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PubMed2006

Biological and molecular characterization of chicken anemia virus isolates from Slovenia.

The presence of chicken anemia virus (CAV) in Slovenia was confirmed by inoculation of 1-day-old chickens without antibodies against CAV and isolation of the virus on the Marek's disease chicken cell-MSB1 line and by polymerase chain reaction (PCR). Experimental inoculation of 1-day-old chickens resulted in lower hematocrit values, atrophy of the thymus, and atrophy of bone marrow. CAV was confirmed by PCR in the thymus, bone marrow, bursa of Fabricius, liver, spleen, ileocecal tonsils, duodenum, and proventriculus. The nucleotide sequence of the whole viral protein (VP)1 gene was determined by direct sequencing. Alignment of VP1 nucleotide sequences of Slovenian CAV isolates (CAV-69/00, CAV-469/01, and CAV-130/03) showed 99.4% to 99.9% homology. The VP1 nucleotide sequence alignment of Slovenian isolates with 19 other CAV strains demonstrated 94.4% to 99.4% homology. Slovenian isolates shared highest homology with the BD-3 isolate from Bangladesh. Alignment of the deduced VP1 amino acids showed that the Slovenian isolates shared 100% homology and had an amino acid sequence most similar to the BD-3 strain from Bangladesh (99.6%) and were 99.1% similar to the G6 strain from Japan and the L-028 strain from the United States. The Slovenian isolates were least similar (96.6%) to the 82-2 strain from Japan. A phylogeneric analysis on the basis of the alignment of the VP1 amino acids showed that CAV isolates used in the study formed three groups that indicated the possible existence of genetic groups among CAV strains. The CAV isolates were grouped together independent of their geographic origin and pathogenicity.

Amino Acid Sequence↗
PubMed1990

Nucleotide sequences of the VP1 capsid proteins of wild poliovirus types 1 and 3 from epidemic areas of Brazil.

The nucleotide sequences encoding the capsid protein VP1 were determined for the wild polioviruses of serotypes 1 and 3 endemic to the northeastern region of Brazil. Compared with the corresponding Sabin vaccine strain sequences, the wild isolates differed at 20% (type 1) and 22% (type 3) of their nucleotide positions, and in 7% (type 1) and 11% (type 3) of their amino acid residues. The highest degree of amino acid heterogeneity occurred within the amino-terminal residues of the VP1 proteins. Intratypic amino acid differences also occurred in VP1 surface residues that form parts of antigenic sites for neutralizing antibodies.

Antigenic Variation↗
PubMed1999

Sequence analysis of VP1 and VP7 genes suggests occurrence of a reassortant of G2 rotavirus responsible for an epidemic of gastroenteritis.

G2 rotavirus was prevalent in a 1993 epidemic of acute gastroenteritis in Taiwan. In this study, the genetic relationship among G2 rotavirus strains was analysed. The VP7 genes were amplified and sequenced. Except for one strain isolated in 1981, the nucleotide sequences of the VP7 genes of most of the G2 rotaviruses were very similar (identity > 97%) and were closely related to that of a Japanese G2 reference strain, S2. The genetic relatedness of G2 rotaviruses was analysed further by RNA-RNA hybridization. The genomes of the major G2 strains of 1993 did not hybridize well with those of the G2 strains of previous seasons in RNA segments 1, 6 and 7. Partial nucleotide sequences of the VP1 gene were analysed and appeared to be similar among the major G2 strains from the same epidemic (identity > 98%), whereas the identity of the VP1 genes of the major G2 strains of the 1993 epidemic to those of previous seasons was only about 84%. Since the numbers of mutations accumulated in the VP1 and VP7 genes over a period of 10 years were comparable, the significant change in the VP1 genes of the major strains of the 1993 epidemic suggests that these G2 rotaviruses had evolved by genetic reassortment.

Amino Acid Sequence↗
PubMed1984

Nucleotide sequence of the VP1 gene of the foot-and-mouth disease virus strain A Venceslau.

The VP1 coat protein of FMDV strain A Venceslau (Aven) consists of 213 amino acid residues. Serum neutralization tests demonstrated that strain Aven is closely related to strain A Argentina/79 (A79) but significantly different from strain A24Cruzeiro (A24). There is a strong correlation between the amino acid sequences and the serological data. Nucleotide and amino acid sequence analyses of VP1 showed that serologically related viruses (Aven and A79) differ less in this region of the genome than those of serologically distinct viruses (Aven vs. A24). The most significant variation between Aven and A24 occurs at amino acid positions 43 to 46, in which all four residues are different.

