Genetic Diversity of the Genus Cosavirus in the Family Picornaviridae: A New Species, Recombination, and 26 New Genotypes

The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses

Molecular characterization of a novel picobirnavirus in a chicken.

Picobirnaviruses (PBVs) are bisegmented viruses with a wide geographical and host species distribution. The number of novel PBV sequences has been increasing with the help of the viral metagenomics. A novel picobirnavirus strain, pbv/CHK/M3841/HUN/2011, was identified by viral metagenomics; the complete segment 1 (MH327933) and 2 (MH327934) sequences were obtained by RT-PCR from a cloacal sample of a diseased broiler breeder pullet in Hungary. Although the conserved nucleotide (e.g., ribosome binding site) and amino acid motifs (e.g., ExxRxNxxxE, S-domain of the viral capsid and motifs in the RNA-dependent RNA polymerase) were identifiable in the chicken picobirnavirus genome, the putative segment 1 showed low (< 30%) amino acid sequence identity to the corresponding proteins of marmot and dromedary PBVs, while segment 2 showed higher (< 70%) amino acid sequence identity to a wolf PBV protein sequence. This is the first full-genome picobirnavirus sequence from a broiler breeder chicken, but the pathogenicity of this virus is still questionable

No Evidence of Murine Leukemia Virus-Related Viruses in Live Attenuated Human Vaccines

The association of xenotropic murine leukemia virus (MLV)-related virus (XMRV) in prostate cancer and chronic fatigue syndrome reported in previous studies remains controversial as these results have been questioned by recent data. Nonetheless, concerns have been raised regarding contamination of human vaccines as a possible source of introduction of XMRV and MLV into human populations. To address this possibility, we tested eight live attenuated human vaccines using generic PCR for XMRV and MLV sequences. Viral metagenomics using deep sequencing was also done to identify the possibility of other adventitious agents.All eight live attenuated vaccines, including Japanese encephalitis virus (JEV) (SA-14-14-2), varicella (Varivax), measles, mumps, and rubella (MMR-II), measles (Attenuvax), rubella (Meruvax-II), rotavirus (Rotateq and Rotarix), and yellow fever virus were negative for XMRV and highly related MLV sequences. However, residual hamster DNA, but not RNA, containing novel endogenous gammaretrovirus sequences was detected in the JEV vaccine using PCR. Metagenomics analysis did not detect any adventitious viral sequences of public health concern. Intracisternal A particle sequences closest to those present in Syrian hamsters and not mice were also detected in the JEV SA-14-14-2 vaccine. Combined, these results are consistent with the production of the JEV vaccine in Syrian hamster cells.We found no evidence of XMRV and MLV in eight live attenuated human vaccines further supporting the safety of these vaccines. Our findings suggest that vaccines are an unlikely source of XMRV and MLV exposure in humans and are consistent with the mounting evidence on the absence of these viruses in humans

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

Interference among viruses circulating and administered in Hungary from 1931 to 2008

Viral interference was discovered about 60 years ago. Molecular epidemiology revealed that this phenomenon possesses important biological implications, it can reduce the epidemic spread of certain viruses from time to time (influenza and enteroviruses) and the efficiency of live vaccination can be impaired, too. Phenomena observed during the last 80 years in Hungary are analyzed. It is suggested to concentrate the distribution of MMR vaccines to seasons of limited influenza and enterovirus circulation. Interference seems to impair the progress of wild poliovirus eradication in the endemic tropical countries. It is recommended to enhance enterovirus surveillance in the region of European countries, since the exchange of the oral poliovirus vaccine to the enhanced inactivated polio vaccine might result in enhanced circulation of non-polio enteroviruses leading to the increase in the number of type I (juvenile) diabetes patients

Real-time PCR assay for rapid qualitative and quantitative detection of Entamoeba histolytica

Simple real-time PCR assay with one set of primer and probe for rapid, sensitive qualitative and quantitative detection of Entamoeba histolytica has been used. Consensus sequences were used to amplify a species-specific region of the 16S rRNA gene, and fluorescence resonance energy transfer hybridization probes were used for detection in a LightCycler platform (Roche). The anchor probe sequence was designed to be a perfect match for the 16S rRNA gene of Entamoeba species, while the acceptor probe sequence was designed for Entamoeba histolytica, which allowed differentiation. The performed characteristics of the real-time PCR assay were compared with ELISA antigen and microscopical detection from 77 samples of individuals with suspected clinical diagnosis of imported E. histolytica infection. Stool and liver abscess pus samples were examined with analytical sensitivity of 5 parasites per PCR reaction. The melting curve means Tms (standard deviation) in clinical isolates were 54°C. The real-time assay was 100% sensitive and specific for differentiation of Entamoeba histolytica, compared with conventional ELISA or microscopy. This real-time PCR assay with melting curve analysis is rapid, and specific for the detection and differentiation of Entamoeba histolytica. The suitability for routine use of this assay in clinical diagnostic laboratories is discussed