Showing papers in "Archives of Virology in 2004"
TL;DR: The new plant virus family Flexiviridae is described, named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlav virus, Foveavirus, Potexvirus, Trichovirus and Vitivirus plus the new genus Mandarivirus together with some related viruses not assigned to any genus.
Abstract: The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.
388 citations
TL;DR: GRP 78 (BiP), which has previously been identified as a co-receptor protein for coxsackievirus A9, is the first non-Fc receptor protein identified for the dengue virus, although GRP78 probably functions as part of a receptor complex.
Abstract: This study sought to identify receptor elements for dengue virus serotype 2 on human liver cells (HepG2) using the viral overlay protein binding assay (VOPBA) technique and Mass Spectrometry fingerprinting. A single major and several minor virus binding bands were observed, and mass spectrometry identified a candidate binding protein for the major binding band as GRP 78 (BiP). GRP78 expression on the cell surface was confirmed, and antibodies directed against both the N and C-terminus of GRP 78 (BiP) altered both the binding of the virus to the cell surface as well as the infectivity profile of HepG2 cells in response to dengue serotype 2 infection. GRP 78 (BiP), which has previously been identified as a co-receptor protein for coxsackievirus A9, is the first non-Fc receptor protein identified for the dengue virus, although GRP78 probably functions as part of a receptor complex.
286 citations
TL;DR: This study characterized twenty-five SAP detected in the laboratory from outbreaks or sporadic cases of acute gastroenteritis in children from different geographical locations and in adults involved in a cruise ship outbreak investigation and a nursing home outbreak, and proposed to classify the currently known SAP into nine genetic clusters within five genogroups, including one genogroup that is represented by an animal calicivirus, the porcine enteric calicvirus (PEC).
Abstract: Norovirus and Sapovirus are two genera of the family Caliciviridae that contain viruses that can cause acute gastroenteritis in humans. Noroviruses (NOR) are genetically highly diverse but limited studies of the genetic diversity of sapoviruses (SAP) have been reported. In this study we characterized twenty-five SAP detected in our laboratory from outbreaks or sporadic cases of acute gastroenteritis in children from different geographical locations and in adults involved in a cruise ship outbreak investigation and a nursing home outbreak. Based on significant differences of partial RNA polymerase sequences (278–286 nt), the 25 strains were grouped into 12 genetic clusters, including 9 potential new clusters. Extended sequence analysis of the capsid gene of selected strains representing five potential new clusters supported this grouping. Four strains (Hou7-1181/90, Mex340/90, Cruise ship/00 and Argentina39) had <84% amino acid (aa) identity to each other and to the published sequences in the GenBank. Mex14917/00 was almost identical to Stockholm/97/SE whose RNA polymerase sequence was unknown. Phylogenetic and distance analyses of the capsid region of the four new strains showed that Hou7-1181/90 and Argentina39 represent two new genogroups and Mex340/90 and Cruise ship/00 belong to two new clusters within the London/92 genogroup. Thus, based on the capsid sequences we propose to classify the currently known SAP into nine genetic clusters within five genogroups, including one genogroup that is represented by an animal calicivirus, the porcine enteric calicivirus (PEC).
250 citations
TL;DR: It is shown that an amino acid substitution caused an antigenic difference demonstrable by monoclonal antibodies and that a similar evolution may have occurred in CPV in Vietnam.
Abstract: Nine isolates of Canine parvovirus (CPV) were obtained from Vietnamese dogs and cats. One canine isolate showed a unique antigenic property which indicates a novel antigenic variant of CPV-2b when examined with hemagglutination inhibition tests using our monoclonal antibodies, 21C3 and 19D7, which were recently developed. This isolate had an amino acid substitution of residue 426, Asp to Glu, and the same substitution has recently been found in CPV from Italian dogs. This study first showed that such substitution caused an antigenic difference demonstrable by monoclonal antibodies and that a similar evolution may have occurred in CPV in Vietnam.
176 citations
TL;DR: It is indicated that co-infection of H9N2 influenza virus with S. aureus or H. paragallinarum enhances the replication of the virus in chickens, resulting in exacerbation of the H 9N2 virus infection.
