Differentiation of field isolates and vaccine strains of infectious laryngotracheitis virus by DNA sequencing

Molecular characterization and phylogenetic analysis of infectious laryngotracheitis virus isolates from commercial chicken flocks in Turkey

Infectious laryngotracheitis virus (ILTV) causes an acute and highly contagious respiratory disease in poultry. Live-attenuated vaccines are generally used to control and prevent infectious laryngotracheitis (ILT). However, these vaccines can revert to a virulent form due to multiple passages and thereby become an ILT source. Hence, monitoring of ILTV in the field through molecular characterization is critically important for controlling infection and differentiating circulating isolates. In this study, we genotypically characterized and phylogenetically analyzed eight ILTV isolates from chicken flocks located in four different cities of Turkey between 2019 and 2022. For all isolates, we analyzed two regions of the infected cell protein 4 gene (ICP4-1 and ICP4-2) and the thymidine kinase (TK) gene. The isolates were 100%, 100%, and 99.8-100% identical to each other in the ICP4-1 and ICP4-2 gene fragments and the TK gene, respectively. None of the ICP4 sequences had a deletion at nt 272-283, confirming that they were field isolates. None of the isolates were predicted to have a T252M mutation in the thymidine kinase, suggesting that they have low virulence. The isolates were 100%, 99.36%, and 99.91% identical to Turkish ILTV isolates in their ICP4-1, ICP4-2, and TK gene region, respectively. Phylogenetic analysis based on the ICP4-1 and TK genes confirmed that the ILTV isolates are closely related to Turkish ILTV isolates. This suggests that these ILTVs were endemic isolates, which in turn suggests that the ILTV isolates circulating in Turkey were evolutionarily close, originated from the field, and had low virulence.

Circulation and Molecular Characterization of Infectious Laryngotracheitis Virus in Poultry Flocks with Respiratory Disorders in Turkey, 2018-2022

Infectious laryngotracheitis (ILT) is a very serious worldwide respiratory disease of poultry, with many countries reporting ILT infections over the last decade. However, few reports are available regarding ILT disease prevalence in poultry in Turkey. Accordingly, the present study investigated ILT infection in Turkish broiler flocks between 2018 and 2022. Circulating ILT strains were characterized by sequence and phylogenetic analysis of two fragments of the infected-cell protein 4 gene. ILT virus (ILTV) was confirmed by quantitative PCR in 8 of the 21 flocks examined. As in other diseases, co-infections with other respiratory pathogens in confirmed ILT cases may worsen the symptoms and prolong the disease course. The present study confirmed co-infections with infectious bronchitis virus (13/21 tested flocks and 5/8 ILTV-positive flocks), indicating the importance of these pathogens in the occurrence of ILT infections.

Protection Efficacy of Recombinant HVT-ND-LT and the Live Attenuated Tissue Culture Origin Vaccines Against Infectious Laryngotracheitis Virus When Administered Individually or in Combination

Infectious laryngotracheitis (ILT) is a respiratory disease that causes significant economic losses to the poultry industry. Control of the disease is achieved by vaccination and implementation of biosecurity measures. The use of bivalent and trivalent recombinant herpesvirus of turkey (rHVT) vaccines expressing infectious laryngotracheitis virus (ILTV) genes has increased worldwide. In the United States, vaccination programs of long-lived birds (broiler breeders and commercial layers) against ILT include immunizations with either HVT recombinant vector vaccines, in ovo or at hatch, or live attenuated vaccines administered via drinking water (chicken embryo origin [CEO]) or eye drop (tissue culture origin [TCO]). The efficacy of bivalent rHVT-LT at hatch followed by drinking water or eye-drop CEO vaccination has been shown to provide more robust protection than rHVT-LT alone. The objective of this study was to evaluate the protection efficacy of a commercial trivalent rHVT-ND-LT when administered at 1 day of age followed by TCO vaccination via eye drop at 10 wk of age. Groups vaccinated with only rHVT-ND-LT or TCO, the combination of rHVT-ND-LT + TCO, and one nonvaccinated group of chickens were challenged with a virulent ILTV strain at 15 wk of age. After challenge, mortalities were prevented only in the group of chickens vaccinated with the rHVT-ND-LT + TCO. Clinical signs of the disease and challenge virus replication in the trachea were significantly reduced for both the rHVT-ND-LT + TCO- and TCO-vaccinated groups of chickens. To assess challenge virus transmission, contact-naive chickens were introduced to all vaccinated groups immediately after challenge. At 8 days postintroduction, infection of contact-naive chickens was evidenced in those introduced to the rHVT-ND-LT and TCO group but prevented in the rHVT-ND-LT + TCO group. Overall, these results indicated that compared to rHVT-ND-LT or TCO when administered alone, the rHVT-ND-LT + TCO vaccination strategy improved protection against disease and reduced shedding of the challenge virus.

