not adenovirus, during early childhood was associated with later coeliac disease. The finding adds new information on the role of viral infections in the aetiology of coeliac disease.

• MeSH
• autoprotilátky krev   MeSH
• celiakie virologie   MeSH
• dítě MeSH
• enterovirové infekce komplikace   epidemiologie   MeSH
• Enterovirus izolace a purifikace   MeSH
• feces virologie   MeSH
• genotyp MeSH
• kojenec MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• lidé MeSH
• longitudinální studie MeSH
• předškolní dítě MeSH
• prospektivní studie MeSH
• rizikové faktory MeSH
• studie případů a kontrol MeSH
• Check Tag
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Norsko MeSH

Enteroviruses have been suggested as triggers of type 1 diabetes (T1D). We aimed to assess whether established T1D susceptibility single nucleotide polymorphisms (SNPs) and candidate SNPs in innate immune genes were associated with the frequency of enterovirus infection in otherwise healthy children. Fifty-six established T1D SNPs and 97 other candidate immunity SNPs were typed in 419 children carrying the T1D high-risk genotype, HLA-DR4-DQ8/DR3-DQ2 genotype, and 373 children without this genotype. Enteroviral RNA was detected using real-time polymerase chain reaction, with primers detecting essentially all enterovirus serotypes, in 7,393 longitudinal stool samples collected monthly (age range 3-36 months). The most significant association was with two T1D SNPs, rs12150079 (ZPBP2/ORMDL3/GSDMB region) (enterovirus frequency: AA 7.3%, AG 8.7%, GG 9.7%, RR = 0.86, overall p = 1.87E-02) and rs229541 (C1QTNF6/SSTR3/RAC2) (enterovirus frequency: CC 7.8%, CT 9.7%, TT 9.4%, RR = 1.13, overall p = 3.6E-02), followed by TLR8 (rs2407992) (p = 3.8E-02), TLR3 (1914926) (p = 4.9E-02), and two other T1D SNPs (IFIH1 rs3747517, p = 4.9E-02 and PTPN22, rs2476601, p = 5.3E-02). However, the quantile-quantile plot of p-values with confidence intervals for all 153 SNPs did not reveal clear evidence for rejection of the complete null hypothesis. Among a number of SNPs in candidate genes, we found no evidence for strong associations with enterovirus presence in stool samples from Norwegian children.

• MeSH
• enterovirové infekce epidemiologie   genetika   MeSH
• Enterovirus izolace a purifikace   MeSH
• feces virologie   MeSH
• genetická predispozice k nemoci * MeSH
• genetické asociační studie MeSH
• jednonukleotidový polymorfismus MeSH
• kojenec MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• lidé MeSH
• longitudinální studie MeSH
• předškolní dítě MeSH
• RNA virová analýza   genetika   MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Norsko MeSH

The aim of this study was to describe the frequency and distribution of Saffold virus in longitudinal stool samples from children, and test for association with development of persistent autoantibodies predictive of type 1 diabetes. A cohort of Norwegian children carrying the HLA genotype associated with highest risk of type 1 diabetes ("DR4-DQ8/DR3-DQ2") was followed with monthly stool samples from 3 to 35 months of age. Blood samples were tested for autoantibodies to insulin, glutamic acid decarboxylase65 and Islet Antigen-2. 2077 stool samples from 27 children with ≥ 2 repeatedly positive islet autoantibodies (cases), and 53 matched controls were analysed for Saffold virus genomic RNA by semi-quantitative real-time reverse transcriptase PCR. Saffold virus was found in 53 of 2077 (2.6%) samples, with similar proportions between cases (2.5%) and controls (2.6%). The probability of being infected by 3 years of age was 28% (95% CI 0.18-0.40). Viral quantities ranged from <1 to almost 105 copies/μl. Estimated odds ratio between islet autoimmunity and infection episodes prior to seroconversion was 1.98 (95% CI: 0.57-6.91, p = 0.29). Saffold virus had no statistically significant association with islet autoimmunity.