Abstract: H9N2 influenza viruses are frequently isolated from chicken meat and bone marrow imported from China to Japan since 2001 These isolates were experimentally inoculated into specific pathogen-free chickens intranasally Viruses were recovered from the meat and bone marrow of birds showing no overt signs On the other hand, chickens co-infected with H9N2 virus and either Staphylococcus aureus or Haemophilus paragallinarum showed clinical signs severer than those shown by birds infected only with the virus alone or each of the bacteria alone In addition, H9N2 viruses were more efficiently recovered from the chickens co-infected with S aureus or H paragallinarum than those from the birds infected with only the virus The present results indicate that co-infection of H9N2 influenza virus with S aureus or H paragallinarum enhances the replication of the virus in chickens, resulting in exacerbation of the H9N2 virus infection
166 citations
TL;DR: It has been difficult to reproduce PMWS experimentally although some protocols have been developed which involve antigenic stimulation with other agents that presumably increase the number of permissive cells entering S phase of the cell cycle.
Abstract: Postweaning multisystemic wasting syndrome (PMWS) is a disease of pigs first recognised in North America in 1997 and subsequently reported worldwide that is caused by Porcine circovirus 2 (PCV2), a member of the family Circoviridae. The most consistent feature of PMWS is a generalized depletion of lymphocytes. Secondary infections with opportunistic organisms are common. There is evidence that the destruction of thymic lymphocytes has a central role in the pathogenesis of PMWS. Pigs with PMWS have altered cytokine responses to mitogens and recall antigens. It remains unknown what cells are primarily infected and are permissive for the replication of PCV2. Macrophages and dendritic cells commonly contain virus in their cytoplasm but may not be the primary source of the large amounts of virus found in tissues of diseased pigs. There is evidence that PCV2, like mammalian parvoviruses, requires cells in the S phase of the cell cycle for replication. It has been difficult to reproduce PMWS experimentally although some protocols have been developed which involve antigenic stimulation with other agents that presumably increase the number of permissive cells entering S phase of the cell cycle. In addition to reviewing the literature attempts are made to identify key unresolved areas that should be the focus of future research.
150 citations
TL;DR: Phylogenetic analysis based on the nucleotide sequence of the structural protein ORF’s showed that the two new Chinese isolates belong to same genetic subgroup, indicating that they were related to the North American PRRSV genotype.
Abstract: The genomes of two isolates of Porcine respiratory and reproductive syndrome virus (PRRSV) from China, designated HB-1(sh)/2002 and HB-2(sh)/2002, were sequenced and analyzed The size of the genomes of HB-1(sh)/2002 and HB-2(sh)/2002 were 15,411 and 15,373 nucleotides respectively, excluding the poly(A) tails Comparative analysis with the genomic sequences of another Chinese isolate (BJ-4) and North American (VR2332) and European (Lelystad virus, LV) viruses revealed that HB-1(sh)/2002 shared 898% identity with BJ-4 and VR2332, but only 547% with LV; while HB-2(sh)/2002 shared 894% and 895% identity with BJ-4 and VR2332 respectively and 543% with LV, indicating that the two new Chinese isolates were related to the North American PRRSV genotype Phylogenetic analysis based on the nucleotide sequence of the structural protein ORF’s showed that the two new Chinese isolates belong to same genetic subgroup HB-2(sh)/2002 additionally exhibited variations in the NSP2 nonstructural protein encoded by ORF1 and the structural protein GP3 encoded by ORF3 in comparison with other North American PRRSV isolates, namely a 12 amino acids deletion in Nsp2 and one amino acid deletion in GP3 were found in HB-2(sh)/2002 Therefore, HB-2(sh)/2002 was a novel strain with unique deletions
130 citations
TL;DR: The full-length sequence of WMV was obtained and it was confirmed that this virus is very closely related to SMV in most of its genome; however, there is evidence for an interspecific recombination in the P1 protein, suggesting that WMV has emerged through an ancestral recombination event.
Abstract: Watermelon mosaic virus (WMV, Potyvirus) is a potyvirus with a worldwide distribution, mostly in temperate and mediterranean regions. According to the partial sequences that were available, WMV appeared to share high sequence similarity with Soybean mosaic virus (SMV), and it was almost considered as a strain of SMV in spite of its different and much broader host range. Like SMV, it was also related to legume-infecting potyviruses belonging to the “Bean common mosaic virus (BCMV) subgroup”. In this paper we obtained the full-length sequence of WMV, and we confirmed that this virus is very closely related to SMV in most of its genome; however, there is evidence for an interspecific recombination in the P1 protein, as the P1 of WMV was 135 amino-acids longer than that of SMV, and the N-terminal half of the P1 showed no relation to SMV but was 85% identical to BCMV. This suggests that WMV has emerged through an ancestral recombination event, and supports the distinction of WMV and SMV as separate taxonomic units.
