Displacement of the Gent/1999 human-like swine H1N2 influenza A virus lineage by novel H1N2 reassortants in Germany.

A swine influenza survey was conducted between 2003 and 2015 in Germany. During this period, 8122 snout swabs or other respiratory specimens from pigs of 5178 herds, mainly from Germany, were investigated for the presence of swine influenza A virus (S-IAV). In total, 1310 S-IAV isolates were collected. Of this collection, the complete genome of 267 H1N2 S-IAV isolates was sequenced and phylogenetically analyzed. The data demonstrate the incursion of human-like swine H1N2 viruses (Gent/1999-like) in 2000 and prevalent circulation until 2010. From 2008 onward, a sustained and broad change of the genetic constellation of the swine H1N2 subtype commenced. The Gent/1999-like swine H1N2 viruses ceased and several new swine H1N2 reassortants emerged and became prevalent in Germany. Of these, the upsurge of the Diepholz/2008-like, Emmelsbuell/2009-like and Papenburg/2010-like viruses is notable. The data reveal the importance of reassortment events in S-IAV evolution. The strong circulation of S-IAV of different lineages in the swine population throughout the year underlines that pigs are important reservoir hosts.

Characterization of a novel picornavirus isolate from a diseased European eel (Anguilla anguilla).

A novel picornavirus was isolated from specimens of a diseased European eel (Anguilla anguilla). This virus induced a cytopathic effect in eel embryonic kidney cells and high mortality in a controlled transmission study using elvers. Eel picornavirus has a genome of 7,496 nucleotides that encodes a polyprotein of 2,259 amino acids. It has a typical picornavirus genome layout, but its low similarity to known viral proteins suggests a novel species in the family Picornaviridae.

Current knowledge on PB1-F2 of influenza A viruses.

Almost 10 years ago, an eleventh protein of influenza A viruses was discovered in a search for CD8+ T-cell epitopes. This protein was named PB1-F2 since it is encoded in the +1 reading frame of the PB1 gene segment. Various studies have shown that PB1-F2 has a pleiotropic effect: (1) The protein can induce apoptosis in a cell type-dependent manner, (2) PB1-F2 is able to promote inflammation, and (3) finally it up-regulates viral polymerase activity by its interaction with the PB1 subunit. These properties could contribute to an enhanced pathogenicity. However, the underlying mechanism is not fully understood yet. New data suggest that some effects of PB1-F2 are strain-specific and host-specific.

Novel reassortant swine H3N2 influenza A viruses in Germany.

Analysis of 228 H3N2 swine influenza A virus isolates collected between 2003 and 2015 in Germany revealed important changes in molecular epidemiology. The data indicate that a novel reassortant, Rietberg/2014-like swine H3N2, emerged in February 2014 in Northern Germany. It is comprised of a hemagglutinin gene of seasonal H3N2 (A/Denmark/129/2005-like), a neuraminidase gene of Emmelsbuell/2009-like swine H1N2 and the internal gene cassette of pandemic H1N1 viruses. Together with Danish swine H3N2 strains of 2013-2015 with identical genome layout, the Rietberg/2014-like viruses represent a second swine H3N2 lineage which cocirculates with a variant of the Gent/1984-like swine H3N2 lineage. This variant, named Gent1984/Diepholz-like swine H3N2, has a Gent/1984-like HA and a Diepholz/2008-like NA; the origin of the internal gene cassette likely derived from avian-like swine H1N1. The first isolate of the Gent1984/Diepholz reassortant emerged in Northern Germany in September 2011 whereas the last German Gent/1984-like isolate was collected in October 2011.

Cocirculation of Swine H1N1 Influenza A Virus Lineages in Germany.

The genome analysis of 328 H1N1 swine influenza virus isolates collected in a 13-year long-term swine influenza surveillance in Germany is reported. Viral genomes were sequenced with the Illumina next-generation sequencing technique and conventional Sanger methods. Phylogenetic analyses were conducted with Bayesian tree inference. The results indicate continued prevalence of Eurasian avian swine H1N1 but also emergence of a novel H1N1 reassortant, named Schneiderkrug/2013-like swine H1N1, with human-like hemagglutinin and avian-like neuraminidase and internal genes. Additionally, the evolution of an antigenic drift variant of A (H1N1) pdm09 was observed, named Wachtum/2014-like swine H1N1. Both variants were first isolated in northwest Germany, spread to neighboring German states and reached greater proportions of the H1N1 isolates of 2014 and 2015. The upsurge of Wachtum/2014-like swine H1N1 is of interest as this is the first documented persistent swine-to-swine spread of A (H1N1) pdm09 in Germany associated with antigenic variation. Present enzootic swine influenza viruses in Germany now include two or more co-circulating, antigenically variant viruses of each of the subtypes, H1N1 and H1N2.

Genotyping of varicella-zoster virus strains after serial passages in cell culture.

There is little information in the literature about the stability of single nucleotide polymorphisms (SNP) used for genotyping of varicella-zoster virus (VZV) in sequencing studies. The objective of this study was to genotype VZV wild-type and vaccine isolates representing the four major clades A, B, C and J before and after serial passages in cell culture. Eleven VZV strains were genotyped by sequencing of the open reading frames (ORF) 1, 21, 37, 50, 54 and 60 as well as by restriction fragment length polymorphism (RFLP) analysis of the ORFs 38 and 62 after 1-16 passages in human embryonic lung fibroblasts (HELF). Results revealed no variations of nucleotide sequences in the ORFs 1, 21, 37, 50, 54 and 60 within 16 cell culture passages. Additionally, there were no changes in the RFLP profile of the ORFs 38 and 62. In conclusion, VZV can be isolated in HELF and propagated for at least 16 passages before genotyping by sequencing without the risk of intra-strain variations. For rapid diagnostic identification of vaccine versus wild-type strains, the RFLP profile that is stable within several cell culture passages can be determined using DNA prepared from clinical specimens.

Isolation and molecular characterization of a second serotype of the encephalomyocarditis virus.

Encephalomyocarditis virus (EMCV) and Theilovirus are the two species of the Cardiovirus genus. Whereas theiloviruses comprise several sero-/genotypes, all known EMCV isolates are serologically very similar and are thought to belong to one serotype, named EMCV-1. Here, a novel EMCV type is described. Strain RD 1338 (D28/05) was isolated from a wood mouse (Apodemus sylvaticus) in Germany and can be distinguished from EMCV-1 by serological and molecular means. Failure of EMCV-1 specific hyperimmune sera to neutralize RD 1338 suggests a distinct serotype. The viral genome was de novo sequenced using next-generation Illumina/Solexa technologies. Considerable differences of the BC-loop/loop I/loop II sequences of VP1, the VP2 puff and the VP3 knob provide a structural basis for deviant serological properties. Sequence alignments reveal amino acid identities of 75 percent for the P1 region and 84 percent for the P2 and P3 regions when comparing RD 1338 to EMCV-1 strains and some 60 percent and less than 50 percent amino acid identities, respectively, for comparisons with theilovirus strains. Phylogenetic analyses of the P1, 2C and 3CD gene regions support the establishment of an EMCV-2 serotype. In contrast to the theilovirus sero-/genotypes that show a narrow host range, EMCV-1 infects a wide variety of hosts. The host range of EMCV-2 remains to be determined.