Variability in sequence of Strawberry vein banding virus

The variability of the Strawberry vein banding virus (SVBV) isolates was investigated. In total 267 strawberry plants from 6 European countries and North America were tested for the presence of SVBV. Only 4 plants were positive. Partial genomic sequences of the capsid protein gene of three North American SVBV isolates were determined. Only minor sequence variability (0.7 %) was observed during a comparison with existing nucleotide data of the European and the North American isolates (9 isolates). No variability at all could be found in the annealing regions of primers and probes used for molecular detection of SVBV for these isolates. However, a comparison to a sequence of a Chinese isolate published recently revealed a much higher DNA sequence difference (9.5 %) of this isolate.     

Genetic characterization of an avian H4N6 influenza virus isolated from the Izumi plain,Japan

An influenza A virus of H4N6 subtype was isolated from the Izumi plain, Japan, in 2013. Genetic analyses revealed that two viral genes (M and NS gene segments) of this isolate were genetically distinct from those of the H4N6 virus isolated from the same place in 2012. Furthermore, three viral genes (PB2, PB1 and M gene segments) of this isolate share high similarity with those of the North American isolates of 2014. These results suggest a high frequency of genetic reassortment of avian influenza viruses in Asian waterfowl and intercontinental movements of avian influenza viruses via migratory waterfowl.

     

Influenza A Virus Migration and Persistence in North American Wild Birds

Wild birds have been implicated in the emergence of human and livestock influenza. The successful prediction of viral spread and disease emergence, as well as formulation of preparedness plans have been hampered by a critical lack of knowledge of viral movements between different host populations. The patterns of viral spread and subsequent risk posed by wild bird viruses therefore remain unpredictable. Here we analyze genomic data, including 287 newly sequenced avian influenza A virus (AIV) samples isolated over a 34-year period of continuous systematic surveillance of North American migratory birds. We use a Bayesian statistical framework to test hypotheses of viral migration, population structure and patterns of genetic reassortment. Our results reveal that despite the high prevalence of Charadriiformes infected in Delaware Bay this host population does not appear to significantly contribute to the North American AIV diversity sampled in Anseriformes. In contrast, influenza viruses sampled from Anseriformes in Alberta are representative of the AIV diversity circulating in North American Anseriformes. While AIV may be restricted to specific migratory flyways over short time frames, our large-scale analysis showed that the long-term persistence of AIV was independent of bird flyways with migration between populations throughout North America. Analysis of long-term surveillance data provides vital insights to develop appropriately informed predictive models critical for pandemic preparedness and livestock protection.     

Variation in phenotype and virulence among enzootic and panzootic amphibian chytrid lineages

The Global Panzootic Lineage of the fungus Batrachochytrium dendrobatidis (Bd-GPL) is threatening amphibians worldwide. In contrast, four lineages (Bd-Brazil, Bd-CH, Bd-Cape, and Bd-Korea) that diverged early in the history of Bd have not yet been directly linked to amphibian declines. Bd likely evolves in response to strong selective pressure imposed by hosts and the environment, leading to differences among pathogen phenotypes and genotypes that may directly affect virulence. Here, we report on variation in phenotype, genotype, and virulence of Bd-Brazil and Bd-GPL. Specifically, we (i) used a controlled infection experiment to compare virulence between one Bd-Brazil and three Bd-GPL isolates on a North American amphibian host (Lithobates sylvaticus), (ii) tested for relative phenotypic and genotypic differentiation among Bd isolates from Brazil, and (iii) tested for possible correlations between environmental variables and Bd phenotypes. We found substantial variation in virulence among Bd-GPL isolates and found that our Bd-Brazil isolate showed virulence comparable to an average North American Bd-GPL. North American hosts infected with a Bd-GPL isolate from Panama did not show significant mortality. Bd phenotypes varied significantly across sampling locations; these phenotypes were neither spatially clustered nor correlated with any environmental variables. Additionally, we found a surprising lack of correlation between genotypic divergence and zoospore and zoosporangium sizes in our sample. Although Bd-Brazil was less virulent infecting L. sylvaticus than one Bd-GPL isolate, this endemic lineage still caused ∼50% mortality in our experimental North American hosts. This indicates that Bd-Brazil has the potential to kill amphibians if introduced to naïve wild populations. Our findings underscore that characterizing virulence of multiple Bd isolates and lineages is important for understanding the evolutionary history and diversity of Bd.     