124 citations
TL;DR: The study indicates that Turkish patients with chronic viral hepatitis show very little genotypic heterogeneity, and subtype ayw and the genotype D of HBV DNA, and the type I of HDV RNA represent almost 100% of related infections.
Abstract: Different genotypes of the hepatitis viruses may influence the clinical outcome of the disease. The distribution of genotypes may vary according to geographical regions. The aim of this study was to evaluate hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis D virus (HDV) genotypes in Turkish patients with chronic hepatitis in a large cohort of patients. Genotyping was performed in 41, 59 and 365 patients with chronic hepatitis B, D and C, respectively, and 36 hemodialysis patients with chronic hepatitis C. Genotypes were determined by direct sequencing in hepatitis B and by polymerase chain reaction-restriction fragment length polymorphism in hepatitis C and D patients. In addition, HBV subtyping by multiplex PCR and subtype specific ELISA were performed in 83 and 71 HBsAg (+) blood donors, respectively. All hepatitis B (100%) and hepatitis D (100%) patients had genotype D and type I, respectively. HBsAg subtyping by two methods yielded that 99% of the patients were subtype ayw. S gene amino acid sequence in the 41 patients included for HBV genotyping revealed the ayw2 subtype. Genotype distribution of 365 patients with chronic C hepatitis were as follows: 306 (84%) patients genotype 1b, 43 (11%) patients genotype 1a, 10 (3%) patients genotype 2, 3 (1%) patients genotype 3, 3 (1%) patients genotype 4. Among 36 patients receiving hemodialysis, 28 (78%) patients had genotype 1b and 8 (22%) patients had genotype 1a. The study indicates that Turkish patients with chronic viral hepatitis show very little genotypic heterogeneity. Subtype ayw and the genotype D of HBV DNA, and the type I of HDV RNA represent almost 100% of related infections. The genotype 1b of HCV RNA was found to be significantly dominant in Turkish patients.
120 citations
TL;DR: Real-time PCR using SYBR Green I dye-based detection is utilized to quantify transcript abundance of the type I interferons (IFN-α and -β) and IFN-β transcriptional enhanceasome genes and suggests that PRRSV infection directly interferes with type I IFN transcriptional activation early in its pathway, at the level of IFN -β gene transcription.
Abstract: Infection by porcine reproductive and respiratory syndrome virus (PRRSV) results in a weak induction of the innate immune response. There are many genes that collectively comprise this response and the extent to which each gene responds to PRRSV infection is unclear and warrants further investigation. To this end, we have utilized real-time PCR using SYBR Green I dye-based detection to quantify transcript abundance of the type I interferons (IFN-alpha and -beta) and IFN-beta transcriptional enhanceasome genes. In MARC-145 cells, both IFN-alpha and -beta transcript abundance were unaffected by PRRSV infection. However, stimulation of MARC-145 cells by exogenous double-stranded RNA, resulted in significant increases in transcript abundance of both IFN-alpha and -beta as well as IFN-beta enhanceasome components, indicating that a type I IFN response could be induced in these cells. The double-stranded RNA induction of type I IFN transcription was significantly inhibited by dual-exposure with PRRSV. These results suggest that PRRSV infection directly interferes with type I IFN transcriptional activation early in its pathway, at the level of IFN-beta gene transcription.
120 citations
TL;DR: Findings suggested that the newly developed ELISA is suitable for PPR diagnosis under field conditions.
