Immunity to Influenza and Future Vaccination Strategies

Influenza viruses are very small pathogens (typically 80-120 nm) belonging to the family of the Orthomyxoviridae together with four other genera: Thogoto virus, Isavirus and influenza B and C viruses. The influenza viruses are distinguished based on the membrane channel protein, genome size and surface glycoproteins. The influenza A viruses are further subdivided into subtypes based on the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). At present, 16 subtypes of the HA and 9 subtypes of the NA are known

Viral metagenomic analysis of feces of wild small carnivores

Background: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods: In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores

Viral metagenomic analysis of feces of wild small carnivores

Background: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods: In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.The authors would like to thank Peter van Run for excellent technical assistance. In addition, the authors wish to thank all the following researchers and institutions for their invaluable help during sampling and for providing the specimens used in this study, specially to Patricia Lizarraga, Ricardo Gutierrez, and Laura Elorza (Martioda Wildlife Rescue Centre-Alava Regional Council), Luis Javier Chueca (UPV-EHU), Asun Gomez (TRAGSATEC), Maddis Podra (European mink Association) and the technical staff and rangers from La Rioja Government and Alava regional council. We would like to thank also La Rioja Government (Agriculture, Livestock and Environmental Council. General Direction of Natural Environment. Nature Conservation and Planning Service) and Alava Regional Council (Department of Environment. Biodiversity Section) for providing the legal permissions required to develop this study. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007 -2013) under the project "European Management Platform for Emerging and Re-emerging Infectious disease Entities" (EMPERIE) EC grant agreement number 223498, the VIRGO Consortium and the Niedersachsen-Research Network on Neuroinfectiology (N-RENNT) of the Ministry of Science and Culture of Lower Saxony. In addition, this research has been partially funded by the Basque Government through the Research group on "Systematics, Biogeography and Population Dynamics" (Ref. IT317-10; GIC10/76). A. Ruiz-Gonzalez holds a Post doc fellowship awarded by the Department of Education, Universities and Research of the Basque Government (Ref. DKR-2012-64) and was awarded by a short visit Research grant from the ConGenOmics Research networking programme of the European Science Foundation (ESF) in order to visit the Department of Viroscience, Erasmus Medical Centre and develop the current research project

Assembly of viral genomes from metagenomes

Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.This work was partially funded by the Virgo Consortium, funded by the Dutch government project number FES0908, by Netherlands Genomics Initiative (NGI) project number 050-060-452 and ZonMW TOP project 91213058. A. Ruiz-Gonzalez holds a Post doc fellowship awarded by the Department of Education, Universities and Research of the Basque Government (Ref. DKR-2012-64) and was partially supported by the Research group on "Systematics, Biogeography and Population Dynamics" (Basque Government; Ref. IT317-10; GIC10/76)

No serological evidence that harbour porpoises are additional hosts of influenza B viruses

Influenza A and B viruses circulate among humans causing epidemics almost annually. While various hosts for influenza A viruses exist, influenza B viruses have been detected only in humans and seals. However, recurrent infections of seals in Dutch coastal waters with influenza B viruses that are antigenetically distinct from influenza B viruses circulating among humans suggest that influenza B viruses have been introduced into this seal population by another, non-human, host. Harbour porpoises (Phocoena phocoena) are sympatric with seals in these waters and are also occasion

Molecular epidemiology of seal parvovirus, 1988-2014

A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina) with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Er

Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands

In the spring and summer 2014, an outbreak of seal influenza A(H10N7) virus infection occurred among harbor seals (Phoca vitulina) off the coasts of Sweden and Denmark. This virus subsequently spread to harbor seals off the coasts of Germany and the Netherlands. While thousands of seals were reported dead in Sweden, Denmark and Germany, only a limited number of seals were found dead in the Netherlands. To determine the extent of exposure of seals in the Netherlands to influenza A/H10N7 virus, we measured specific antibody titers in serum samples from live-captured seals and seals admitted for rehabilitation in the Netherlands by use of a hemagglutination inhibition assay and an ELISA. In harbor seals in 2015, antibodies against seal influenza A(H10N7) virus were detected in 41% (32 out of 78) pups, 10% (5 out of 52) weaners, and 58% (7 out of 12) subadults or adults. In gray seals (Halichoerus grypus) in 2015, specific antibodies were not found i