Amino Acid Sequence↗
PubMed2001

Presumed common source outbreaks of hepatitis A in an endemic area confirmed by limited sequencing within the VP1 region.

Hepatitis A virus isolates from anti-HAV IgM positive sera of 70 hepatitis cases in two outbreaks and 216 other cases in Central America, 136 sporadic cases and 53 cases from an hyper-endemic region in Costa Rica, were compared by phylogenetic analyses within the VP1 region. The outbreaks in all 531 cases, in 1992 and 1999, respectively, were presumed water borne. In the first outbreak, HAV RNA could be detected in 70% of the cases sampled during 6 weeks after onset of jaundice. In the hyper-endemic region of San Ramón in Costa Rica, 1,932 cases were registered between 1972 and 1985. All isolates belonged to subtype 1A. Background isolates from Costa Rica and El Salvador tended to form separate subclusters in the phylogenetic tree construction and were mostly unrelated to subtype 1A strains from other parts of the world. Based on their amino acid sequences, four HAV strains, all related to CR326 sampled in Costa Rica in 1960, were found to have circulated in the area during the last three decades. However, on the basis of nucleotide variability the isolates from the outbreaks could be distinguished from the strains from sporadic cases and sequence analysis could confirm the epidemiological homogeneity of both outbreaks. In the hyper-endemic region, 16 different sequences were encountered forming one single subcluster. Thus, limited sequencing within the VP1 region proved useful to identify outbreaks of hepatitis A in a highly endemic area, where most strains were local and only one subtype was prevalent.

Adolescent↗
PubMed2026

Performance comparison of rapid and native barcoding methods for Oxford Nanopore sequencing of Poliovirus Viral Protein 1 (VP1) amplicons.

Accurate and timely sequencing of poliovirus is critical for global eradication efforts, particularly for molecular epidemiology based on the typing region of the genome, viral protein 1 (VP1). While Oxford Nanopore Technologies (ONT) sequencing has expanded capabilities for poliovirus surveillance, the relative performance of different ONT library preparation methods, including ligation-based (Native Barcoding) and transposase-based (Rapid Barcoding) approaches, has not been systematically evaluated. In this study, we compared rapid barcoding and native barcoding workflows for sequencing VP1 amplicons from 17 type 2 poliovirus-positive samples, each processed in triplicate. Native barcoding generated significantly more sequencing output, producing approximately 2.3-fold greater total read yield than rapid barcoding, and demonstrated higher run-to-run reproducibility (R2 = 0.979-0.998 vs. 0.847-0.929, respectively; p&#x202f;<&#x202f;0.001). In addition, native barcoding generated 80% of the total yield achieved by rapid barcoding within approximately 7&#x202f;h, whereas rapid barcoding required approximately 40&#x202f;h to reach the same output. Despite these differences, both methods produced identical VP1 consensus sequences across all samples, with comparable read quality (median per-base Q-scores of approximately Q17-Q18). Rapid barcoding provided substantial practical advantages, reducing hands-on library preparation time (55 vs. 200&#x202f;min) and per-sample cost ($12.82 vs. $16.54), while simplifying workflow and reducing technical complexity. These findings indicate that sequencing yield may not be a determinant of downstream analytical outcomes for poliovirus VP1 ONT sequencing. Rapid barcoding therefore represents a cost-effective and efficient approach for routine poliovirus surveillance, whereas native barcoding remains advantageous in applications requiring rapid data generation or maximal sequencing depth.

Poliovirus↗
PubMed2006

Molecular characterization of foot-and-mouth disease virus in Hong Kong during 2001-2002.