Detection and molecular characterization of infectious laryngotracheitis virus (ILTV) in chicken with respiratory signs in Brazil during 2015 and 2016

Avian infectious laryngotracheitis (ILT) is a respiratory disease that causes severe economic losses in the poultry industry, mainly due to high morbidity and mortality and reduced egg production. Molecular characterization was performed on samples collected from flocks in the Brazilian States of São Paulo, Pernambuco, and Minas Gerais during 2015 and 2016 that presented clinical signs of respiratory disease. End-point PCR was used for viral detection, and DNA sequencing was used for differentiation of vaccine and field strains. Molecular analysis based on the infected cell protein (ICP4) gene separated four of the nine samples together with previous Brazilian isolates (São Paulo and Minas Gerais), one sample was grouped on the same branch as Minas Gerais strains (along with another related sample), one sample was separately branched but still related to the tissue culture origin (TCO) vaccine strain, and two samples were grouped on the same branch as the TCO vaccine strain. Molecular analysis of the thymidine kinase (TK) gene showed the existence of strains of both high and low virulence. The characterization of two fragments of the ICP4 gene and a fragment of the TK gene in this study suggested that the virus circulating in Guatapará, as well as those in Barretos and Itanhandu, that is causing respiratory problems in birds is a highly virulent field strain. The clinical signs point to a TCO vaccine strain that most likely underwent some reversal event and is a latent reactivated infection.

Molecular and genetic detection of infectious laryngeotrachitis disease virus in broiler farms after a disease outbreak in Egypt

Infectious laryngotracheitis (ILT) is a viral respiratory illness in poultry that causes massive financial losses. This research aimed to isolate and identify the ILT virus in suspected outbreaks of broiler flocks in Egypt during 2020-2021, besides investigating its genetic link with other circulating strains. Real-time-PCR was used to test 57 samples taken from unvaccinated broiler farms. Ten samples are positive for ILTV, and the virus is being isolated in SPF chicken embryos. The Sanger sequencing was used to conduct (partial) sequencing of the infected cell protein4 gene (ICP4) for eight isolates. Phylogenetic analysis conducted Maximum Likelihood, comparative sequencing analysis of ICP4 of strains under study with vaccination ILT reference strains reveled that all isolates were clustered into two major groups. The (OM291843and OM291846) clustered together with the chicken embryo origin vaccine strains (IV and V group). The remaining six strains belong to the TCO vaccine(I, II and III group). The total sequence similarity between the strains under study and the various Egyptian strains varied from (97 to 100%) while the similarity with TCO or chicken embryo origin -vaccine strains ranged from (95to 100%). There were no deletions detected in the 272-283-bp region of the ICP4 gene. Detection of arginine to methionine substitutions at position 180 (R180M) and change of Serine to Asparagine at position 227 (S227N) in the (OM291843 and OM291846) which were previously described in chicken embryo origin -vaccine strains. This reveals that field strains may have evolved from vaccine strains, notably identification of non-synonymous substitutions which might be linked to the virulence strains' attenuation. Finally, independent of geographical distribution, both chicken embryo origin-vaccine-like and TCO-Vaccine-like virus strains were circulating in Egyptian non-vaccinated broiler flocks in 2020 and 2021. Despite their genetic differences, both viruses caused significant illnesses in the field.

Characterization of infectious laryngotracheitis virus isolates from laying hens during 2019-2020 outbreaks in Tamil Nadu, India

