Showing papers in "Virus Genes in 2010"
TL;DR: Most of the findings on the biological properties and molecular mechanisms of the oncoproteins E6 and E7 from mucosal and cutaneous HPV types are reviewed.
Abstract: More than 100 different human papillomavirus (HPV) types have been isolated so far, and they can be sub-grouped in cutaneous or mucosal according to their ability to infect the skin or the mucosa of the genital or upper-respiratory tracts. A sub-group of human mucosal HPVs, referred to as high-risk HPV types, is responsible for approximately 5% of all human cancers, which represents one-third of all the tumours induced by viruses. Epidemiological and biological studies have shown that HPV16 is the most oncogenic type within the high-risk group. Emerging lines of evidence suggest that, in addition to the high-risk mucosal HPV types, certain cutaneous HPVs are involved in skin cancer. HPV-associated cancers are intimately linked to HPV persistence and the accumulation of chromosomal rearrangements. The products of the early genes, E6 and E7, of the high-risk mucosal HPV types play a key role in both events. Indeed, these proteins have developed a number of strategies to evade host immuno-surveillance allowing viral persistence, and to alter cell cycle and apoptosis control, facilitating the accumulation of DNA damage/mutations. Often, the two oncoproteins target the same cellular pathways with different mechanisms, showing a strong synergism in promoting cellular transformation and neutralizing the immune response. Here, we review most of the findings on the biological properties and molecular mechanisms of the oncoproteins E6 and E7 from mucosal and cutaneous HPV types.
294 citations
TL;DR: A phylogenetic tree constructed from the VP2 genes showed that most of the Chinese strains classified in a cluster consisting of Chinese and Korean field isolates, which were distinct from Thai, U.S., and Italian isolates.
Abstract: Sequences of the full-length gene encoding the main capsid protein VP2 of 22 strains of canine parvovirus (CPV), isolated from domestic dogs in China between 1983 and 2008, were determined and analyzed in comparison with the sequences of 30 other strains of CPV from China and reference CPV isolates retrieved from GenBank. Three types of CPV, including CPV-2, CPV-2a, and CPV-2b, were detected, and CPV-2a (with 297-Ala mutation) was predominant in China. The unique Ile-324 mutation in the VP2 of Chinese CPV isolates was detected, as compared with a Tyr-324 in the VP2 of the reference CPV strains. A phylogenetic tree constructed from the VP2 genes showed that most of the Chinese strains classified in a cluster consisting of Chinese and Korean field isolates, which were distinct from Thai, U.S., and Italian isolates.
72 citations
TL;DR: 29 previously enterovirus positive samples from 28 patients diagnosed with hand, foot and mouth disease, meningitis and encephalitis, were molecularly typed and revealed that the viruses were mostly of Far-Eastern or Asia-Pacific origin.
Abstract: Human enteroviruses are associated with various clinical syndromes from minor febrile illness to severe, potentially fatal conditions like aseptic meningitis, paralysis, myocarditis, and neonatal enteroviral sepsis. Between June 2000 and August 2008 echovirus (E) type 2, 4, 6, 7, 9, 11, 13, 25, 30, coxsackievirus (CV) -A16, -A19, -B5, and enterovirus 71 (EV71) were reported in Hungary. In this study, 29 previously enterovirus positive samples from 28 patients diagnosed with hand, foot and mouth disease, meningitis and encephalitis, were molecularly typed. The genetic relationships of identified serotypes CV-A16, EV71, and E30 were assessed by direct sequencing of genomic region encoding the capsid protein VP1. The sequences were compared to each other and sequences from other geographical regions possessed in Genbank. The phylogenetic analysis of CV-A16 revealed that the viruses were mostly of Far-Eastern or Asia-Pacific origin. Typing of EV71 showed that one virus from 2000 belonged to genotype C1 and five viruses observed in 2004 and 2005 were identified as genotype C4. The 11 echovirus 30 strains showed homology with those of neighbor European countries. The molecular examination of E30 revealed that three separate lineages circulated in 2000, 2001, and 2004-2006 in Hungary.
68 citations
TL;DR: In this paper, the authors quantified the genetic diversity of two Citrus tristeza virus (CTV) genes and determined the complete genomic sequence for two strains of Hawaiian CTV.
Abstract: The Hawaiian Islands are home to a widespread and diverse population of Citrus tristeza virus (CTV), an economically important pathogen of citrus. In this study, we quantified the genetic diversity of two CTV genes and determined the complete genomic sequence for two strains of Hawaiian CTV. The nucleotide diversity was estimated to be 0.0565 ± 0.0022 for the coat protein (CP) gene (n = 137) and 0.0822 ± 0.0033 for the p23 gene (n = 30). The genome size and organization of CTV strains HA18-9 and HA16-5 were similar to other fully sequenced strains of CTV. The 3′-terminal halves of their genomes were nearly identical (98.5% nucleotide identity), whereas the 5′-terminal halves were more distantly related (72.3% nucleotide identity), suggesting a possible recombination event. Closer examination of strain HA16-5 indicated that it arose through recent recombination between the movement module of an HA18-9 genotype, and the replication module of an undescribed CTV genotype.