Most of the molecular epidemiological studies of foot-and-mouth disease virus (FMDV) are based on comparison of VP1 gene sequence. In this report, The nucleotide sequences of the VP1 coding region of FMDV type O strains O/HKN/3/01, O/HKN/5/01, O/HKN/12/01, O/HKN/7/02 and O/HKN/10/02, isolated from the disease outbreak that occurred in Hong Kong Special Administrative Region (Hong Kong SAR) of China during 2001-2002, were determined and compared with the sequences of other FMDVs. The results revealed that the VP1 gene of the five isolates had the same nucleotide (nt) sequences (639 nt), coding for 213 amino acids, and no changes were found either at the critical amino acid sites 144 (Val), 148 (Leu), 154 (Lys) and 208 (Pro) within the VP1 protein epitope (amino acids 140-160, 200-213), or in the amino acids 145-147 comprising the arginine-glycine-aspartic acid (RGD) sequence that is involved in the adsorption of virus to host cell. Analysis of the VP1 gene nucleotide sequence revealed that the five isolates examined were most closely related to FMDVs found in Hong Kong from 1991 to 1999 and Taiwan in 1997. Furthermore, although the critical amino acids on the antigen epitope of the prevalent Hong Kong isolates and the serotype O vaccine strain, O1/Manisa/Turkey/69, showed relative conservativeness, they were distantly related genetically, which showed that there existed variation between the prevalent Hong Kong FMDV strains and the vaccine strain.

Amino Acid Sequence↗
PubMed1981

Nucleotide sequence at polyoma VP1 mRNA splice sites.

Double-stranded DNA complementary to total cytoplasmic polyadenylated RNA isolated late in infection from polyoma virus-infected mouse 3T6 cells was cloned in Escherichia coli by using the large HindIII-BamHI fragment of pBR322 plasmid DNA. Polyoma-specific DNA inserts were detected by hybridization, and then nucleotide sequences were determined from two clones. The sequence of the (formula see text) with prototypical mammalian splice sites, and the dashed arrows indicate possible alternative splice sites leading to the same spliced product. A sequence of 897 nucleotides was spliced out of the primary transcript during the processing of the mature VP1 mRNA. Restriction enzyme mapping with four other independently isolated clones indicates that these are the major splicing signals for the VP1 message. The distal splice site is 48 nucleotides upstream from the initiator codon.

Base Sequence↗
PubMed2002

Sequence and phylogenetic analysis of the L and VP1 genes of foot-and-mouth disease virus serotype Asia1.

Most of the molecular epidemiological studies of foot-and-mouth disease virus (FMDV) are based on comparison of VP1 gene sequence. In this report, we determine the nucleotide (nt) sequence of the L (603 nt) and VP1 (633 nt) genes of 27 FMDV serotype Asia 1 isolates recovered from different outbreaks in India, and compared with each other and the vaccine strain, IND 63/72, used in the country. Independent phylogenetic analyses on both the aligned gene sequences identified two major lineages (designated A & B) in the Asia 1 isolates. Both L- and VP1-based trees were congruent with respect to the major branching pattern of the isolates. The lineage A is represented by the isolates of 1986-2000 including the vaccine strain IND 63/72, whereas, lineage B appeared to be dominant and responsible for most of the recent outbreaks. A correlation was observed between the clustering of the isolates in the phylogenetic tree and the amino acid changes at many of the positions in VP1 as well as in L protein. The annual rate of evolution in L and VP1 genes was found similar and estimated to be 4.0 x 10(-3) and 3.8 x 10(-3) substitutions per nucleotide, respectively. Our result, largely from the congruence in phylogenetic trees and the rate of evolution in both the genes, suggests the possibility for the use of L gene sequence in phylogenetic comparison of FMDV.

Amino Acid Sequence↗
PubMed2005

Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses.

Phylogenetic analysis of the capsid protein VP1 coding sequences of all 101 human rhinovirus (HRV) prototype strains revealed two major genetic clusters, similar to that of the previously reported VP4/VP2 coding sequences, representing the established two species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Pairwise nucleotide identities varied from 61 to 98 % within and from 46 to 55 % between the two HRV species. Interserotypic sequence identities in both HRV species were more variable than those within any Human enterovirus (HEV) species in the same family. This means that unequivocal serotype identification by VP1 sequence analysis used for HEV strains may not always be possible for HRV isolates. On the other hand, a comprehensive insight into the relationships between VP1 and partial 2A sequences of HRV and HEV revealed a genus-like situation. Distribution of pairwise nucleotide identity values between these genera varied from 41 to 54 % in the VP1 coding region, similar to those between heterologous members of the two HRV species. Alignment of the deduced amino acid sequences revealed more fully conserved amino acid residues between HRV-B and polioviruses than between the two HRV species. In phylogenetic trees, where all HRVs and representatives from all HEV species were included, the two HRV species did not cluster together but behaved like members of the same genus as the HEVs. In conclusion, from a phylogenetic point of view, there are no good reasons to keep these two human picornavirus genera taxonomically separated.