• MeSH
• autoprotilátky krev   MeSH
• Cardiovirus izolace a purifikace   MeSH
• diabetes mellitus 1. typu krev   genetika   imunologie   MeSH
• feces virologie   MeSH
• glutamát dekarboxyláza imunologie   MeSH
• HLA-DQ antigeny genetika   MeSH
• infekce viry z rodu Cardiovirus krev   imunologie   virologie   MeSH
• inzulin imunologie   MeSH
• kojenec MeSH
• lidé MeSH
• longitudinální studie MeSH
• předškolní dítě MeSH
• tyrosinfosfatasy receptorového typu, třída 8 imunologie   MeSH
• virová nálož MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

AIMS/HYPOTHESIS: Only a few longitudinal molecular studies of enterovirus and islet autoimmunity have been reported, and positive results seem to be limited to Finland. We aimed to investigate an association between enterovirus RNA in blood and islet autoimmunity in the MIDIA study from Norway, a country which largely shares environmental and economic features with Finland. METHODS: We analysed serial blood samples collected at ages 3, 6, and 9 months and then annually from 45 children who developed confirmed positivity for at least two autoantibodies (against insulin, GAD65 and IA-2) and 92 matched controls, all from a cohort of children with a single high-risk HLA-DQ-DR genotype. Enterovirus was tested in RNA extracted from frozen blood cell pellets, using real-time RT-PCR with stringent performance control. RESULTS: Out of 807 blood samples, 72 (8.9%) were positive for enterovirus. There was no association between enterovirus RNA and islet autoimmunity in samples obtained strictly before (7.6% cases, 10.0% controls, OR 0.75 [95% CI 0.36, 1.57]), or strictly after the first detection of islet autoantibodies (10.5% case, 5.8% controls, OR 2.00 [95% CI 0.64, 6.27]). However, there was a tendency towards a higher frequency of enterovirus detection in the first islet autoantibody-positive sample (15.8%) compared with the corresponding time point in matched controls (3.2%, OR 8.7 [95% CI 0.97, 77]). Neither of these results was changed by adjusting for potential confounders, restricting to various time intervals or employing various definitions of enterovirus positivity. CONCLUSIONS/INTERPRETATION: Positivity for enterovirus RNA in blood did not predict the later induction of islet autoantibodies, but enterovirus tended to be detected more often at the islet autoantibody seroconversion stage.

• MeSH
• autoimunita genetika   MeSH
• autoprotilátky krev   MeSH
• diabetes mellitus 1. typu genetika   imunologie   virologie   MeSH
• Enterovirus genetika   izolace a purifikace   MeSH
• geny MHC třídy II genetika   MeSH
• HLA-DQ antigeny genetika   MeSH
• lidé MeSH
• novorozenec MeSH
• RNA virová krev   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

OBJECTIVE: Polymorphisms in the IFIH1 (common rs1990760 and four rare rs35667974, rs35337543, rs35744605, rs35732034) have been convincingly associated with type 1 diabetes. The encoded protein (interferon-induced helicase C domain-containing protein 1) senses double-stranded RNA during replication of Picornavirales, including Enterovirus, a genus suspected in the etiology of type 1 diabetes. We therefore investigated whether the polymorphisms are associated with differences in the frequency of enterovirus RNA in blood. RESEARCH DESIGN AND METHODS: The study included 1001 blood samples, each from a child participating in the Norwegian 'Environmental Triggers of Type 1 Diabetes: the MIDIA study'. The enterovirus RNA was tested using qualitative semi-nested real-time reverse transcriptase PCR on RNA extracted from frozen cell packs after removal of plasma. Stool samples previously analyzed for enterovirus RNA were available in 417 children. RESULTS: The genotypes of IFIH1 rs1990760 were associated with different frequencies of enterovirus RNA in blood (7.0%, 14.4% and 9.5% bloods were enterovirus positive among children carrying the Ala/Ala, Ala/Thr and Thr/Thr genotypes, respectively, p = 0.012). This association remained essentially unchanged after adjustment for age and calendar year. The presence of enterovirus in the concomitantly sampled stool further increased the likelihood of enterovirus RNA in blood (odds ratio 2.40, CI 95% 1.13-4.70), but did not affect the association with IFIH1 rs1990760. The rare polymorphisms (individually, or pooled) were not significantly associated with enterovirus RNA in blood. CONCLUSIONS: The common IFIH1 SNP may modify the frequency of enterovirus RNA in blood of healthy children. This effect can help explain the association of IFIH1 with type 1 diabetes.