67 citations
TL;DR: Enterovirus 71 (EV71) strains from children were characterized by full-length VP1 nucleotide sequencing and represents the first record of genotype A EV71 in China since the BrCr prototype strain was discovered in the USA in 1969.
Abstract: Enterovirus 71 (EV71) strains from children were characterized by full-length VP1 nucleotide sequencing Out of 22 clinical specimens, five isolates identified as EV71 were recovered by virus isolation The VP1 sequences of the five isolates had more than 974% sequence identity with prototype virus BrCr, clustering in the genotype A lineage This represents the first record of genotype A EV71 in China since the BrCr prototype strain was discovered in the USA in 1969
65 citations
TL;DR: It is revealed that CHIK virus with novel genetic changes were present in the severe Chikungunya outbreaks in 2007 and 2008 in South India.
Abstract: Chikungunya virus (CHIKV), a positive-stranded alphavirus, causes epidemic febrile infections characterized by severe and prolonged arthralgia. In the present study, six CHIKV isolates (2006 RGCB03, RGCB05; 2007 RGCB80, RGCB120; 2008 RGCB355, RGCB356) from three consecutive Chikungunya outbreaks in Kerala, South India, were analyzed for genetic variations by sequencing the 11798 bp whole genome of the virus. A total of 37 novel mutations were identified and they were predominant in the 2007 and 2008 isolates among the six isolates studied. The previously identified E1 A226V critical mutation, which enhances mosquito adaptability, was present in the 2007 and 2008 samples. An important observation was the presence of two coding region substitutions, leading to nsP2 L539S and E2 K252Q change. These were identified in three isolates (2007 RGCB80 and RGCB120; 2008 RGCB355) by full-genome analysis, and also in 13 of the 31 additional samples (42%), obtained from various parts of the state, by sequencing the corresponding genomic regions. These mutations showed 100% co-occurrence in all these samples. In phylogenetic analysis, formation of a new genetic clade by these isolates within the East, Central and South African (ECSA) genotypes was observed. Homology modeling followed by mapping revealed that at least 20 of the identified mutations fall into functionally significant domains of the viral proteins and are predicted to affect protein structure. Eighteen of the identified mutations in structural proteins, including the E2 K252Q change, are predicted to disrupt T-cell epitope immunogenicity. Our study reveals that CHIK virus with novel genetic changes were present in the severe Chikungunya outbreaks in 2007 and 2008 in South India.
59 citations
TL;DR: Results suggest that recombinant DENV VLPs can be efficiently produced in the GAP promoter-based P. pastoris expression system, which may be useful for the development of effective and economic dengue subunit vaccine.
Abstract: The envelope glycoprotein (E) of flavivirus is the major structural protein on the surface of the mature virions. The complexes of premembrane (prM) and E play important roles in virus assembly and fusion modulation and in potential immunity-inducing vaccines. In the present study, the cDNA encoding prM and E proteins of dengue virus type 2 (DENV-2) was subcloned into the pGAPZαA vector and further integrated into the genome of Pichia pastoris under the control of the glyceraldehyde-3-phosphate dehydrogenase (GAP) constitutive promoter. The high-level constitutive expression of recombinant E antigen was achieved in P. pastoris. Both the cell lysate and the culture supernatant, examined by electron microscopy, were found to contain DENV-2 virus-like particles (VLPs) with diameters of about 30 nm. After immunization of BALB/c mice, the VLPs exhibited similar efficacies as inactivated virus in terms of antibody induction and neutralization titer. These results suggest that recombinant DENV VLPs can be efficiently produced in the GAP promoter-based P. pastoris expression system. This system may be useful for the development of effective and economic dengue subunit vaccine.
56 citations
TL;DR: It indicated that PCV2b predominated in PMWS occurrences in eastern China and a few recombinants of different genotypes existed in nature.
Abstract: Porcine circovirus type 2 (PCV2) is the essential infectious agent of postweaning multisystemic wasting syndrome (PMWS). In the present study, we obtained sequences of 31 PCV2 isolates from different farms of 11 provinces of eastern China and analyzed the genetic characterization of 136 eastern China-derivate PCV2 isolated during 2001–2009. The results showed that these PCV2 isolates could be divided into two groups, PCV2b (108 of 1A/1B, 19 of 1C) and PCV2a (1 of 2A, 2 of 2D, 6 of 2E). Among the 9 PCV2a isolates, eight were found before the year 2005. Meanwhile, three major heterogenic regions were observed in amino acid positions 53–91, 121–151, and 190–210; a few specific substitution patterns were found in each subgroup and several variant or conserved epitopes were also observed in the Cap protein. It indicated that PCV2b predominated in PMWS occurrences in eastern China and a few recombinants of different genotypes existed in nature.