Infectious laryngotracheitis (ILT) is an acute respiratory disease in chickens that is a serious threat to poultry-producing countries worldwide. In the present study, we isolated and characterized infectious laryngotracheitis (ILTV) virus isolates by sequencing and restriction fragment length polymorphism analysis of PCR-amplified products (PCR-RFLP). A total of 26 ILTV outbreaks were investigated that occurred between 2019 and 2020 in flocks that had not been vaccinated against ILTV. ILTV was isolated by cultivating tracheal samples in embryonated chicken eggs, which showed multiple opaque pock lesions and thickening of the chorioallantoic membrane after 120 hours of infection. The ILTV isolates were identified and characterized by PCR and sequencing a portion of the ICP4 and TK genes. Phylogenetic analysis based on the ICP4 region showed that the sequences clustered with chicken-embryo-origin vaccine-like strains. Sequence analysis of the ICP4 region differentiated chicken-embryo-origin (CEO), tissue-culture-origin (TCO), and field ILTV strains, with significant differences in nucleotide and amino acid sequences. Furthermore, PCR-RFLP analysis of the TK gene showed that the patterns were identical to those obtained with low-virulence and vaccine strains. In conclusion, sequencing of a portion of the ICP4 region of ILTV allowed differentiation of ILTV field, CEO, and TCO vaccine strains. In this study, CEO-vaccine-like strains were found to be the cause of ILTV outbreaks between 2019 and 2020 in Tamil Nadu in southern India.

Evaluation of Recombinant Herpesvirus of Turkey Laryngotracheitis (rHVT-LT) Vaccine against Genotype VI Canadian Wild-Type Infectious Laryngotracheitis Virus (ILTV) Infection

In Alberta, infectious laryngotracheitis virus (ILTV) infection is endemic in backyard poultry flocks; however, outbreaks are only sporadically observed in commercial flocks. In addition to ILTV vaccine revertant strains, wild-type strains are among the most common causes of infectious laryngotracheitis (ILT). Given the surge in live attenuated vaccine-related outbreaks, the goal of this study was to assess the efficacy of a recombinant herpesvirus of turkey (rHVT-LT) vaccine against a genotype VI Canadian wild-type ILTV infection. One-day-old specific pathogen-free (SPF) White Leghorn chickens were vaccinated with the rHVT-LT vaccine or mock vaccinated. At three weeks of age, half of the vaccinated and the mock-vaccinated animals were challenged. Throughout the experiment, weights were recorded, and feather tips, cloacal and oropharyngeal swabs were collected for ILTV genome quantification. Blood was collected to isolate peripheral blood mononuclear cells (PBMC) and quantify CD4+ and CD8+ T cells. At 14 dpi, the chickens were euthanized, and respiratory tissues were collected to quantify genome loads and histological examination. Results showed that the vaccine failed to decrease the clinical signs at 6 days post-infection. However, it was able to significantly reduce ILTV shedding through the oropharyngeal route. Overall, rHVT-LT produced a partial protection against genotype VI ILTV infection.

Isolation of infectious laryngotracheitis virus in broiler chicken in Iran: First report

In February 2019, a severe respiratory distress with co-infection of infectious laryngotracheitis (ILT) and Newcastle disease accompanied with SalmonellaEnteritidis occurred in a broiler flock in the western region of Iran. Clinical signs included paralysis, torticollis, nasal discharge, conjunctivitis, gasping and respiratory rale with high mortality. At necropsy, caseous diphtheritic membrane adherent to the larynx and trachea was observed. Microscopically, syncytial cells formation with dense eosinophilic intranuclear inclusion bodies were main histopathological findings in tracheal tissues. Conventional polymerase chain reaction (PCR) for ICP4 gene amplification as a definitive diagnosis was utilized for the detection of ILT virus nucleic acid in suspected tracheal samples inoculated on to the chorioallantioc membrane of 11-day-old specific pathogen free (SPF) chicken eggs. Tracheal tissues taken from these SPF birds were positive by nested ILT PCR. In conclusion, because of no vaccination policy against ILT in broilers, the most probable scenario is that virus-laden dust or other fomites can be vectors and virus persistence and disease outbreak can be a sequel of wild virus introduction to the farm.

Detection of Laryngotracheitis Virus in Poultry Flocks with Respiratory Disorders in Slovenia

Infectious laryngotracheitis (ILT) is an acute, highly contagious infectious disease of the upper respiratory tract in chickens and other poultry species that causes significant economic losses in countries worldwide. Between 2017 and 2019, seven outbreaks of mild to severe respiratory disorders with high suspicion of ILT occurred in commercial and backyard poultry flocks in Slovenia. In all submissions, infection with ILT virus (ILTV) was confirmed by PCR, which is the first report of ILT in Slovenia. Circulating ILT strains were characterized by the sequence and phylogenetic analysis of two fragments of the ICP4 gene. Four strains—three detected in non-vaccinated flocks and one in a flock vaccinated against ILT—were identical or very similar to the chicken embryo–origin live virus vaccines, and the other three were closely related to Russian, Chinese, Australian, and American field strains and to tissue culture origin vaccine strains. As in other diseases, coinfections with other respiratory pathogens in confirmed ILT cases may cause a more severe condition and prolong the course of the disease. In our study, coinfections with Mycoplasma synoviae (7/7 tested flocks), infectious bronchitis virus (5/5 tested flocks), Mycoplasma gallisepticum (4/7 tested flocks), Ornithobacterium rhinotracheale (3/4 tested flocks), and avian pox virus (1/2 tested flocks) were confirmed, indicating the importance of these pathogens in the occurrence of ILT infections.