• MeSH
• DEAD-box RNA-helikasy genetika   MeSH
• diabetes mellitus 1. typu krev   genetika   virologie   MeSH
• Enterovirus genetika   MeSH
• feces virologie   MeSH
• genetická predispozice k nemoci * MeSH
• genetické asociační studie * MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• kojenec MeSH
• lidé MeSH
• multivariační analýza MeSH
• RNA virová krev   MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Norsko MeSH

Enterovirus infections may be involved in the etiology of type 1 diabetes (T1D), which is strongly associated with certain human leukocyte antigen (HLA) class II haplotypes. Our aim was to assess whether HLA genotypes conferring varying degrees of risk for T1D were associated with enterovirus gut infections. From the general Norwegian population, 190 healthy infants at high-risk for T1D (DR4-DQ8/DR3-DQ2), and 383 infants without this genotype were identified. Non-DR4-DQ8/DR3-DQ2 genotypes were further categorized as conferring either an increased-to-moderate risk (DR4-DQ8 or DR3-DQ2), were protective (DQB1*06:02), or were neutral (all other genotypes). A total of 4626 monthly fecal samples taken between age 3 and 12mo were tested for enterovirus RNA using real-time PCR. Enterovirus prevalence was 11.5% among high-risk children, and 12.2% in other children (adjusted odds ratio: 1.23, p=0.12). The prevalence was 11.3% in those with increased-to-moderate risk, 13.0% in the protective group, and 12.6% in the neutral group (likelihood ratio test, 3 d.f.: p=0.37). In conclusion, there was no statistically significant association between HLA genotype and the occurrence of human enterovirus gut infections.

• MeSH
• diabetes mellitus 1. typu genetika   virologie   MeSH
• enterovirové infekce * MeSH
• Enterovirus genetika   izolace a purifikace   MeSH
• feces * virologie   MeSH
• genetická predispozice k nemoci MeSH
• genotyp MeSH
• HLA-DQ alfa řetězec * genetika   MeSH
• HLA-DQ beta řetězec * genetika   MeSH
• HLA-DRB1 řetězec * genetika   MeSH
• kojenec MeSH
• lidé MeSH
• testování histokompatibility MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH

Interferon induced with helicase C domain 1 (IFIH1) senses and initiates antiviral activity against enteroviruses. Genetic variants of IFIH1, one common and four rare SNPs have been associated with lower risk for type 1 diabetes. Our aim was to test whether these type 1 diabetes-associated IFIH1 polymorphisms are associated with the occurrence of enterovirus infection in the gut of healthy children, or influence the lack of association between gut enterovirus infection and islet autoimmunity.After testing of 46,939 Norwegian newborns, 421 children carrying the high risk genotype for type 1 diabetes (HLA-DR4-DQ8/DR3-DQ2) as well as 375 children without this genotype were included for monthly fecal collections from 3 to 35 months of age, and genotyped for the IFIH1 polymorphisms. A total of 7,793 fecal samples were tested for presence of enterovirus RNA using real time reverse transcriptase PCR.We found no association with frequency of enterovirus in the gut for the common IFIH1 polymorphism rs1990760, or either of the rare variants of rs35744605, rs35667974, rs35337543, while the enterovirus prevalence marginally differed in samples from the 8 carriers of a rare allele of rs35732034 (26.1%, 18/69 samples) as compared to wild-type homozygotes (12.4%, 955/7724 samples); odds ratio 2.5, p = 0.06. The association was stronger when infections were restricted to those with high viral loads (odds ratio 3.3, 95% CI 1.3-8.4, p = 0.01). The lack of association between enterovirus frequency and islet autoimmunity reported in our previous study was not materially influenced by the IFIH1 SNPs.We conclude that the type 1 diabetes-associated IFIH1 polymorphisms have no, or only minor influence on the occurrence, quantity or duration of enterovirus infection in the gut. Its effect on the risk of diabetes is likely to lie elsewhere in the pathogenic process than in the modification of gut infection.

• MeSH
• autoimunita * genetika   MeSH
• časové faktory MeSH
• DEAD-box RNA-helikasy * genetika   MeSH
• diabetes mellitus 1. typu MeSH
• Enterovirus * MeSH
• feces * virologie   MeSH
• IFIH1 MeSH
• jednonukleotidový polymorfismus * MeSH
• kohortové studie MeSH
• kojenec MeSH
• Langerhansovy ostrůvky * imunologie   virologie   MeSH
• lidé MeSH
• přirozená imunita * MeSH
• střeva imunologie   virologie   MeSH
• studie případů a kontrol MeSH
• virová nálož genetika   MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH