Genome sequence comparison of two United States live attenuated vaccines of infectious laryngotracheitis virus (ILTV)

This study was conducted to identify unique nucleotide differences in two U.S. chicken embryo origin (CEO) vaccines [LT Blen (GenBank accession: JQ083493) designated as vaccine 1; Laryngo-Vac^? (GenBank accession: JQ083494) designated as vaccine 2] of infectious laryngotracheitis virus (ILTV) genomes compared to an Australian Serva vaccine reference ILTV genome sequence [Gallid herpesvirus 1 (GaHV-1); GenBank accession number: HQ630064]. Genomes of the two vaccine ILTV strains were sequenced using Illumina Genome Analyzer 2X of 36 cycles of single-end reads. Results revealed that few nucleotide differences (23 in vaccine 1; 31 in vaccine 2) were found and indicate that the US CEO strains are practically identical to the Australian Serva CEO strain, which is a European-origin vaccine. The sequence differences demonstrated the spectrum of variability among vaccine strains. Only eight amino acid differences were found in ILTV proteins including UL54, UL27, UL28, UL20, UL1, ICP4, and US8 in vaccine 1. Similarly, in vaccine 2, eight amino acid differences were found in UL54, UL27, UL28, UL36, UL1, ICP4, US10, and US8. Further comparison of US CEO vaccines to several ILTV genome sequences revealed that US CEO vaccines are genetically close to both the Serva vaccine and 63140/C/08/BR (GenBank accession: HM188407) and are distinct from the two Australian-origin CEO vaccines, SA2 (GenBank accession: JN596962) and A20 (GenBank accession: JN596963), which showed close similarity to each other. These data demonstrate the potential of high-throughput sequencing technology to yield insight into the sequence variation of different ILTV strains. This information can be used to discriminate between vaccine ILTV strains and further, to identify newly emerging mutant strains of field isolates.     

Comparative genomic sequence analysis of the Marek’s disease vaccine strain SB-1

Marek’s disease virus (MDV), an oncogenic alphaherpesvirus, induces a rapid onset T-cell lymphoma and demyelinating disease in chickens. Since the 1970s the disease has been controlled through mass vaccination with herpesvirus of turkeys [meleagrid herpesvirus type 1 (MeHV-1)]. Over time this vaccine’s efficacy decreased, and in the 1980s a bivalent vaccine consisting of MeHV-1 and a non-oncogenic gallid herpesvirus type 3 (GaHV-3) strain known as SB-1 was introduced. The complete DNA sequence (165,994 bp) of this GaHV-3 strain was determined using 454 pyrosequencing. A total of 524 open reading frames (ORFs) were examined for homology to protein sequences present in GenBank using BLAST (E-values <0.9). Of the 128 ORF hits, 75 ORFs showed homology to well-characterized alphaherpesviral proteins. Phylogenetically, this strain partitions in its own branch along with the GaHV-3 strain HPRS24 and shows more relatedness to MeHV-1 than gallid herpesvirus type 2 (GaHV-2, Marek’s disease virus). When comparing the GaHV-3 ORFs to their homologues in MeHV-1 and GaHV-2, a greater percentage of amino acid similarity was found with homologous ORFs in the genome of SB-1 than with those in the HPRS24 genome. Overall, twice as many of the 75 ORFs within the SB-1 genome showed greater sequence identities and similarities to homologous ORFs in the Marek’s disease genome than those within the HPRS24 genome. This paper describes the sequence difference between the two GaHV-3 genomes. Overall 19 ORFs differ in the number of predicted amino acids; of these, eight (U_L3.5, U_L5, U_L9, U_L28, U_L30, U_L36, U_L37, and U_L50) encode well-characterized alphaherpesviral proteins A sequence within the unique short region of the SB-1 genome exhibited significant sequence homology to long terminal repeat (LTR) sequences of avian retroviruses. This sequence was only found in the SB-1 genome and not the HPRS24 genome.     

Molecular epidemiology of infectious laryngotracheitis: a review

Infectious laryngotracheitis (ILT) is an economically important respiratory disease of poultry that affects the poultry industry worldwide. The disease is caused by gallid herpesvirus I (GaHV-1), a member of the genus Iltovirus, family Herpesviridae, subfamily Alphaherpesvirinae. The current incidence of the disease is heavily influenced by live attenuated vaccines, which have been used extensively since their introduction in the mid-twentieth century. The capability of current live attenuated vaccine viruses to revert to virulence and spread from bird to bird has shaped the molecular epidemiology of ILT. Because of the antigenic homogeneity among GaHV-1 strains, differentiation of strains has been achieved by targeting genomic differences between outbreak-related isolates and vaccine strains. Numerous genes and genomic regions have been utilized in the development of DNA-based diagnostic assays to differentiate outbreak-related isolates from vaccine strains in countries where ILT outbreaks have occurred. More recently, full genome sequences have allowed determination of the origin of some of the outbreak-related isolates circulating in some poultry production countries. Overall, molecular typing data collected worldwide have identified live attenuated vaccine-related isolates as the primary source for outbreaks of the disease.     

Comparison of the replication and transmissibility of two infectious laryngotracheitis virus chicken embryo origin vaccines delivered via drinking water

Infectious laryngotracheitis (ILT) is an acute infectious viral disease that affects chickens, causing respiratory disease, loss of production and mortality in severe cases. Biosecurity measures and administration of attenuated viral vaccine strains are commonly used to prevent ILT. It is notable that most recent ILT outbreaks affecting the intensive poultry industry have been caused by vaccine-related virus strains. The purpose of this study was to characterize and compare viral replication and transmission patterns of two attenuated chicken embryo origin ILT vaccines delivered via the drinking water. Two groups of specific pathogen free chickens were each inoculated with SA-2 ILT or Serva ILT vaccine strains. Unvaccinated birds were then placed in contact with vaccinated birds at regular intervals. Tracheal swabs were collected every 4 days over a period of 60 days and examined for the presence and amount of virus using a quantitative polymerase chain reaction. A rapid increase in viral genome copy numbers was observed shortly after inoculation with SA-2 ILT virus. In contrast, a comparatively delayed virus replication was observed after vaccination with Serva ILT virus. Transmission to in-contact birds occurred soon after exposure to Serva ILT virus but only several days after exposure to SA-2 ILT virus. Results from this study demonstrate in vivo differences between ILT vaccine strains in virus replication and transmission patterns.     

Characterization by restriction fragment length polymorphism and sequence analysis of field and vaccine strains of infectious laryngotracheitis virus involved in severe outbreaks

At the end of 2002 and throughout 2003, there was a severe outbreak of infectious laryngotracheitis (ILT) in an intensive production area of commercial hens in the São Paulo State of Brazil. ILT virus was isolated from 28 flocks, and 21 isolates were genotyped by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) using four genes and eight restriction enzymes, and by partial sequencing of the infected cell protein 4 (ICP4) and thymidine kinase (TK) genes. Three groups resulted from the combinations of PCR-RFLP patterns: 19 field isolates formed Group I, and the remaining two isolates together with the chicken embryo origin (CEO) vaccine strains formed Group II. Group III comprised the tissue-culture origin (TCO) vaccine strain by itself. The PCR-RFLP results agreed with the sequencing results of two ICP4 gene fragments. The ICP4 gene sequence analysis showed that the 19 field isolates classified into Group I by RFLP-PCR were identical among themselves, but were different to the TCO and CEO vaccines. The two Group II isolates could not be distinguished from one of the CEO vaccines. The nucleotide and amino acid sequence analyses discriminated between the Brazilian and non-Brazilian isolates, as well as between the TCO and CEO vaccines. Sequence analysis of the TK gene enabled classification of the field isolates (Group I) as virulent and non-vaccine. This work shows that the severe ILT outbreak was caused by a highly virulent, non-vaccine strain.     

Map location of lactate dehydrogenase-elevating virus (LDV) capsid protein (Vp1) gene

Lactate dehydrogenase-elevating virus (LDV) is currently classified within the Togaviridae family. In an effort to obtain further information on the characteristics of this virus, we have begun to sequence the viral RNA genome and to map the virion structural protein genes. A sequence of 1064 nucleotides, which represents the 3' terminal end of the genome, was obtained from LDV cDNA clones. A 3' noncoding region of 80 nucleotides followed by two complete open reading frames (ORFs) were found within this sequence. The two ORFs were in different reading frames and overlapped each other by 11 nucleotides. One ORF encoded a protein of 170 amino acids and the other ORF, located adjacent to the 3' noncoding region of the viral genome, encoded a 114 amino acid protein. Thirty-three N-terminal residues were sequenced directly from purified LDV capsid protein, Vp1, and this amino acid sequence mapped to the ORF adjacent to the 3' noncoding region. The presence of overlapping ORFs and the 3' terminal map position of Vp1 indicate that LDV differs significantly from the prototype alpha togaviruses.     