Abstract: A sandwich ELISA test using PPR specific monoclonal antibody (clone 4G6) to an epitope of nucleocapsid protein has been developed. The test uses polyclonal sera to capture the antigen from clinical samples (swabs and tissues). Captured antigens from clinical samples are detected using PPR specific monoclonal antibody. The test is specific to PPR as it failed to detect rinderpest vaccine virus (RBOK strain). Varieties of clinical samples originating from laboratory experiments (n = 231) and from field (n = 259) were employed to test the efficacy of sandwich-ELISA test. The test compared very well with an internationally accepted commercial Immune-capture ELISA kit, which uses biotinylated monoclonal antibody against the nucleocapsid protein. On a parallel testing using 490 clinical samples, 4G6 MAb based sandwich ELISA had an overall relative diagnostic specificity of 92.8% and diagnostic sensitivity of 88.9% compared to the commercial kit. The newly developed test is free from prozone phenomenon. PPR outbreaks from various parts of India have been confirmed using the test. Findings suggested that the newly developed ELISA is suitable for PPR diagnosis under field conditions.
TL;DR: The genomic differences between three completely sequenced WSSV isolates, originating from Thailand, China and Taiwan, are mapped and highly invariable genomic loci are identified, which may be used for reliable monitoring of W SSV infections and for shrimp health certification.
Abstract: White spot syndrome virus (WSSV), member of a new virus family called Nimaviridae, is a major scourge in worldwide shrimp cultivation. Geographical isolates of WSSV identified so far are very similar in morphology and proteome, and show little difference in restriction fragment length polymorphism (RFLP) pattern. We have mapped the genomic differences between three completely sequenced WSSV isolates, originating from Thailand (WSSV-TH), China (WSSV-CN) and Taiwan (WSSV-TW). Alignment of the genomic sequences of these geographical isolates revealed an overall nucleotide identity of 99.32%. The major difference among the three isolates is a deletion of approximately 13 kb (WSSV-TH) and 1 kb (WSSV-CN), present in the same genomic region, relative to WSSV-TW. A second difference involves a genetically variable region of about 750 bp. All other variations >2 bp between the three isolates are located in repeat regions along the genome. Except for the homologous regions (hr1, hr3, hr8 and hr9), these variable repeat regions are almost exclusively located in ORFs, of which the genomic repeat regions in ORF75, ORF94 and ORF125 can be used for PCR based classification of WSSV isolates in epidemiological studies. Furthermore, the comparison identified highly invariable genomic loci, which may be used for reliable monitoring of WSSV infections and for shrimp health certification.
TL;DR: Genetic comparisons were made of the fusion protein sequences of 155 Newcastle disease virus isolates collected in South Africa between 1990 and 2002 and it was shown that almost all mesogenic isolates had avirulent F0 cleavage site sequences.
Abstract: Genetic comparisons were made of the fusion protein sequences of 155 Newcastle disease virus isolates collected in South Africa between 1990 and 2002. Their evolutionary relationships and origins are described. All of the lentogenic field isolates were shown to be derived from commercial vaccines. No true South African lentogenic wild type strain was identified. Furthermore, it was shown that almost all mesogenic isolates had avirulent F(0) cleavage site sequences. Three major epizootics occurred in South Africa during the period of this study. The first outbreak (1990/1991) was caused by viruses endemic to South Africa since the 1960's (genotype VIII) but were occasionally also isolated in 2000. Genotype VIIb viruses, implicated in the severe outbreaks during 1993/1994, persisted until 1999. Genotype VIId viruses, responsible for the most recent outbreak in 1999/2000, had their origins in the Far East like those of the two previous outbreaks.
TL;DR: Comparisons of the SARS-CoV genomic sequence with those of six other coronaviruses failed to find evidence of recombination or genomic rearrangement using computational methods designed for that purpose.
Abstract: Different tree-building methods consistently place the SARS corona-virus (SARS-CoV) as a basal Group 2 coronavirus rather than as an ungrouped species as concluded by others. Detailed comparisons of the SARS-CoV genomic sequence with those of six other coronaviruses failed to find evidence of recombination or genomic rearrangement using computational methods designed for that purpose.
TL;DR: The NoV prevailed at the end of the rainy season and the beginning of the dry season during this one-year study, and further epidemiological studies may be necessary to determine whether the GII/4 strains continue to dominant in this region.