55 citations
TL;DR: It is suggested that monopartite begomoviruses may associate with distinct satellites that are prevalent in the region as well as satellites shown previously to be associated with other begomviruses in Pakistan.
Abstract: A begomovirus disease complex associated with Sonchus arvensis, a common weed in Pakistan was studied using cloning, nucleic acid sequencing and phylogenetic analysis The complex associated with this weed consists of a monopartite begomovirus and several distinct betasatellites and alphasatellites The monopartite begomovirus associated with yellow vein disease of Sonchus arvensis showed 95-99% nucleotide sequence identity with Alternanthera yellow vein virus (AlYVV) reported from China, Vietnam and India Two betasatellites were isolated from S arvensis: one sharing between 914 and 953% nucleotide sequence identity with isolates of Ageratum yellow leaf curl betasatellite (AYLCB), and the other sharing between 782 and 999% identity with isolates of Cotton leaf curl Multan betasatellite (CLCuMB) Two alphasatellites were identified: one was homologous to Potato leaf curl alphasatellite (PotLCuA), while the other was closely related to Hibiscus leaf curl alphasatellite (HLCuA) Thus, AlYVV in S arvensis is associated with satellites shown previously to be associated with other begomoviruses in Pakistan Our results suggest that monopartite begomoviruses may associate with distinct satellites that are prevalent in the region
54 citations
TL;DR: The present study determined the full-length nucleotide sequences of VP1, VP3, and NSP1-3 genes and nearly full- length nucleotide sequence of VP2 gene of RU172 and provided important insights into the possible patterns of evolution of the porcine G12 strain.
Abstract: Human group A rotavirus (GAR) G12 strains are regarded as potentially important pathogens for acute gastroenteritis. On the other hand, to date, the only report of detection of G12 in animals was that of a porcine G12P[7] strain RU172. Strain RU172 formed a separate G12 lineage, distinct from human G12 strains, and by analyses of deduced amino acid sequences, had a VP4, VP6, NSP4-5 of porcine origin. In the present study, we determined the full-length nucleotide sequences of VP1, VP3, and NSP1-3 genes and nearly full-length nucleotide sequence of VP2 gene of RU172. By nucleotide sequence identities and phylogenetic analyses, the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes of RU172 were assigned to G12-P[7]-I5-R1-C1-M1-A1-N1-T1-E1-H1 genotypes, respectively. Within their respective genotypes, (i) VP1 gene of RU172 exhibited higher genetic relatedness to Wa-like human G12 GARs than porcine strains, (ii) VP2-3 and NSP2 genes clustered separately from the Wa-like human (including G12) and porcine clusters, while (iii) the VP6, NSP1 and NSP3-5 genes clustered with porcine and porcine-like human strains. These observations suggested that (i) the porcine G12 strain might have originated from porcine–human reassortment events, or alternatively, (ii) the Wa-like human and porcine G12 strains might have originated from a common ancestor, and eventually evolved (by genetic drift and shift) with time. Our findings provided important insights into the possible patterns of evolution of the porcine G12 strain.
52 citations
TL;DR: It is demonstrated that infection with type I PRRSV is not uncommon in Korean pig farms, which suggests that diagnosis and control of type IPRRSV should be considered in Korea and a new approach to vaccination against, and epidemiological analysis of, Korean PR RSV is urgently needed.
Abstract: The first Korean strain of porcine reproductive and respiratory syndrome virus (PRRSV) was isolated in 1997, and it exhibited high similarity to strain VR-2332 (type II PRRSV; North American type). Recently, however, infection with type I PRRSV (European type) has also been reported in Korea. To date, preliminary data about type I PRRSV prevalence in Korea have not been reported. Here, using reverse transcriptase (RT)-PCR, we analyzed 383 archived field samples from 101 pig farms in Korea that were collected from 2007 to 2008. We identified 155 samples from 68 farms that were positive for PRRSV. Fifty-one samples (51/155; 32.9%) and 20 farms (20/68; 29.4%) were type I PRRSV-positive/type II PRRSV-negative. Furthermore, we tried to isolate the type I PRRSV from positive samples and seven type I PRRSV were isolated using PAM. The phylogenetic analysis using the type I PRRSV isolates (7 isolates) was performed based on open reading frame (ORF)5 (accession numbers GU325642 to GU325648) and ORF7 (accession numbers GU325635 to GU325641). In the phylogenetic study, seven type I PRRSV isolates were closely related with panEuropean based on ORF7, while they were genetically distinct from Lelystad virus and made a unique clade based on ORF5. The results of this study demonstrate that infection with type I PRRSV is not uncommon in Korean pig farms, which suggests that diagnosis and control of type I PRRSV should be considered in Korea. A new approach to vaccination against, and epidemiological analysis of, Korean PRRSV is urgently needed.