Infectious laryngotracheitis: Etiology, epidemiology, pathobiology, and advances in diagnosis and control - a comprehensive review

Infectious laryngotracheitis (ILT) is a highly contagious upper respiratory tract disease of chicken caused by a Gallid herpesvirus 1 (GaHV-1) belonging to the genus Iltovirus, and subfamily Alphaherpesvirinae within Herpesviridae family. The disease is characterized by conjunctivitis, sinusitis, oculo-nasal discharge, respiratory distress, bloody mucus, swollen orbital sinuses, high morbidity, considerable mortality and decreased egg production. It is well established in highly dense poultry producing areas of the world due to characteristic latency and carrier status of the virus. Co-infections with other respiratory pathogens and environmental factors adversely affect the respiratory system and prolong the course of the disease. Latently infected chickens are the primary source of ILT virus (ILTV) outbreaks irrespective of vaccination. Apart from conventional diagnostic methods including isolation and identification of ILTV, serological detection, advanced biotechnological tools such as PCR, quantitative real-time PCR, next generation sequencing, and others are being used in accurate diagnosis and epidemiological studies of ILTV. Vaccination is followed with the use of conventional vaccines including modified live attenuated ILTV vaccines, and advanced recombinant vector vaccines expressing different ILTV glycoproteins, but still these candidates frequently fail to reduce challenge virus shedding. Some herbal components have proved to be beneficial in reducing the severity of the clinical disease. The present review discusses ILT with respect to its current status, virus characteristics, epidemiology, transmission, pathobiology, and advances in diagnosis, vaccination and control strategies to counter this important disease of poultry.

Molecular detection and genetic characterization of infectious laryngotracheitis virus in poultry in Myanmar

BACKGROUND

Avian infectious laryngotracheitis (ILT) is a highly contagious viral disease that causes severe economic losses to the poultry industry worldwide. In Southeast Asian countries, including Myanmar, poultry farming is a major industry. Although it is known that infectious respiratory pathogens, including infectious laryngotracheitis virus (ILTV), are a major threat to poultry farms, there are no data currently available on the epidemiology of ILTV in Myanmar. Therefore, in this study, we conducted a molecular detection of ILTV in 20 poultry farms in Myanmar.

RESULTS

Of the 57 tested oropharyngeal swabs, 10 were positive for ILTV by polymerase chain reaction of a 647 bp region of the thymidine kinase (TK) gene, giving a prevalence of ILTV of 17.5% (10/57). Further sequencing analysis of infected cell protein 4 (ICP4) gene and glycoprotein B, G, and J (gB, gG, and gJ) genes indicated that these isolates were field strains. Phylogenetic analysis revealed that the Myanmar strains clustered together in a single branch and were closely related to other reference strains isolated from Asian countries.

CONCLUSIONS

This study demonstrated the presence of ILTV in poultry farms in Myanmar. The genetic characterization analysis performed provides the fundamental data for epidemiological studies that monitor circulating strains of ILTV in Myanmar.

Superinfection and recombination of infectious laryngotracheitis virus vaccines in the natural host

Infectious laryngotracheitis virus (ILTV, Gallid alphaherpesvirus 1) causes severe respiratory disease in chickens and has a major impact on the poultry industry worldwide. Live attenuated vaccines are widely available and are administered early in the life of commercial birds, often followed by one or more rounds of revaccination, generating conditions that can favour recombination between vaccines. Better understanding of the factors that contribute to the generation of recombinant ILTVs will inform the safer use of live attenuated herpesvirus vaccines. This study aimed to examine the parameters of infection that allow superinfection and may enable the generation of recombinant progeny in the natural host. In this study, 120 specific-pathogen free (SPF) chickens in 8 groups were inoculated with two genetically distinct live-attenuated ILTV vaccine strains with 1-4 days interval between the first and second vaccinations. After inoculation, viral genomes were detected in tracheal swabs in all groups, with lowest copies detected in swabs collected from the groups where the interval between inoculations was 4 days. Superinfection of the host was defined as the detection of the virus that was inoculated last, and this was detected in tracheal swabs from all groups. Virus could be isolated from swabs at a limited number of timepoints, and these further illustrated superinfection of the birds as recombinant viruses were detected among the progeny. This study has demonstrated superinfection at host level and shows recombination events occur under a very broad range of infection conditions. The occurrence of superinfection after unsynchronised infection with multiple viruses, and subsequent genomic recombination, highlight the importance of using only one type of vaccine per flock as the most effective way to limit recombination.