Abstract: This report describes norovirus (NoV) and sapovirus (SaV) infections in hospitalized children with acute sporadic gastroenteritis in Ho Chi Minh City, Vietnam. Stool specimens collected between December 1999 and November 2000 were examined for NoV and SaV using reverse transcription-PCR and phylogenetic analysis. NoVs were detected in 72 of 448 rotavirus-negative specimens, counted as part of an overall annual detection rate of 5.4% (72 of 1,339 children). This included four NoV genogroup I (GI) strains and 68 NoV GII strains. Only one SaV GI strain was detected in the rotavirus-negative specimens. Over 73% of the NoV sequences belonged to GII/4 (Lordsdale cluster) and were detected in all months except March. We also detected GII/3 strains (Saitama U201 cluster), a naturally occurring recombinant NoV, between January 2000 and March 2000 but not after this period. Other NoV strains belonging to GI/4, GI/8, GII/1, and GII/7 were also detected but were infrequent. In addition, two almost identical NoV GII strains (strains 026 and 0703) collected six months apart were classified into a new genotype that includes the Mc37 strain, which was previously shown to be a recombinant NoV. During this one-year study, the NoV prevailed at the end of the rainy season and the beginning of the dry season. Further epidemiological studies may be necessary to determine whether the GII/4 strains continue to dominant in this region.
TL;DR: PTGS induced in Gynura aurantiaca infected with two closely-related variants of Citrus exocortis viroid, a member of family Pospiviroidae, was not directly related to viroid titer with initiation of symptoms.
Abstract: Evidence of post-transcriptional gene silencing (PTGS) in avocado infected by Avocado sunblotch viroid (ASBVd), the type species of family Avsunviroidae, was suggested by detection of ASBVd-specific 22-nucleotide RNAs. PTGS was observed in infected bleached and variegated symptomatic tissues as well as symptomless carrier foliar sources and fruit with typical sunblotch disease lesions. Tissues with the different symptom expressions, characterized by the presence of different predominant ASBVd variants, were found to induce PTGS at differential levels. Detection of the PTGS-associated small interfering RNAs (siRNAs) as well as relative concentration was also related to viroid titer. PTGS induced in Gynura aurantiaca infected with two closely-related variants of Citrus exocortis viroid, a member of family Pospiviroidae, was not directly related to viroid titer with initiation of symptoms.
TL;DR: The results show that a coinfection of begomoviruses can persist over decades, producing a reservoir of partially recombined but distinct geminiviruses.
Abstract: We report on the nucleotide sequences of geminiviruses of the genus Bemogovirus infecting Sida micrantha Schr., a common weed in Brazil. For decades, the mosaic frequently associated with Sida plants was considered to be caused by a Brazilian strain of Abutilon mosaic virus (AbMV). By infection studies and sequence comparisons, we demonstrate that it is associated with a complex of at least two begomoviruses as different from AbMV as most South American geminiviruses. Two molecules of DNA A (A1, A2) and three of DNA B (B1, B2, B3) were cloned and sequenced. According to the high homology in their common regions, DNA A1 and DNA B3, as well as DNA A2 and DNA B2, are cognate components of two begomoviruses, which were infectious in Nicotiana benthamiana plants. No trans-replication was found for any other A/B combination. The intergenic region of DNA B2 appears to be the product of the recombination between DNA B1 and DNA A2. These results show that a coinfection of begomoviruses can persist over decades, producing a reservoir of partially recombined but distinct geminiviruses.
TL;DR: The genome of an isolate of Newcastle disease virus (NDV) obtained following an outbreak in geese consists of 15192 nt, which is six nt longer than the published full length genome of the NDV strains La Sota, B1, Clone-30, Beaudette C and HB V4.
Abstract: We have completely sequenced the genome of an isolate of Newcastle disease virus (NDV) obtained following an outbreak in geese. The genomic sequence consists of 15192 nt, which is six nt longer than the published full length genome of the NDV strains La Sota, B1, Clone-30, Beaudette C and HB V4. The six nt insertion was located in the non-coding region of the nucleoprotein (NP) gene between nt 1646 and nt 1647 of the NDV genome (numbered according to the genomic sequence of the La Sota strain). An additional 22 NDV strains were searched for the existence of this six nt insertion. NDVs in genotypes VI, VII, VIII and IX had this insertion while NDV's in genotypes I, II, III, IV, and V did not. The significance of this insertion in NDV evolution is discussed.
TL;DR: Conserved genomic sequences distinctive of Staphylococcus aureus phage types 3A, 11, 77, 187 and Twort, representative of phage serogroups A, B, F, L and D, were identified and characterized.