TL;DR: The results from this study and other published results in the GenBank database showed that isolates circulating in Sichuan province in recent years were mainly LX4 genotype, which is the predominant genotype circulated in China in recently years.
Abstract: Between 2008 and 2010, 19 strains of infectious bronchitis virus (IBV) were isolated from the vaccinated chicken flocks in Sichuan province, China. The S1 genes of the isolates were amplified and sequenced. Phylogenetic analysis revealed that the 19 isolates and 37 reference IBV strains can be grouped into eight genotypes. Although IBVs of Taiwan-I type, massachusetts type, and proventriculitis type were isolated, but most isolates were LX4 genotype. Homology analysis of the sequences of S1 genes of the 19 isolates and 37 reference IBV strains revealed that the identity of the nucleotides and amino acid sequences of the S1 genes between the 15 LX4-type isolates and other IBV strains were 71.9-99.3% and 72.1-99.1%, respectively, while those of the analyzed IBV of LX4 type were 96.0-99.9% and 94.3-99.8%, respectively. The results from this study and other published results in the GenBank database showed that isolates circulating in Sichuan province in recent years were mainly LX4 genotype, which is the predominant genotype circulated in China in recent years.
TL;DR: The sequence analyses showed that the parvoviruses detected in southeastern China formed a distinct sublineage within the subfamily ParVovirinae, which is proposed to be a novelParvovirus sublineages, Cnvirus, to describe these parviviruses.
Abstract: Parvoviridae, which are classified into two subfamilies Parvovirinae and Densovirinae, can infect both vertebrate and insects and are related to a wide range of diseases in insects, animals, and humans. In this report, several new parvoviruses were identified in swine sera collected in southeastern China. The sequence analyses showed that the parvoviruses detected in southeastern China formed a distinct sublineage within the subfamily Parvovirinae. Based on these results, we propose a novel parvovirus sublineage, Cnvirus, to describe these parvoviruses.
TL;DR: Phylogenetic analyses of the polyprotein and deduced mature protein amino acid sequences reveal that SCSMV, together with TriMV, forms a distinct group in the family at the genus level, and should represent a new genus, Susmovirus, in the Potyviridae.
Abstract: The complete genomic sequence of a Pakistani isolate of Sugarcane streak mosaic virus (SCSMV-PAK) is determined to be 9782 nucleotides in length, excluding the 3' poly(A) tail, and it comprises a large open reading frame encoding a polyprotein of 3130 amino acid residues. The deduced polyprotein is likely to be cleaved at nine putative protease sites by three viral proteases to ten mature proteins. Conserved motifs of orthologous proteins of other potyviruses are identified in corresponding positions of SCSMV-PAK. The genomic organization is virtually identical to the genera Ipomovirus, Potyvirus, Rymovirus, and Tritimovirus in the family Potyviridae. Sequence analyses indicate that the SCSMV-PAK genomic sequence is different from those of Sugarcane mosaic virus and Sorghum mosaic virus, two viruses with very similar symptoms and host range to SCSMV-PAK. SCSMV-PAK shares 52.7% identity with Triticum mosaic virus (TriMV) and 26.4-31.5% identities with species of the existing genera and unassigned viruses in the Potyviridae at the polyprotein sequence level. Phylogenetic analyses of the polyprotein and deduced mature protein amino acid sequences reveal that SCSMV, together with TriMV, forms a distinct group in the family at the genus level. Therefore, SCSMV should represent a new genus, Susmovirus, in the Potyviridae.
TL;DR: Long term pathogenicity tests in specific pathogen free (SPF) chickens reveal that the recombinant GX0101 has a higher virulence than GA, but less virulent than Md5, the very virulent pathotype of MDV.
