Happy K. Shieh

Identification and subtyping of avian influenza viruses by reverse transcription-PCR

Avian influenza viruses have 15 different hemagglutinin (HA) subtypes (H1-H15). We report a procedure for the identification and HA-subtyping of avian influenza virus by reverse transcription-PCR (RT-PCR). The avian influenza virus is identified by RT-PCR using a set of primers specific to the nucleoprotein (NP) gene of avian influenza virus. The HA-subtypes of avian influenza virus were determined by running simultaneously 15 RT-PCR reactions, each using a set of primers specific to one HA-subtype. For a single virus strain or isolate, only one of the 15 RT-PCR reactions will give a product of expected size, and thus the HA-subtype of the virus is determined. The result of HA-subtyping was then confirmed by sequence analysis of the PCR product. A total of 80 strains or isolates of avian influenza viruses were subtyped by this RT-PCR procedure, and the result of RT-PCR gave an excellent (100%) correlation with the result of the conventional serological method. The RT-PCR procedure we developed is rapid and sensitive, and could be used for the identification and HA-subtyping of avian influenza virus in organ homogenates.

Complete nucleotide sequence of avian paramyxovirus type 6 isolated from ducks

There are nine serotypes of avian paramyxovirus (APMV). Only the genome of APMV type 1 (APMV-1), also called Newcastle disease virus (NDV), has been completely sequenced. In this study, the complete nucleotide sequence of an APMV-6 serotype isolated from ducks is reported. The 16236 nt genome encodes eight proteins, nucleocapsid protein (NP), phosphoprotein (P), V protein, matrix protein (M), fusion protein (F), small hydrophobic (SH) protein, haemagglutinin-neuraminidase (HN) protein and large (L) protein, which are flanked by a 55 nt leader sequence and a 54 nt trailer sequence. Sequence comparison reveals that the protein sequences of APMV-6 are most closely related to those of APMV-1 (NDV) and -2, with sequence identities ranging from 22 to 44%. However, APMV-6 contains a gene that might encode the SH protein, which is absent in APMV-1, but present in the rubulaviruses simian virus type 5 and mumps virus. The presence of an SH gene in APMV-6 might provide a link between the evolution of APMV and rubulaviruses. Phylogenetic analysis demonstrates that APMV-6, -1, -2 (only the F and HN sequences were available for analysis) and -4 (only the HN sequences were available for analysis) all cluster into a single lineage that is distinct from other paramyxoviruses. This result suggests that APMV should constitute a new genus within the subfamily Paramyxovirinae.

Genetic and Pathogenic Characterization of H6N1 Avian Influenza Viruses Isolated in Taiwan Between 1972 and 2005

Abstract This article reports the genetic and pathogenic characteristics of 34 isolates of H6N1 avian influenza viruses isolated in Taiwan between 1972 and 2005. Genetic analyses showed that a unique lineage of H6N1 viruses has been established in domestic chickens in Taiwan since 1997, and this lineage of viruses differs from the H6N1 viruses circulating in Hong Kong and Southeastern China. Pathogenicity tests showed that all Taiwanese H6N1 viruses were of low pathogenicity but might lead to economic loss when associated with other diseases. Hemagglutination inhibition tests showed that antigenic drift has occurred in Taiwanese H6N1 viruses, and sequence comparison has identified a total of five possible antigenic sites on the hemagglutinin molecule of the H6N1 viruses. Some Taiwanese H6N1 viruses could replicate in mice without preadaptation, indicating that these viruses have the potential to cause cross-species infection into mammals.

Rapid differentiation of vaccine strains and field isolates of infectious laryngotracheitis virus by restriction fragment length polymorphism of PCR products.