Abstract: Conserved genomic sequences distinctive of Staphylococcus aureus phage types 3A, 11, 77, 187 and Twort, representative of phage serogroups A, B, F, L and D, were identified and characterized. PCR primers designed for the above sequences were used for development of a multiplex PCR assay which enabled us not only to classify all phages of the International Typing Set plus 16 additional phages, but also to detect prophages in S. aureus genomes. One to four different prophages were unambiguously detected in experimentally lysogenized S. aureus strains, and substantial variation in prophage content was found in 176 S. aureus clinical strains of different provenance. In addition, by using a comparative genomics approach, all the prophages in the S. aureus genomes sequenced to date could be revealed and classified.
TL;DR: Serial passages of the viruses derived from the above vectors in C. quinoa showed that the size of duplications affected the stability of the GFP gene, and the version of the RNA2-vector with the shortest duplications and its silent mutant version could stably express GFP in leaves even after at least nine serial passages.
Abstract: Infectious cDNA clones of Apple latent spherical virus (ALSV)-RNA1 (pEALSR1) and -RNA2 (pEALSR2) were constructed using an enhanced 35S promoter. A viral vector was constructed from pEALSR2 by creating artificial protease processing sites by duplicating the Q/G protease cleavage site between 42KP and Vp25. Eight RNA2-derived vectors expressing GFP with varied sizes of duplications around the 42KP/Vp25 junction were constructed and tested for infectivity in Chenopodium quinoa. The results indicated that greater than five aa from the C-terminus of 42KP and N-terminus of Vp25 in duplication are necessary for systemic infection. In infected C. quinoa plants, GFP fluorescence was observed in both inoculated and upper leaves. Serial passages of the viruses derived from the above vectors in C. quinoa showed that the size of duplications affected the stability of the GFP gene. The version of the RNA2-vector (pER2L5R5GFP) with the shortest duplications and its silent mutant version could stably express GFP in leaves even after at least nine serial passages. ALSV-RNA2 vector has a capacity to maintain a DNA insert as long as 1300 bp because Apple chlorotic leaf spot virus movement protein (50KP) gene could be expressed in C. quinoa. Inoculation of a virus derived from pER2L5R5GFP to apple seedlings resulted in the expression of GFP fluorescence in uninoculated upper leaves, indicating that the vector is available for the expression of foreign genes in apple trees.
TL;DR: It is argued that sheep with the AHQ allele are not generally less susceptible to scrapie and support the hypothesis that the influence of this allele on scrapie susceptibility may vary from flock to flock depending on genetic and/or epidemiological factors.
Abstract: Prion protein (PrP) genotypes were determined in eight sheep that have been tested positive for atypical scrapie from purebred or crossbred Merinoland sheep flocks in Germany and compared with the PrP genotypes of their flock mates. Two restriction fragment length polymorphism (RFLP) analyses were developed to determine all PRNP haplotypes occurring by variations at codons 136, 154 and 171. At least one copy of the A136H154Q171 (AHQ) allele was found in all scrapie-positive sheep while the frequency of AHQ varied from over 23% to less than 3% in the whole flocks. There was a significant association between PrP genotype and a positive scrapie diagnosis over all flocks, suggesting a high scrapie susceptibility of PrP genotypes including the AHQ allele, at least in sheep of Merinoland type. These results argue that sheep with the AHQ allele are not generally less susceptible to scrapie and support the hypothesis that the influence of this allele on scrapie susceptibility may vary from flock to flock depending on genetic and/or epidemiological factors. This has to be considered when strategies for the eradication of scrapie in sheep are based on PrP genotypes.
TL;DR: A new genotyping method, based on PCR amplification of the pre-S/S genome region and subsequent restriction fragment length polymorphism (RFLP) analysis, was developed, that established a correlation between RFLP subtypes and subgroups within genotype A, suggesting an African origin for a large number of Brazilian HBVs.