Cysteine Endopeptidases↗
PubMed1978

Nucleotide sequence of the simian virus 40 Hind II + III restriction fragment J and the total amino acid sequence of the major structural protein VP1.

The HindII + III restriction fragment J (Hind-J) represents 4.58% of the simian virus 40 genome. The information present in Hind-J is expressed as part of the major, late 16-S messenger RNA, which codes for the structural protein VP1. The nucleotide sequence of the 240-base-pairs-long Hind fragment J has been determined by analysis of each oligonucleotide from both strands resulting from T1 or pancreatic RNase digestion of RNA transcribed from the DNA and from RNase digestion of ribo-substituted DNA. Large oligonucleotide blocks which could be constructed mainly on the basis of complementarity were subsequently ordered by partial chemical degradation of terminally labeled DNA. This direct DNA sequencing approach also completely confirmed the results obtained by both aforementioned RNase degradation methods. In the strand with the same polarity as the late mRNA, triplets corresponding to termination codons are present in two of the three reading frames. The one open reading frame connects in phase with the open reading frame of the neighboring HindII/ III fragments K, F and G, which have been published previously and which together with Hind-J span the total VP1 gene. Some features of the primary nucleotide sequence of this VP1 gene and the derived VP1 amino acid sequence are discussed.

Amino Acid Sequence↗
PubMed2006

Prospective identification of HEV-B enteroviruses during the 2005 outbreak.

Enteroviruses (EVs) represent the main etiological agents of epidemics of viral meningitis and especially the serotypes related to the human enterovirus B species. Genetic typing by sequencing a PCR-amplified portion of the genome has proved to be useful for identifying EVs and is more rapid than standard seroneutralization tests. However, prospective genotyping has not been reported in routine practice within a clinical diagnostic laboratory. A genetic typing assay using two sets of primers was developed for the amplification and sequencing of the VP1 coding sequence of the HEV-B serotypes. Identification was carried out by sequence comparisons with EV sequences in GenBank using the BLAST search tool and confirmed by phylogenetic analysis. This method was used to identify prospectively the 48 enteroviruses isolated in patients with either enterovirus-proved meningitis (n = 41) or other clinical manifestations (n = 7) admitted to the University Hospital of Clermont-Ferrand (France) in 2005. The assay was also used to type retrospectively EVs isolated in cerebrospinal fluid specimens of 25 patients admitted to the Trousseau Paediatric Hospital in Paris (France) between February and August 2005. In both prospective and retrospective investigations of meningitis, echovirus 30 (E30) was the most frequent serotype, followed in decreasing order by E18, E13, coxsackievirus B5, B3, E6, E4, E7, E11, E33, and coxsackievirus A9. In patients with other manifestations, coxsackievirus B3, B5, and E3 were each identified twice, and E2 once. In E30 infected patients, nine different lineages were demonstrated by phylogenetic analysis. Genetic typing allowed the prospective, effective and rapid identification of all EV isolates involved in the 2005 outbreak. Molecular typing in combination with phylogenetic analysis will be a reliable means to confirm the emergence of new EV variants, and is of interest of both individual patients and public health.

Adolescent↗
PubMed2002

Polyomavirus infection in hamsters and trichoepitheliomas/cutaneous adnexal tumours.

Multiple skin nodules, with histological features of adnexal tumours consistent with trichoepithelioma, were observed on the head and trunk of Syrian hamsters. Skin biopsies from 20 hamsters from five different colonies were affected, and two of the affected hamsters also had lymphoma. Two owners reported that 16 of 70 hamsters and 50 of 100 hamsters in their colonies had similar skin lesions. These tumours have previously been associated in laboratory colonies with hamster polyomavirus (HaPV) infection. Examination of skin tissues by electron microscopy failed to reveal intranuclear virus particles. Using recombinant major capsid protein VP1 of HaPV, VP1-specific antibodies were detected in sera from 12 of 12 affected hamsters and in four of four unaffected in-contact hamsters, by ELISA. The ELISA data were verified by immunoblot analysis. Eleven of 13 serum samples contained antibodies which reacted with at least one recombinant structural HaPV protein (VP2), including samples from three in-contact unaffected hamsters. Nine of the 11 anti-VP2-positive samples also reacted with recombinant VP3 of HaPV, and six reacted with VP1. Amplification by PCR and sequencing detected VP1 -encoding sequences showing a high degree of homology with HaPV. The findings suggest a possible infection by HaPV or a HaPV-like virus and it is likely that such an infection was enzootic within the affected colonies.