Comparing Competitive Fitness of West Nile Virus Strains in Avian and Mosquito Hosts

Enzootic transmission of West Nile virus (WNV; Flaviviridae, Flavivirus) involves various species of birds and ornithophilic mosquitoes. Single nucleotide substitutions in the WNV genome may impact viral fitness necessary for WNV adaptation and evolution as previously shown for the WN02 genotype. In an effort to study phenotypic change, we developed an in vivo fitness competition model in two biologically relevant hosts for WNV. The House Finch (HOFI; Haemorhous mexicanus) and Culex tarsalis mosquitoes represent moderately susceptible hosts for WNV, are highly abundant in Western North America and frequently are infected with WNV in nature. Herein, we inoculated HOFIs and Cx. tarsalis competitively (dually) and singly with infectious-clone derived viruses of the founding California isolate COAV997-2003 (COAV997-IC), the founding North American isolate NY99 (NY99-IC), and a 2004 field isolate from California (CA-04), and compared the replicative capacities (fitness) of these viruses to a genetically marked virus of COAV997 (COAV997-5nt) by measuring RNA copy numbers. COAV997 and COAV997-5nt exhibited neutral fitness in HOFIs and Cx. tarsalis, and the temperature-sensitive phenotype of COAV997 did not affect replication in HOFIs as none of the infected birds became febrile. The NY99 and CA-04 isolates demonstrated elevated fitness in HOFIs compared to COAV997-5nt, whereas all viruses replicated to similar titers and RNA copies in Cx. tarsalis, and the only fitness differences were related to infection rates. Our data demonstrated that competitive replication allows for the sensitive comparison of fitness differences among two genetically closely related viruses using relevant hosts of WNV while eliminating host-to-host differences. In conclusion, our approach may be helpful in understanding the extent of phenotypic change in fitness associated with genetic changes in WNV.     

Phylogenetic relationships among New World Scrophularia L. (Scrophulariaceae): new insights inferred from DNA sequence data

The genus Scrophularia L. (Scrophulariaceae) comprises 200?C300 species, of which approximately 19 are distributed in North America and the Greater Antilles. To investigate phylogenetic and biogeographic relationships of the New World species, two intergenic spacers (trnQ-rps16 and psbA-trnH) of chloroplast DNA and nuclear ribosomal ITS were sequenced. Phylogenetic analyses revealed three distinct New World clades that correspond to their geographical distribution and are corroborated by morphological characters. Phylogenetic inference indicates the eastern American S. marilandica L. as sister to all Antillean species; for colonization of the Caribbean archipelago, a late Miocene dispersal event from the North American mainland is assumed. There is evidence for a hybrid origin of the most widespread North American species, S. lanceolata Pursh. The results further suggest that S. nodosa L. is sister to all New World and three Japanese species of Scrophularia. The latter form an Eastern Asian?CEastern North American (EA-ENA) disjunction with six New World species. We propose an eastern Asian origin for the New World taxa of Scrophularia. Divergence times estimated using a relaxed molecular clock model suggest one or more Miocene migration events from eastern Asia to the New World via the Bering Land Bridge followed by diversification in North America.     

Some properties of the virus causing the mosaic of sweet peas in Czechoslovakia

Identification trials were carried out to determine what virus causes a mosaic disease of sweet peas in Czechoslovakia. The found properties of the identified sweet pea mosaic virus, the character of its transmission and its host range prove that sweet peas in Czechoslovakia are attacked by common pea mosaic virus (CPMV). Some insignificant differences in properties between our virus isolate and CPMV were observed in the course of the determination of properties of our virus isolate on various host plants. The possible existence of more strains of CPMV is discussed. The transmission of sweet pea mosaic to the plants ofPhaseolus vulgaris L. was negative. For this reason bean yellow mosaic virus (BYMV) was eliminated as a possible pathogen of our virus isolate. At the same time the indicator plantsChenopodium giganteum Don. andChenopodium guinoa Willd. with eight developed leaves were established to be most suitable for the determination of the properties of the isolate by the half-leaf test. The transmission of the virus isolate by seeds was not proved.     