Abstract: Hepatitis B virus (HBV) genotype A has been divided recently into two subgroups, designated A-A' (genotype A excluding A') and A'. Isolates belonging to subgroup A' have been identified in Africa. A new genotyping method, based on PCR amplification of the pre-S/S genome region and subsequent restriction fragment length polymorphism (RFLP) analysis, was developed, that established a correlation between RFLP subtypes and subgroups within genotype A. To investigate the occurrence of subgroup A' in South America, 119 Brazilian HBV isolates were analyzed. Ninety-three (78%) of them belonged to genotype A, with three predominating RFLP subtypes: 44 (37%) isolates were classified as AI, 30 (25%) were AII, and 18 (15%) were AIII. Pre-S/S nucleotide sequences of 15 genotype A isolates were determined. Phylogenetic analysis performed with these 15 and an additional 41 sequences revealed that isolates AI and AII clustered in subgroup A', whereas isolates AIII were classified into subgroup A-A'. The correlation RFLP subtypes-subgroups was confirmed by the presence of amino acid residues specific for subgroup A' in the surface antigens and polymerase of isolates AI and AII. The high proportion (63%) of isolates from subgroup A' suggested an African origin for a large number of Brazilian HBVs.
TL;DR: Investigation of whether PCV-2 DNA was present in archival tissues, and if so, to investigate the relatedness of these viruses with contemporary strains of PCVs, demonstrates that similar isolates of PCv-2 have been present in the UK pig population for more than 30 years.
Abstract: Porcine circovirus 2 (PCV-2) is implicated as the causative agent of post-weaning multisystemic wasting syndrome (PMWS) and is also associated with porcine dermatitis and nephropathy syndrome (PDNS). The recent emergence of epidemic PMWS in the United Kingdom was predated by sporadic cases of PDNS dating back to the early 1980’s. The aim of this study was to investigate whether PCV-2 DNA was present in archival tissues, and if so, to investigate the relatedness of these viruses with contemporary strains of PCV-2. DNA extracted from paraffin wax-embedded tissue blocks (n = 68), was subjected to a TaqMan® polymerase chain reaction (PCR) targeting a fragment of ORF1 of PCV-2. Positive results were obtained from 41% (9/22), 31% (4/13) and 32% (8/25) of submissions from the 1990’s, 1980’s and 1970’s respectively. The presence of PCV-2 antigen in some of these tissues was confirmed by immunohistochemistry (IHC). A PCR targeting ORF2 was used to obtain sequence data for phylogenetic analysis. Sequences from 5 archival tissues were unique but showed high genetic identity to PCV-2 sequence obtained from a 2000 PDNS case. These data demonstrate that similar isolates of PCV-2 have been present in the UK pig population for more than 30 years.
TL;DR: Sequence analysis demonstrated that the variable (V) domain was very conserved among the cachexia variants and five nucleotide differences, affecting both the upper and lower strands of the V domain, were identified as a motif discriminating cachexia and non-cachexia sequences.
Abstract: Seven citrus isolates of Hop stunt viroid (HSVd) were subjected to retrotranscription and DNA amplification (RT-PCR), cloning and sequencing. Single stranded polymorphism (SSCP) analysis demonstrated the existence of variability among and within cachexia inducing sources of HSVd. The electrophoretic profiles of SSCP appeared to be able to discriminate between non-cachexia and cachexia sources of HSVd. Sequence analysis demonstrated that the variable (V) domain was very conserved among the cachexia variants. Five nucleotide differences, affecting both the upper (3 nucleotides) and the lower (2 nucleotides) strands of the V domain, were identified as a motif discriminating cachexia and non-cachexia sequences. These five nucleotides affect the organization of a short helical region and two flanking loops of the V domain probably modifying the three-dimensional geometry of the molecule. The stability of the minimum free energy rod-like conformation of the cachexia sequences is lower than the non-cachexia. Information regarding the host effect on the evolution and variability of viroid quasispecies is also provided.
TL;DR: Agroinoculation with mixed cultures of Agrobacterium with partial dimers of DNA A and allFive DNA Bs proved that all five DNA B components can co-infect a single V. mungo plant.
Abstract: One DNA A (KA30) and five different DNA B components (KA21, KA22, KA27, KA28 and KA34) of a geminivirus, Mungbean yellow mosaic virus-Vigna (MYMV-Vig) were cloned from a pooled sample of field-infected Vigna mungo plants from Vamban, South India. MYMV-Vig DNA A (KA30) and one of the DNA B components (KA27) exhibited 97% and 95% sequence identities, respectively, to those of MYMV reported from Thailand. However, the DNA B components KA21, KA22, KA28 and KA34 exhibited only 71 to 72% sequence identity to MYMV DNA B. Co-existence of multiple DNA B components in field-infected V. mungo was proved by Southern and PCR analyses. Each of the five DNA B components was infective together with the DNA A upon agroinoculation. Agroinoculation with mixed cultures of Agrobacterium with partial dimers of DNA A and all five DNA Bs proved that all five DNA B components can co-infect a single V. mungo plant.