Abstract: A Marek's disease virus (MDV) field strain designated GX0101 was isolated from a layer flock and confirmed to be a recombinant virus with an insert of a long terminal repeat (LTR) from the reticuloendotheliosis virus (REV). A chimeric molecule containing an REV-LTR insert of 539 bp and its flanking sequences from MDV was amplified and sequenced. An REV-LTR downstream from the Internal Repeat Short (IRS) region has 77.4-98.6% homology to seven REV field strains isolated from different avian species in different parts of the world. The insertion site is located downstream of SORF 1 and upstream of SORF2 in the IRS region near the junction with the Unique Short (US) region in the MDV serotype 1 genome. Chicken experiments were conducted to determine the oncogenicity of the recombinant GX0101 virus and its transmissibility to contact chickens. Dot blot hybridization was used to detect the presence of the pp38 gene in feather tips from GX0101 or Md5 infected and contact birds. The pp38 was detected in GX0101 contact birds about 1-2 weeks earlier than in Md5 birds when both groups were vaccinated with HVT vaccine. Long term pathogenicity tests in specific pathogen free (SPF) chickens reveal that the recombinant GX0101 has a higher virulence than GA, but less virulence than Md5, the very virulent pathotype of MDV. This is the first report on an oncogenic serotype 1 MDV field strain with LTR insert and its pathogenicity.
TL;DR: Computer based analysis, recombination detection Program (RDP) supports the recombination hypothesis, indicated that recombination with other begomoviruses had taken place within V1 ORF and AC1 ORf of CLCuV-SG01 and AC2 ORF of CLP-SG02 and also in noncoding intergenic region (IR).
Abstract: Diseased cotton plants showing typical leaf curl symptoms were collected from experimental plot of Agriculture Research Station—Sriganganagar, Rajasthan. Complete DNA-A component from samples taken from two areas were amplified through rolling circle amplification (RCA) using templiphi kit (GE Healthcare) and characterized. DNA-A of one isolate consists of 2751 nucleotides and second isolate of 2759 nucleotide. Both sequences comprised six ORF’s. Genome organization of DNA-A of one isolate shows high sequence similarity with other characterized local begomovirus isolates of Rajasthan, while other isolate shows high sequence similarity with CLCuV reported from Pakistan. The maximum similarity of first isolate, CLCuV-SG01, shows highest sequence identity with Cotton leaf curl Abohar (Rajasthan) virus, and second isolate, CLCuV-SG02, shows highest sequence identity with cotton leaf curl virus from Pakistan. Both isolates showed 85% similarities with each other. The sequence data revealed probable infiltration of some strains of Cotton leaf curl virus from Pakistan to India, or co-existence of different isolates under similar geographical conditions. While CLCuV-SG01 shows highest nt sequence similarity with CLCuV Rajasthan (Abohar), nt identity of V1 ORF (encoding coat protein) of SG01 shows the highest nt identity (100%) with CLCuV Multan (Bhatinda) and Abohar virus while AC1 region also showed difference. Complete nucleotide sequence of SG01 shows only 86% similarity with CLCuV Multan virus. Similarity search revealed significant difference in AV1 and AC1 regions with respect to DNA-A suggesting an evolutionary history of recombination. Computer based analysis, recombination detection Program (RDP) supports the recombination hypothesis, indicated that recombination with other begomoviruses had taken place within V1 ORF and AC1 ORF of CLCuV-SG01 and AC1 ORF of CLCuV-SG02 and also in noncoding intergenic region (IR).
TL;DR: Results indicated that both types are currently prevalent field CPV circulating in Thailand and type 2a is the predominant genotype.
Abstract: Canine parvovirus (CPV) causes a very severe enteric disease especially in puppies. Twenty-six isolates of CPV were obtained from dogs at the Animal Hospital, Kasetsart University, Thailand. Whole VP2 gene of 26 isolates was amplified using polymerase chain reaction (PCR) and its sequences were analyzed. Nineteen out of 26 isolates were characterized as CPV type 2a variants and the rest of the isolates were characterized as CPV type 2b. These results indicated that both types are currently prevalent field CPV circulating in Thailand and type 2a is the predominant genotype. Neither CPV type 2 nor type 2c was observed in this study.
TL;DR: Results showed that HBX gene increased telomerase activity and human telomersase reverse transcriptase (hTERT) expression in HBx-transfected cells and HBx -positive HCC samples, and evidence of that HBx increased binding of Sp1 to its target DNA was shown.
Abstract: It is well known that telomerase activation and virus infection are strongly associated with human hepatocellular carcinoma (HCC). Hepatitis B virus X protein (HBx) plays an important role in HCC pathogenesis. However, the mechanisms of HBx on telomerase activity are not well understood. To determine the potential roles of HBx in telomerase activity, both transfection and antisense assay were designed to examine the effects of HBx on telomerase in this report. Results showed that HBX gene increased telomerase activity and human telomerase reverse transcriptase (hTERT) expression in HBx-transfected cells and HBx-positive HCC samples. Co-transfection and luciferase reporter assay showed that HBx could stimulate hTERT promoter in a dose-dependent manner in different cells. Truncated and mutant reporter assays revealed that Sp1 binding sites mapped at −132 to +5 nt in hTERT promote were important for HBx-mediated upregulation of hTERT. Western blot did not show any change of Sp1 expression in HBx-transfected cells, but EMSA showed evidence of that HBx increased binding of Sp1 to its target DNA. These results provide new insights into the role of HBx in liver carcinogenesis.