Genetic analysis of infectious salmon anaemia virus (ISAV) from Scotland

The nucleotide sequences of segments 2 and 8 of infectious salmon anaemia virus (ISAV) isolates from Scotland were determined. These were used to predict amino acid sequences of the products of these segments. The sequences were compared with those previously published for ISAV from Norway and North America. Nucleotide and amino acid variations were found in the Scottish isolate, indicating that it is not identical to those Norwegian or North American strains. Although phylogenetic analysis of the sequences was not possible, it was clear that the Scottish isolate is more closely related to the Norwegian strain than the North American. Sequencing further isolates that are geographically or temporally separated will be important in advancing understanding of the epidemiology of this important disease.     

Pathogenesis and antigenic characterization of a new East European subtype 3 porcine reproductive and respiratory syndrome virus isolate

Background  

Porcine reproductive and respiratory syndrome virus (PRRSV) is divided into a European and North American genotype. East European PRRSV isolates have been found to be of the European genotype, but form different subtypes. In the present study, PRRSV was isolated from a Belarusian farm with reproductive and respiratory failure and designated "Lena". Analyses revealed that Lena is a new East European subtype 3 PRRSV isolate. The main purpose of this investigation was to study the pathogenesis and antigenic characteristics of PRRSV (Lena).     

Novel Host-Related Virulence Factors Are Encoded by Squirrelpox Virus,the Main Causative Agent of Epidemic Disease in Red Squirrels in the UK

Squirrelpox virus (SQPV) shows little evidence for morbidity or mortality in North American grey squirrels (Sciurus carolinensis), in which the virus is endemic. However, more recently the virus has emerged to cause epidemics with high mortality in Eurasian red squirrels (S. vulgaris) in Great Britain, which are now threatened. Here we report the genome sequence of SQPV. Comparison with other Poxviridae revealed a core set of poxvirus genes, the phylogeny of which showed SQPV to be in a new Chordopoxvirus subfamily between the Molluscipoxviruses and Parapoxviruses. A number of SQPV genes were related to virulence, including three major histocomaptibility class I homologs, and one CD47 homolog. In addition, a novel potential virulence factor showing homology to mammalian oligoadenylate synthetase (OAS) was identified. This family of proteins normally causes activation of an endoribonuclease (RNaseL) within infected cells. The putative function of this novel SQPV protein was predicted in silico.     

Advances toward DNA-based identification and phylogeny of North American Armillaria species using elongation factor-1 alpha gene

The translation elongation factor-1 alpha (EF-1α) gene was used to examine the phylogenetic relationships among 30 previously characterized isolates representing ten North American Armillaria species: A. solidipes (=A. ostoyae), A. gemina, A. calvescens, A. sinapina, A. mellea, A. gallica, A. nabsnona, North American biological species X, A. cepistipes, and A. tabescens. The phylogenetic relationships revealed clear separation of all ten North American Armillaria species, with the exception of one A. gallica isolate that perhaps represents an unnamed cryptic species. These results indicate that the EF-1α gene could potentially serve as a diagnostic tool for distinguishing among currently recognized North American biological species of Armillaria.     

Divergence of West African and North American Communities of Aspergillus Section Flavi

West African Aspergillus flavus S isolates differed from North American isolates. Both produced aflatoxin B₁. However, 40 and 100% of West African isolates also produced aflatoxin G₁ in NH₄ medium and urea medium, respectively. No North American S strain isolate produced aflatoxin G₁. This geographical and physiological divergence may influence aflatoxin management.     