TL;DR: It is reported that several begomoviruses are associated with tomato leaf curl disease in Yunnan province, China, and sequences showed that Y72β, Y77β and Y79β seem to be different from other characterised DNAβ, sharing the highest nucleotide sequence identity with TbCSV.
Abstract: The importance of diseases of tomato caused by begomoviruses is increasing worldwide. Here, we report that several begomoviruses are associated with tomato leaf curl disease in Yunnan province, China. 14 tomato samples showing leaf curl symptoms were collected in three districts in Yunnan, and they fell into four groups according to their reaction with a panel of 16 monoclonal antibodies in TAS-ELISA. Comparison of partial DNA-A sequences amplified with degenerate primers confirmed the existence of several types of begomoviruses. The complete DNA-A sequences of 4 isolates (Y25, Y41, Y72, Y161), corresponding to the four groups, were determined. Sequence comparisons and phylogenetic analysis revealed that they corresponded to four previously identified begomoviruses. Groups I, II and IV are most closely related to Tomato yellow leaf curl China virus (TYLCCNV), Tobacco curly shoot virus (TbCSV) and Tobacco leaf curl Yunnan virus (TbLCYNV), respectively, while Group III shows close relationships with Tomato yellow leaf curl Thailand virus (TYLCTHV). In addition, all isolates in Groups I and III were found to be associated with DNAβ molecules, while satellite DNA was not found in virus isolates in Groups II and IV. The complete DNAβ sequences of three isolates from Group III (Y72, Y77, Y79) were determined. Sequence analysis showed that Y72β, Y77β and Y79β seem to be different from other characterised DNAβ, sharing the highest nucleotide sequence identity with DNAβ of TbCSV.
TL;DR: To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed and three major genetic groups were associated with the recent outbreaks.
Abstract: To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). Among them, three major genetic groups were associated with the recent outbreaks of IB in Japan. One group is indigenous to Japan and could not be placed within the known existing groups in other countries. The remaining two groups, which have emerged recently, are related to isolates in China and Taiwan.
TL;DR: Here the satellites group by geographic location and are considerably more diverse than previously indicated, probably reflects the limited movement of begomovirus/DNA β complexes in this region and their subsequent diversification from a common ancestor to a variety of hosts.
Abstract: Two previous analyses of the diversity of begomovirus-associated DNA β satellites focused predominantly on molecules originating from the Indian sub-continent and southern China. They showed the satellites to group according to the hosts from which they were isolated, either malvaceous or non-malvaceous plants, and then to form sub-groups based upon geographic origin and host. In this study we analysed the diversity of DNA β satellites in east and south east Asia. Here the satellites group by geographic location and are considerably more diverse than previously indicated. This probably reflects the limited movement of begomovirus/DNA β complexes in this region and their subsequent diversification from a common ancestor to a variety of hosts.
TL;DR: A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.
Abstract: Degenerate primers for RT-PCR were designed and used to amplify genome fragments (c. 750 nt in the coat protein-ORF6 region) of allexiviruses from a total of 28 garlic samples from 24 provinces in China. Many samples contained more than one distinct sequence. A total of 60 different sequences were obtained. Phylogenetic analysis and two-way comparisons were used to assess the status of the sequences and to re-examine the criteria for distinguishing species within the genus. Most of the sequences could be allocated to either Garlic virus D or Garlic virus X on the basis of sequence similarity but some appeared to be intermediate between existing species. There were no sequences of Garlic virus C or Shallot virus X. A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.
TL;DR: Some recent findings on the final steps of the HIV-1 life cycle are summarized and some unanswered questions are touched upon, particularly regarding the processes involved in virus maturation and infectivity.
Abstract: HIV-1 particles have been studied by structural and chemical approaches, however, the processes of assembly, budding and maturation are just beginning to be characterized, and molecular details of these processes remain poorly defined. This brief review summarizes some recent findings on the final steps of the HIV-1 life cycle and touches upon some unanswered questions, particularly regarding the processes involved in virus maturation and infectivity.