Animals↗
PubMed1984

The use of a monoclonal antibody and of DNA recombinant technology for the localization of a poliovirus neutralization epitope in viral capsid polypeptide VP1.

Poliovirus cDNA sequences encoding type 1 capsid polypeptide VP1 were fused in phase into the beta-lactamase sequence of pBR322. The resulting recombinant plasmid pSW119 expressed in E. coli a VP1-beta-lactamase fusion protein which reacted with antibodies raised against poliovirus capsid polypeptide VP1 and with a monoclonal poliovirus type 1 neutralizing antibody C3. Deletions of various length were introduced into the VP1 sequence. The truncated proteins expressed by the deleted plasmids did not react further with C3 when the region of VP1 amino acids 91-104 was deleted. A synthetic peptide corresponding to this region of VP1 (amino acids 93-104) was chemically synthesized. It was found to inhibit the seroneutralization of poliovirus by C3 antibodies and, once coupled to keyhole limpet hemocyanin, it was specifically immunoprecipitated with C3. Therefore, the C3 epitope recognized by the poliovirus neutralizing monoclonal antibody is located within the region of amino acids 93-104 of capsid polypeptide VP1.

Antibodies, Monoclonal↗
PubMed2001

Analysis of minimal sequences on JC virus VP1 required for capsid assembly.

Human JC virus (JCV) belongs to the family of Polyomaviridae. The viral capsid is composed of 72 capsomeres. Five VP1 molecules make up a capsomere structure. To investigate the minimal sequences on JCV VP1 polypeptide required for capsid assembly, the first 12 (Delta N12) and 19 (Delta N19) amino acids at the N-terminus and the last 16 (Delta C16), 17 (Delta C17), and 31 (Delta C31) amino acids at the C-terminus of VP1 were truncated and expressed in E. coli. The VP1 proteins of Delta N12 and Delta C16 were able to self-assemble into a virus-like particle similar to that of wild-type (WT) VP1. However, the mutant proteins of Delta N19, Delta C17, and Delta C31 formed a pentameric capsomere structure as demonstrated by a 10-50% sucrose gradient centrifugation and electron microscopy. These results suggest that the 12 amino-terminal and 16 carboxy-terminal amino acids of VP1 are dispensable for the formation of virus-like particles, and further truncation at either end of VP1 leads to the loss of this property.

Capsid↗
PubMed1995

Molecular epidemiology of foot-and-mouth disease (FMD) in Israel in 1994 and in other Middle-Eastern countries in the years 1992-1994.

The reverse transcriptase-polymerase chain reaction (RT-PCR) and direct sequencing were employed in the diagnosis and typing of foot-and-mouth disease virus (FMDV) in samples taken during the 1994 disease outbreak in Israel. Using PCR, virus isolation and serological methods it was shown that the 1994 disease outbreak in Israel and other Middle-Eastern countries was caused by O1 type virus. Direct PCR sequencing of VP1 genes and homology analysis of the virus isolates revealed that there were two distinct outbreaks in Israel. The first originated in Jordan, moved to the West Bank territory and then to the Lower Galilee. The second outbreak, caused by another virus, was responsible for disease outbreaks in South Lebanon, Upper Galilee and the Golan Heights. When viral sequences of isolates from the 1993 outbreaks in Egypt and Lebanon were included in the analysis, they showed a high degree of VP1 sequence homology between themselves, suggesting a common origin.

Animals↗
PubMed1998

[Synthesis and immunogenic properties of peptides--fragments of the immunodominant regions of the VP1 protein of the Asia-1 type of foot- and-mouth disease virus].

Potential immunodominant epitopes were predicted on the basis of a theoretical analysis of the antigenic structure of the VP1 protein of the type Asia-1 foot-and-mouth disease virus. Peptides corresponding to the 140-153, 136-153, 132-153, 143-157, 137-157, and 193-208 fragments of the VP1 protein sequence were synthesized by the solid phase method, and the immunogenic properties of the peptides were studied on guinea pigs. The shortest peptide exhibiting the protective effect was found to correspond to the, 140-153 fragment of the VP1 sequence. The Plm-(Gly)3-(140-153)-(Gly)2-Lys(Plm)-Leu and [Ac-(140-153)-(Gly)3]8-(Lys)7-Gly synthetic constructions in combination with adjuvants provided up to 80% protection of immunized animals against infection with the foot-and-mouth disease virus.

Adjuvants, Immunologic↗