A procedure was developed for differentiation of vaccine strains and field isolates of infectious laryngotracheitis virus (ILTV) by restriction fragment length polymorphism (RFLP) of DNA fragments amplified from the genome of ILTV by polymerase chain reaction (PCR). RFLP patterns of viral thymidine kinase (TK) gene, glycoprotein C (gC) gene, glycoprotein X (gX) gene and ICP4 gene amplified from different ILT viruses were compared. The results showed that the vaccine strain of tissue-culture-origin (TCO) could be readily distinguished from other ILT viruses. Moreover, two out of the four field isolates could be differentiated from vaccine strains of chicken embryo origin (CEO); but the remaining two field isolates were identical to the CEO vaccine strains. These results suggested that both vaccine-like and vaccine-unlike ILT viruses were involved in the field outbreak of this disease, and that the PCR/RFLP procedure could serve as a fast and sensitive method for the detection and differentiation of vaccine strains and field isolates of ILT viruses.

Development of a polymerase chain reaction procedure for detection and differentiation of duck and goose circovirus

Abstract This article reports the complete nucleotide sequences of four duck circovirus (DuCV) isolates from sick ducks in Taiwan and development of a polymerase chain reaction (PCR) for detection and differentiation of goose circovirus (GoCV) and DuCV. Sequence comparison showed that Taiwanese DuCV isolates had 82.5%–83.8% nucleotide sequence identity to the German and North American DuCV isolates. This is the first report on the presence of DuCV and its associated diseases outside Germany. A PCR test was developed using a universal primer pair based on conserved sequences present in the genomes of GoCV and DuCV. This PCR test could detect and differentiate between GoCV and DuCV by the size of PCR product each virus produced (256 bp for GoCV and 228 bp for DuCV). Application of this PCR test to samples of bursa of Fabricius from sick birds in the field showed that 9 of 26 goose samples contained GoCV, while 13 of 34 duck samples contained DuCV. This PCR test could serve as a fast and sensitive method for detection and differentiation of DuCV and GoCV.

Detection of infectious bursal disease virus infection using the polymerase chain reaction

The method of reverse transcription (RT) followed by the polymerase chain reaction (PCR) was used to amplify two different fragments of the infectious bursal disease virus (IBDV) genome. Two sets of primer framed two different regions within the genes coding for proteins VP2 and VP3, respectively. Both sequences were detected in five strains of IBDV, whereas, none were obtained from uninfected control cells. The sensitivity of RT-PCR was carried out on nucleic acids from the IBDV infected cell cultures. The detection limit was 10(0) to 10(-1) TCID50 in ethidium bromide stained gels and could be enhanced further to 10(-1) to 10(-3) TCID50 by hybridization after southern transfer. In addition, detection of IBDV infection in 12 out of 14 bursal specimens examined by this technique was shown to be entirely consistent with the clinical history and an alternative diagnostic method. The speed, sensitivity, and specificity of this method is relevant for the diagnosis of infection with IBDV.

analysis of the double-stranded RNA genome segments among avian reovirus field isolates

Nine isolates of avian reovirus (ARV) from both healthy birds and birds with different clinical illness and one commercially available vaccine strain were selected and characterized by analysis of the migration pattern of their genomic double-stranded RNA (dsRNA) segments following separation by polyacrylamide gel electrophoresis. Different electropherotypes were observed and analyzed. The results show that the dsRNA segments of ARV were markedly polymorphic among isolates within the same serotype as well as among different serotypes. The results also show no correlation between electropherotype and disease state.

Identification of sequence changes in live attenuated goose parvovirus vaccine strains developed in Asia and Europe