TL;DR: The results suggest that the begomovirus identified in this study was a new recombinant virus proposed as Cyamopsis tetragonoloba leaf curl virus (CyTLCuV).
Abstract: Monopartite begomoviruses comprise DNA-A as the main genome and associated satellite DNAs. Viral DNA extracted from guar (Cyamopsis tetragonoloba) showing leaf curl symptoms exhibited positive amplification of coat protein (CP) gene of DNA-A component, suggesting the presence of begomovirus. Full length DNA-A was amplified by primer pair re-designed from CP gene nucleotide sequence. The associated alphasatellite and betasatellite DNA molecules were amplified and sequenced, confirming the presence of monopartite begomovirus. Sequence comparisons showed 89% identity with other begomoviruses. The Neighbor-Joining tree based on full length DNA-A nucleotide sequence showed that the guar infecting begomovirus clustered separately from other known begomoviruses. The betasatellite shared a high (96%) nucleotide identity to Cotton leaf curl Multan betasatellites. The alphasatellite showed 91% nucleotide identity to alphasatellite associated with begomovirus infecting Okra. Recombination analyses showed three recombinant fragments in DNA-A, two in betasatellite, and four in alphasatellite. The results suggest that the begomovirus identified in this study was a new recombinant virus. Its name was proposed as Cyamopsis tetragonoloba leaf curl virus (CyTLCuV).
TL;DR: Results confirmed that the KS07 virus is highly virulent in pigs and easily transmitted to sentinel animals, and justifies the need for continued surveillance of influenza viruses in swine.
Abstract: A highly virulent H1N1 influenza A virus, A/Swine/Kansas/77778/2007 (KS07), which caused approximately 10% mortality in finishing pigs, was isolated from herds in the Midwestern United States. Molecular and phylogenic analysis revealed this swine isolate was a triple reassortant virus, similar to an H1N1 virus that infected humans and pigs at an Ohio county fair in August 2007. A pig challenge model was developed to evaluate the pathogenicity and transmission capacity of the KS07 virus. The results confirmed that the KS07 virus is highly virulent in pigs and easily transmitted to sentinel animals. The KS07 virus failed to cross-react with a panel of H1-specific swine sera. Interestingly, the KS07 virus shed for a prolonged period up to 7 days in infected pigs, indicating that this virus can spread efficiently between animals. The highly virulent H1N1 swine influenza virus is further evidence of reassortment among avian, human and swine influenza viruses and justifies the need for continued surveillance of influenza viruses in swine.
TL;DR: Data present in this article confirm that the 30 aa deletion in the NSP2-coding region alone is not a reliable genomic indicator for the high virulence of PRRSV strains emerged in China.
Abstract: Two strains of porcine reproductive and respiratory syndrome virus (PRRSV) were isolated, designated GDQJ and GDBY1. Experimental inoculation showed that GDBY1, caused 100% morbidity and 67% mortality, while GDQJ, caused 100% morbidity but no death. Full-length genomes were sequenced. Homologic and phylogenetic analyses indicated that these two strains were closely related to Chinese highly pathogenic PRRSV strains. Surprisingly, identical 30 amino acids (aa) deletion in the NSP2-coding region, a presumed high virulence marker, was present in low virulent strain GDQJ. Further comprehensive analysis of GDQJ genome in comparison with Chinese highly pathogenic PRRSV strains revealed multiple genomic variations, distributing in 5′ UTR, NSP1b, NSP2, NSP3, NSP5, NSP7, NSP9, NSP10, GP5, and N regions. Data present in this article confirm that the 30 aa deletion in the NSP2-coding region alone is not a reliable genomic indicator for the high virulence of PRRSV strains emerged in China. The genomic variations of GDQJ strain provided the basis for further studies of virulence determinants for PRRSVs.
TL;DR: It is proved that house sparrow can carry the virulent NDV strains and the same genotype of viruses that are circulating in poultry are existing in house sp Sparrows living around poultry farm in southern China.
Abstract: House sparrow (Passer domesticus) is one of the most widely distributed wild birds in China. Five Newcastle disease virus (NDV) strains were isolated from house sparrows living around the poultry farms in southern China. These isolates were characterized by pathogenic assays and phylogenetic analysis. The results showed that all NDV isolates except one were velogenic and virulent for chickens. These four virulent strains for chickens possess the amino acid sequence 112R/K-R-Q-K/R-R-F117 in the F0 cleavage site which is typical of velogenic NDV. Phylogenetic analysis indicated that these isolates belong to genotype VII and were closely related to the strains which were isolated from NDV outbreaks in chickens since 2000. One isolate of NDV from house sparrow belong to genotype II and was proved to be vaccine strain (Chicken/U.S./LaSota/46). The result of this study proved that house sparrow can carry the virulent NDV strains and the same genotype of viruses that are circulating in poultry are existing in house sparrows living around poultry farm in southern China.