Characterization of field isolates of infectious laryngotracheitis virus from Ontario.

Five cases of infectious laryngotracheitis (ILT) occurred in the fall of 2004 in the Niagara Peninsula, in Southern Ontario. At about the same time two more cases occurred in Eastern Ontario and one case in South-Western Ontario. We examined, at a molecular level, 10 Ontario ILT virus field isolates from 2004 and early 2005 as well as four ILT vaccine viruses by polymerase chain reaction-restriction fragment length polymorphism analyses of ICP4 and glycoprotein E genes, and partial sequencing of UL47 and glycoprotein G genes. We determined that the five Niagara Peninsula ILT viruses were identical among themselves. They represented an independent cluster of ILT cases and were not related to other cases that occurred during 2004 and early 2005. Viruses isolated during the outbreaks in Eastern and South-Western Ontario could not be differentiated from chicken embryo origin ILT vaccine viruses. Niagara Peninsula isolates were different, at a molecular level, from all four vaccine viruses that were examined and from ILT viruses that had been previously analysed and reported in the literature. Taken together our data indicate that both "wild-type" and vaccine-derived viruses are involved in ILT cases in Ontario.     

A genomic map of infectious laryngotracheitis virus and the sequence and organization of genes present in the unique short and flanking regions

We present a genomic map of infectious laryngotracheitis virus (ILT) and an 18,912 bp sequence containing the entire unique short region and a portion of the flanking short repeats. In determining the genomic map, an 856 bp region repeated as many as 13 times was identified within the short repeats. The unique short sequence contains nine potential open reading frames (ORFs). Six of these ORFs show homology to other known herpesvirus unique short genes. Using the herpes simplex virus nomenclature, these genes are the US2, protein kinase, and glycoproteins G, D, I, and E (ORF 1, 2, 4, 6, 7, and 8, respectively). Interestingly, an open reading frame with homology to HSV-1 UL47 (ORF 3) is found in the unique short. One very large open reading frame (ORF 5) is present and contains a threonine-rich, degenerate repeat sequence. This gene appears to be unique to ILT among sequenced herpesviruses. Two ORFs were identified within the short repeat (SR) region. SRORF 1 is homologous to a gene (SORF3) found in the unique short region in both MDV and HVT, and appears to be specific to avian herpesviruses. SRORF 2 has homology to HSV US10.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence data-base and have been assigned the accession number U28832.     

A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus

We describe a novel lipothrixvirus, SIFV, of the crenarchaeotal archaeon Sulfolobus islandicus. SIFV (S. islandicus filamentous virus) has a linear virion with a linear double-stranded DNA genome. These two features coincide in several crenarchaeotal but not in any other viruses. The SIFV core is formed by a zipper-like array of DNA-associated protein subunits and is covered by a lipid envelope containing host lipids. We sequenced approximately 96% of the virus genome excepting the DNA termini, which were modified in an unusual, yet uncharacterized, manner. Both, the 5' and the 3' DNA termini were insensitive to enzymatic degradation and labelling. Two open reading frames (ORFs) of the SIFV genome are likely to encode helicases and resemble uncharacterized ORFs from other archaea in sequence. Three ORFs showed sequence similarity with each other and each contained a glycosyl transferase motif. Another ORF of the SIFV genome showed significant sequence similarity to the ORF a291 from the well characterized, spindle-shaped Sulfolobus virus SSV1. Due to its structure, SIFV is classified as a lipothrixvirus.     

Characterization of infectious laryngotracheitis virus isolates from the US by polymerase chain reaction and restriction fragment length polymorphism of multiple genome regions.

Infectious laryngotracheitis (ILT) is an acute viral respiratory disease, primarily of chickens. Economic losses attributable to ILT affect many poultry-producing areas throughout the United States (US) and the world. Despite efforts to control the disease by vaccination, prolonged epidemics of ILT remain a threat to the poultry industry. Earlier epidemiological and molecular evidence indicated that outbreaks in the US are caused by vaccine-related strains. In this study, polymerase chain reaction and restriction fragment polymorphism (PCR-RFLP) of four genome regions was utilized to characterize 25 isolates from commercial poultry and backyard flocks from the US. Combinations of PCR-RFLP patterns classified the ILT virus isolates into nine groups. Backyard flock isolates were categorized in three separate groups. The ILT virus US Department of Agriculture (USDA) reference strain and the tissue culture origin (TCO) vaccine strain were categorized into two separate groups. Twenty-two isolates from commercial poultry were categorized into four groups: one group, of six isolates, showed patterns identical to the chicken embryo origin (CEO) vaccines; a second group, of nine isolates, differed in only one pattern from the CEO vaccines; a third group, of two isolates, differed in only one pattern from the TCO vaccine; a fourth group, of five isolates, differed in six and nine patterns from the CEO and TCO vaccines, respectively. Results obtained from this study clearly demonstrated that most of the commercial poultry isolates (17 of 22 isolates) were closely related to the vaccine strains. However, isolates different to the vaccine strains were also identified in commercial poultry.     

Characterization of a Gallid herpesvirus 2 strain with novel reticuloendotheliosis virus long terminal repeat inserts

A bacterial artificial chromosome clone, designated LCY, was constructed from a Gallid herpesvirus 2 (GaHV-2) isolate from a GaHV-2 and reticuloendotheliosis virus co-infected clinical sample. The LCY GaHV-2 insert was sequenced and found to consist of 175,319 nucleotides. LCY GaHV-2 open reading frames (ORFs) had a high sequence identity to those of reference strains. The major difference was that two REV long terminal repeats (LTRs), in the same direction, were inserted at the internal repeat short (IRs)/unique short (Us) and Us/terminal repeat short (TRs) junctions. In addition, the a-like sequence and UL36 were different from other strains. Phylogenetic analysis revealed that LCY was closely related to pandemic strains in China. A pathogenicity study and a vaccination-challenge test were performed on LCY and the reference strain, GA. The results showed that LCY induced gross Marek’s disease (MD) lesions and mortality in 71.4 and 7.1% of chickens, respectively, which are lower rates than those observed for the reference strain GA (85.7 and 35.7%). The commercially available CVI988 vaccine provided complete protection against LCY and GA (100%). These results showed that the isolate exhibited lower pathogenicity in SPF chickens. This study revealed that a novel pattern of LTR inserts was found in the strain LCY and that the strain was of low virulence. The present work expands the available genetic information for GaHV-2 and will be useful for the control of MD in China.     

Complete genomic sequence of turkey coronavirus

Turkey coronavirus (TCoV), one of the least characterized of all known coronaviruses, was isolated from an outbreak of acute enteritis in young turkeys in Ontario, Canada, and the full-length genomic sequence was determined. The full-length genome was 27,632 nucleotides plus the 3' poly(A) tail. Two open reading frames, ORFs 1a and 1b, resided in the first two thirds of the genome, and nine additional downstream ORFs were identified. A gene for hemagglutinin-esterase was absent in TCoV. The region between the membrane (M) and nucleocapsid (N) protein genes contained three potential small ORFs: ORF-X, a previously uncharacterized ORF with an associated putative TRS within the M gene (apparently shared among all group III coronaviruses), and previously described ORFs 5a and 5b. The TCoV genome is organized as follows: 5' UTR--replicase (ORFs 1a, 1b)--spike (S) protein--ORF3 (ORFs 3a, 3b)--small envelop (E or 3c) protein--membrane (M) protein--ORF5 (ORFs X, 5a, 5b)--nucleocapsid (N) protein--3' UTR--poly(A). TCoV genome structure and sequence was most similar, but distinct from, avian infectious bronchitis virus (IBV). This is the first complete genome sequence for a TCoV and confirms that TCoV belongs to group III coronaviruses.     

Short communication: Molecular analysis of Potato leafroll virus isolates from the Czech Republic

The complete genomes of three Czech isolates VIRUBRA 1/045, VIRUBRA 1/046, and VIRUBRA 1/047 of Potato leafroll virus (PLRV) were sequenced and compared with 13 complete sequences of PLRV isolates available in GenBank. Among the Czech isolates, VIRUBRA 1/046 and 1/047 showed the highest nucleotide (nt) identity (98.7%). PLRV was the most conserved virus in both open reading frames (ORFs) 3 and 4. The most variable regions were ORFs 0 and Rap1. Interestingly, isolate VIRUBRA 1/045 significantly differed from the other two Czech isolates in ORFs 0 and 1. Moreover, we identified mutations in the amino acid (aa) sequences, which were specific for the Czech isolates. Phylogenetic analysis based on ORF0 showed that the Czech isolates could be classified in two of the three groupings of the phylogenetic tree obtained. This is the first report on sequence analysis of the genome sequences of PLRV isolates from the Czech Republic. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.