DSP toxin production de novo in cultures of Dinophysis acuminata (Dinophyceae) from North America

For decades, many aspects of Dinophysis biology have remained intractable due to our inability to maintain these organisms in laboratory cultures. Recent breakthroughs in culture methods have opened the door for detailed investigations of these important algae. Here, for the first time, we demonstrate toxin production in cultures of North American Dinophysis acuminata, isolated from Woods Hole, MA. These findings show that, despite the rarity of Dinophysis-related DSP events in North America, D. acuminata from this area has the ability to produce DSP toxins just as it does in other parts of the world where this species is a major cause of DSP toxicity. In our cultures, D. acuminata cells were observed feeding on Myrionecta rubra using a peduncle. Culture extracts were analyzed using LC–MS/MS, providing unequivocal evidence for the toxin DTX1 in the Dinophysis cultures. In addition, a significant amount of an okadaic acid diol ester, OA-D8, was detected. These results suggest that this Dinophysis isolate stores much of its OA as a diol ester. Also, toxin PTX-2 and a hydroxylated PTX-2 with identical fragmentation mass spectrum to that of PTX-11, but with a different retention time, were detected in this D. acuminata culture. This demonstration of toxin production in cultured North American Dinophysis sets the stage for more detailed studies investigating the causes of geographic differences in toxicity. It is now clear that North American Dinophysis have the ability to produce DSP toxins even though they only rarely cause toxic DSP events in nature. This may reflect environmental conditions that might induce or repress toxin production, genetic differences that cause modifications in toxin gene expression, or physiological and biochemical differences in prey species.     

Protection against Pseudomonas aeruginosa lung infection in mice by recombinant OprF-pulsed dendritic cell immunization

Background

Porcine reproductive and respiratory syndrome (PRRS) has now been widely recognized as an economically important disease. The objective of this study was to compare the molecular and biological characteristics of porcine reproductive and respiratory syndrome virus (PRRSV) field isolates in China to those of the modified live virus (MLV) PRRS vaccine and its parent strain (ATCC VR2332).

Results

Five genes (GP2, GP3, GP4, GP5 and NSP2) of seven isolates of PRRSV from China, designated LS-4, HM-1, HQ-5, HQ-6, GC-2, GCH-3 and ST-7/2008, were sequenced and analyzed. Phylogenetic analyses based on the nucleotide sequence of the ORF2-5 and NSP2 showed that the seven Chinese isolates belonged to the same genetic subgroup and were related to the North American PRRSV genotype. Comparative analysis with the relevant sequences of another Chinese isolate (BJ-4) and North American (VR2332 and MLV) viruses revealed that these isolates have 80.8-92.9% homology with VR-2332, and 81.3-98.8% identity with MLV and 80.7-92.9% with BJ-4. All Nsp2 nonstructural protein of these seven isolates exhibited variations (a 29 amino acids deletion) in comparison with other North American PRRSV isolates. Therefore, these isolates were novel strain with unique amino acid composition. However, they all share more than 97% identity with other highly pathogenic Chinese PRRSV strains. Additionally, there are extensive amino acid (aa) mutations in the GP5 protein and the Nsp2 protein when compared with the previous isolates.

Conclusions

These results might be useful to study the genetic diversity of PRRSV in China and to track the infection sources as well as for vaccines development.     

Susceptibility of North-American and European crickets to Acheta domesticus densovirus (AdDNV) and associated epizootics