TL;DR: Preliminary phylogenetic analysis using the amino acid sequences of the RNA-dependent RNA polymerases protein encoded by S2 revealed that HZ08 formed a cluster close to the aquareovirus, but was far from the other isolates, which indicated that Hz08 is likely to be a new member of Aquareov virus.
Abstract: A new grass carp reovirus, assigned HZ08, was isolated from a diseased grass carp case during routine examination in Huzhou City, Zhejiang Province, China. The complete nucleotide sequences of genomic segments S1-S3 and S5-S6 were obtained and comprised 3927, 3870, 3753, 2229, and 2030 bp, respectively. Each segment contained a single open reading frame which encoded putative proteins of 143.6, 143.1, 135.9, 80.5, and 68.4 kDa, respectively. Conserved motifs 5' (GUAAUUU...UUCAUC) 3' were found at the ends of each segment. At the amino acid level, HZ08 S1-S3 and S5-S6 showed similarity to the corresponding segments of Aquareovirus. Further phylogenetic analysis using the amino acid sequences of the RNA-dependent RNA polymerases protein encoded by S2 revealed that HZ08 formed a cluster close to the aquareovirus, but was far from the other isolates, which indicated that HZ08 is likely to be a new member of Aquareovirus.
TL;DR: It is suggested that H120 might have contributed to the emergence of new IBV variants through both virulence reversion and recombination.
Abstract: The strain H120 of infectious bronchitis virus (IBV) is one of the earliest and representative attenuated live Infectious Bronchitis vaccine strains. To investigate the genomic feature of H120 and further understand its role in the epidemiology of IBV, complete genome of H120 was sequenced and compared with sequences of other IBV strains by phylogenetic and recombination analysis. The complete genome of H120 is 27631 nucleotides in length and has a similar structure with that of Beaudette strain. We found that strain ZJ971 is probably a virulence revertant of H120. Nine amino acids changes and a three-nucleotide deletion were identified in ZJ971. Besides, potential recombination events associated with H120 were found in five IBV strains including H52, KQ6, SAIBK, Ark DPI 11, and Ark DPI 101. This study suggested that H120 might have contributed to the emergence of new IBV variants through both virulence reversion and recombination.
TL;DR: This study has reaffirmed the epidemiological utility of the CVR genome region for distinguishing between geographically and temporally constrained genotype I viruses, and has revealed the presence of multiple ASFV variants in Nigeria.
Abstract: Samples collected from wild and domestic suids in Nigeria, over a 3-year period (2003–2006), were evaluated for African swine fever (ASF) virus genome presence by targeting three discrete genome regions, namely the 478-bp C-terminal p72 gene region advocated for genotype assignment, a 780-bp region spanning the 5′-ends of the pB125R and pB646L (p72) genes and the hypervariable central variable region (CVR) encoded within the 9RL ORF (pB602L). ASF virus (ASFV) presence was confirmed in 23 of the 26 wild and domestic pigs evaluated. No evidence of ASF infection was found in two warthogs from Adamawa State; however, one bushpig from Plateau State was positive. Nucleotide sequences of the 478-bp and 780-bp amplicons were identical across all ASFV-positive samples sequenced. However, five discrete CVR variants were recovered, bringing the total number identified to date, from Nigeria, to six. The largest of the CVR variants, termed ‘Tet-36’ was identical to a virus causing outbreaks in neighbouring Benin in 1997, indicating a prolonged persistence of this virus type in Nigeria. Co-circulation of three tetramer types (Tet-36, Tet-27 and Tet-20) was found in Plateau State in July 2004, whilst in Benue State, two tetramer types (Tet-20 and Tet-21) were present in August 2005. Despite simultaneous field presence, individual co-infection was not observed. This study has reaffirmed the epidemiological utility of the CVR genome region for distinguishing between geographically and temporally constrained genotype I viruses, and has revealed the presence of multiple ASFV variants in Nigeria.
TL;DR: It is concluded that PRRSVs isolated during 2006–2008 in China underwent accelerated evolution, and predicted that this accelerated evolution equip these viruses more adapted to their primary hosts.
Abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is reported to have evolved at a higher evolutionary rate than other RNA viruses. However, whether this virus is capable of evolutionary acceleration during outbreaks remains unknown. In this study, we analyze the data based on ORFs of eight newly obtained epidemic PRRSVs from Hebei province with other viral genomes from GenBank. Phylogenetic analysis suggested that all isolates during recent outbreaks (2006–2008) are grouped together. We also find that ORF5 genes of this viral group are positively selected, suggesting their higher evolutionary rates and coinciding with that period of large-scale outbreaks in China. The evolutionary rate of 3.29 × 10−3 substitutions per nucleotide site per year also suggests the higher evolutionary rate of these viruses. We concluded that PRRSVs isolated during 2006–2008 in China underwent accelerated evolution, and predicted that this accelerated evolution equip these viruses more adapted to their primary hosts.
TL;DR: The complete genome sequence of a Newcastle disease virus isolated from a chicken in Sweden was determined and compared with other NDV sequences and was shown to belong to genotype VIIb, which arose in the Far East and spread around the world during the 1990s.
Abstract: The complete genome sequence of a Newcastle disease virus (NDV) isolated from a chicken in Sweden was determined and compared with other NDV sequences. The isolate was shown to belong to genotype VIIb, which arose in the Far East and spread around the world during the 1990s. It had a length of 15,192 bases and consisted of six genes in the order 3′-NP-P-M-F-HN-L-5′. The F protein cleavage site was 112-RRQRRF-117, corresponding to that of a virulent pathotype.
TL;DR: Surprisingly, it was found that the levels of CMV and the foreign protein expressed from the CMV vector were much higher in the HC-Pro-transgenic plants than the levels detected in the plants mixed-infected withCMV and PVY.
Abstract: The mixed infection of Cucumber mosaic virus (CMV) and a potyvirus has been known to increase CMV titer in Nicotiana benthamiana plants, resulting in synergistic viral symptoms. We found that among three potyviruses—Potato virus Y (PVY), Turnip mosaic virus (TuMV), and Clover yellow vein virus (C1YVV)—synergistic effects on CMV (or a recombinant CMV vector) titers were most efficiently induced by a co-infection with PVY in N. benthamiana plants. In addition, the helper component-proteinase (HC-Pro) gene of PVY expressed by transgenic plants, which is a viral RNA silencing suppressor, was sufficient to cancel the cycling pattern of CMV titer, resulting in increased levels of overall CMV accumulation. Surprisingly, we found that the levels of CMV and the foreign protein expressed from the CMV vector were much higher in the HC-Pro-transgenic plants than the levels detected in the plants mixed-infected with CMV and PVY. The mechanism for canceling the cyclic infection of CMV by the HC-Pro protein alone is discussed in view of the interaction between RNA silencing and HC-Pro, as well as the possible involvement of the 3a protein.
TL;DR: Findings indicate that H5N1 highly pathogenic avian influenza viruses are circulating in wild birds in addition to domestic poultry in Asia and exhibit antigenic variation that may be due to vaccination.
Abstract: In April and May 2008, whooper swans (Cygnus cygnus) were found dead in Hokkaido in Japan. In this study, an adult whooper swan found dead beside Lake Saroma was pathologically examined and the identified H5N1 influenza virus isolates were genetically and antigenically analyzed. Pathological findings indicate that the swan died of severe congestive edema in the lungs. Phylogenetic analysis of the HA genes of the isolates revealed that they are the progeny viruses of isolates from poultry and wild birds in China, Russia, Korea, and Hong Kong. Antigenic analyses indicated that the viruses are distinguished from the H5N1 viruses isolated from wild birds and poultry before 2007. The chickens vaccinated with A/duck/Hokkaido/Vac-1/2004 (H5N1) survived for 14 days after challenge with A/whooper swan/Hokkaido/1/2008 (H5N1), although a small amount of the challenge virus was recovered from the tissues of the birds. These findings indicate that H5N1 highly pathogenic avian influenza viruses are circulating in wild birds in addition to domestic poultry in Asia and exhibit antigenic variation that may be due to vaccination.
TL;DR: A phylogenetic analysis of the fusion protein gene of isolates obtained from outbreaks of ND in Sudan found that all contemporary strains isolated between 2003 and 2006 were of genotype 5d, containing the virulent fusion protein cleavage site (F0) motif 112RRQKRF117.
Abstract: Newcastle disease (ND) is a serious neurological and respiratory disease of poultry that affects all types of birds but has traditionally not caused symptoms in wild aquatic birds, the natural hosts. In the late 1990s, a new genotype, viz. 5d that is pathogenic to all types of birds, including waterfowl, arose in China and has since spread from East Asia into parts of Europe, the Middle East and Africa. We performed a phylogenetic analysis of the fusion protein gene of isolates obtained from outbreaks of ND in Sudan and found that all contemporary strains isolated between 2003 and 2006 were of genotype 5d, containing the virulent fusion protein cleavage site (F0) motif 112RRQKRF117. Introduction via a Middle Eastern trade partner is likely to be the source of infection since phylogenetic analysis excluded the possibility of introduction from western and southern Africa.