Live attenuated vaccines have been used for control of the disease caused by goose parvovirus (GPV), but the mechanism involved in attenuation of GPV remains elusive. This report presents the complete nucleotide sequences of two live attenuated strains of GPV (82-0321V and VG32/1) that were independently developed in Taiwan and Europe, together with the parental strain of 82-0321V and a field strain isolated in Taiwan in 2006. Sequence comparisons showed that 82-0321V and VG32/1 had multiple deletions and substitutions in the inverted terminal repeats region when compared with their parental strain or the field virus, but these changes did not affect the formation of the hairpin structure essential for viral replication. Moreover, 82-0321V and VG32/1 had five amino acid changes in the non-structural protein, but these changes were located at positions distant from known functional motifs in the non-structural protein. In contrast, 82-0321V had nine changes and VG32/1 had 11 changes in their capsid proteins (VP1), and the majority of these changes occurred at positions close to the putative receptor binding sites of VP1, as predicted using the structure of adeno-associated virus 2 as the model system. Taken together, the results suggest that changes in sequence near the receptor binding sites of VP1 might be responsible for attenuation of GPV. This is the first report of complete nucleotide sequences of GPV other than the virulent B strain, and suggests a possible mechanism for attenuation of GPV.

Detection of avian reovirus RNA and comparison of a portion of genome segment S3 by polymerase chain reaction and restriction enzyme fragment length polymorphism

A reverse transcription-polymerase chain reaction (RT-PCR) was established to amplify a 672-base pairs fragment on the segment S3 of avian reovirus (ARV). The amplified fragments were detected in nine strains of ARV as well as three tendon tissue specimens, indicating that the primer regions were well conserved. The RT-PCR was able to detect as low as 0.2 pg using an ethidium bromide stained gel. The detection limit could be enhanced further to 0.04 pg by hybridisation after southern transfer. The amplified DNA fragments from nine ARV strains and two tissue specimens showed different restriction enzyme cleavage patterns. Analysis of the data revealed that these 11 strains were classified into four groups. The results suggest that PCR followed by restriction enzyme analysis may provide a simple and rapid method for the characterisation of ARV isolates.

Molecular Characterization of Plasmids with Antimicrobial Resistant Genes in Avian Isolates of Pasteurella multocida

Abstract SUMMARY. The complete nucleotide sequences of two plasmids from avian isolates of Pasteurella multocida that caused outbreaks of fowl cholera in Taiwan were determined. The entire sequences of the two plasmids, designated as pJR1 and pJR2, were 6792 bp and 5252 bp. Sequence analysis showed that the plasmid pJR1 contained six major genes: the first gene (sulII) encoded a type II sulfonamide resistant dihydropteroate synthase, the second gene (tetG) encoded a tetracycline resistance protein, the third gene (catB2) encoded a chloramphenicol acetyltransferase, the fourth gene (rep) encoded a replication protein, and the fifth and sixth genes (mbeCy and ΔmbeAy) encoded proteins involved in the mobilization of plasmid. The plasmid pJR2 contained five major genes: the first gene (ΔintI1) encoded a truncated form of a type I integrase, the second gene (aadA1) encoded an aminoglycoside adenylyltransferase that confers resistance to streptomycin and spectinomycin, the third gene (blaP1) encoded a beta-lactamase that confers resistance to ampicillin and carbenicillin, and the fourth and fifth genes might encode proteins involved in the plasmid replication or segregation. Sequence comparisons showed that the antibiotic resistance genes found in pJR1 and pJR2 exhibited a high degree of sequence homology to the corresponding genes found in a great variety of gram-negative bacteria, including Escherichia coli, Salmonella enterica Typhimurium DT104, Pseudomonas spp., P. multocida, Mannheimia spp., and Actinobacillus pleuropneumoniae, which suggests that these resistance genes were disseminated in these bacteria. Although sulII and tetG genes were found previously in P. multocida or Mannheimia spp., this is the first report on the presence of catB2, aadA1, and blaP1 genes in bacteria of the family Pasteurellaceae. Moreover, the aadA1 and blaP1 genes found in pJR2 were organized into an integron structure, which is a site-specific recombination system capable of capturing and mobilizing antibiotic resistance genes. This is also the first report on the presence of an integron in bacteria of the family Pasteurellaceae. The presence of a P. multocida integron might facilitate the spreading of antibiotic resistance genes between P. multocida and other gram-negative bacteria.