The European house cricket, Acheta domesticus L., is highly susceptible to A. domesticus densovirus (AdDNV). Commercial rearings of crickets in Europe are frequently decimated by this pathogen. Mortality was predominant in the last larval stage and young adults. Infected A. domesticus were smaller, less active, did not jump as high, and the adult females seldom lived more than 10-14 days. The most obvious pathological change was the completely empty digestive caecae. Infected tissues included adipose tissue, midgut, epidermis, and Malpighian tubules. Sudden AdDNV epizootics have decimated commercial mass rearings in widely separated parts of North America since the autumn of 2009. Facilities that are producing disease-free crickets have avoided the importation of crickets and other non-cricket species (or nonliving material). Five isolates from different areas in North America contained identical sequences as did AdDNV present in non-cricket species collected from these facilities. The North American AdDNVs differed slightly from sequences of European AdDNV isolates obtained in 1977, 2004, 2006, 2007 and 2009 and an American isolate from 1988. The substitution rate of the 1977 AdDNV 5 kb genome was about two nucleotides per year, about half of the substitutions being synonymous. The American and European AdDNV strains are estimated to have diverged in 2006. The lepidopterans Spodoptera littoralis and Galleria mellonella could not be infected with AdDNV. The Jamaican cricket, Gryllus assimilis, and the European field cricket, Gryllus bimaculatus, were also found to be resistant to AdDNV.     

Evidence of Lymphocytic Choriomeningitis Virus (LCMV) in Domestic Mice in Gabon: Risk of Emergence of LCMV Encephalitis in Central Africa

Lymphocytic choriomeningitis virus (LCMV) can cause acute fatal disease on all continents but was never detected in Africa. We report the first detection of LCMV RNA in a common European house mouse (Mus musculus domesticus) in Africa. Phylogenetic analyses show a close relationship with North American strains. These findings suggest that there is a risk of the appearance of LCMV acute encephalitis cases. This is a perfect example of virus dissemination by its natural host that may have dramatic public health consequences.     

Amyloidity is not diagnostic for species in the Mycena pearsoniana complex (Mycena sectio Calodontes)

In Mycena sectio Calodontes with otherwise amyloid spores, the inamyloid spores of Mycena pearsoniana Dennis ex Singer were a distinguishing feature for this species and its subsection Violacella. Although the original concept of this species was European, Singer chose to typify it with material collected in Mexico. The name has since been applied to all European collections with inamyloid spores and decurrent lamellae. Our phylogenetic analysis of 91 ITS sequences from European, North and South American Calodontes collections shows that European collections identified as M. pearsoniana fall into two well-supported sibling clades together with both inamyloid and weakly amyloid North American collections. Since the holotype of M. pearsoniana is in an advanced state of decay, we have selected an epitype from a North American locality with a climate comparable to the Mexican type locality. Our results show weakly and inamyloid spore reactions to be homoplastic in Calodontes, and furthermore that spores of M. pearsoniana can show either amyloid or inamyloid reactions interchangeably. This raises doubt about the taxonomic value of this trait in Mycena systematics.     

The marsupial MHC: The Tammar Wallaby,Macropus eugenii,contains an expressed DNA-like gene on chromosome 1

Isolates of cauliflower mosaic virus (CaMV) differ in host range and symptomatology. Knowledge of their sequence relationships should assist in identifying nucleotide sequences responsible for isolate-specific characters. Complete nucleotide sequences of the DNAs of eight isolates of CaMV were aligned and the aligned sequences were used to analyze phylogenetic relationships by maximum likelihood, bootstrapped parsimony, and distance methods. Isolates found in North America clustered separately from those isolated from other parts of the world. Additional isolates, for which partial sequences were available, were incorporated into phylogenetic analysis of the sequences of genome segments corresponding to individual protein coding regions or the large intergenic region of CaMV DNA. The analysis revealed several instances where the position of an isolate on a tree for one coding region did not agree with the position of the isolate on the tree for the complete genome or with its position on trees for other coding regions. Examination of the distribution of shared residue types of phylogenetically informative positions in anomalous regions suggested that most of the anomalies were due to recombination events during the evolution of the isolates. Application of an algorithm that searches for segments of significant length that are identical between pairs of isolates or contain a significantly high concentration of polymorphisms suggested two additional recombination events between progenitors of the isolates studied and an event between the XinJing isolate and a CaMV not represented in the data set. An earlier phylogenetic origin for CaMV than for carnation etched ring virus, the caulimovirus used as outgroup in these analyses, was deduced from the position of the outgroup with North American isolates in some trees, but with non-North American isolates in other trees. Correspondence to: U. Melcher