Genotyping of Infectious Laryngotracheitis Virus (ILTV) Isolates from Western Canadian Provinces of Alberta and British Columbia Based on Partial Open Reading Frame (ORF) a and b

Simple Summary

Infectious laryngotracheitis virus is an economically important acute upper respiratory tract disease in chickens. To control the disease, there are two types of vaccines commercially available, the recombinant viral vector and the live attenuated vaccines. The live attenuated vaccines are effective in disease control, but because of their residual virulence, they can replicate, cause disease, and revert to their original virulent form. Strains of the virus can be categorized as vaccine-related or wild type related. Information is scarce on the type of strains that are circulating in Canada. This study aims to discriminate between wild type and vaccine strains associated with infectious laryngotracheitis cases in the provinces of Alberta and British Columbia between the years 2009–2018. To accomplish this objective, the sequencing of two specific partial genes was performed. As a result, 27 samples from Alberta, and 5 samples from British Columbia were successfully sequenced. From the total samples, ~85% were related to vaccine strains and the rest categorized as wild type. These results reinforce the concern on current practices surrounding vaccination and the need to implement better biosecurity measures.

Abstract

Infectious laryngotracheitis virus (ILTV) causes an acute upper respiratory disease in chickens called infectious laryngotracheitis (ILT). Live attenuated vaccines are effective in disease control; however, they have residual virulence, which makes them able to replicate, cause disease and revert to the original virulent form. Information is scarce on the molecular nature of ILTV that is linked to ILT in Canada. This study aims to determine whether isolates originating from ILT cases in Western Canada are a wild type or vaccine origin. Samples submitted for the diagnosis of ILT between 2009–2018 were obtained from Alberta (AB, n = 46) and British Columbia (BC, n = 9). For genotyping, a Sanger sequencing of open reading frame (ORF) a and b was used. A total of 27 from AB, and 5 from BC samples yielded a fragment of 1751 base pairs (bp). Three of the BC samples classified as group IV (CEO vaccine strains) and 2 as group V (CEO revertant). Of the AB samples, 22 samples clustered with group V, 3 with group VI (wild type), and 2 with group VII, VIII, and IX (wild type). Overall, 17 non-synonymous single nucleotide polymorphisms (SNPs) were detected. Further studies are underway to ascertain the virulence and transmission potential of these isolates.

Application of recombinase polymerase amplification method for rapid detection of infectious laryngotracheitis virus

Infectious laryngotracheitis is a significant respiratory disease of chickens that causes huge economic losses due to high morbidity and mortality and reduced egg production. A real-time recombinase polymerase amplification (RPA) assay was developed to accurately detect ILTV. The specific probe and primer sets were carefully designed and screened. The real-time RPA assay was carried out at 39 °C for 30 min, and results were obtained within 15 min. The results of the specificity assay showed no fluorescence signals with other avian-related viruses. The sensitivity of the assay was 1 × 10² copies/μL. The low CV value showed that the assay was reproducible. A total of 115 clinical samples were tested using the real-time RPA assay and the real-time PCR assay in parallel; the coincidence rates of the two detection methods were 100%. The results indicated that the real-time RPA assay is a specific, sensitive, rapid, and useful tool for epidemiological studies and clinical diagnosis, especially in the field and in resource-poor areas.

Molecular characterization and genetic diversity of the infectious laryngotracheitis virus strains circulating in Egypt during the outbreaks of 2018 and 2019

Infectious laryngotracheitis (ILT) is a respiratory disease that causes significant economic losses in the poultry industry worldwide. In this study, ILT outbreaks were reported on 30 farms located in eight Egyptian governorates between January 2018 and May 2019. Gross examination of diseased chickens revealed congestion and hemorrhage of laryngeal and tracheal mucosa with fibrinohemorrhagic casts and/or caseous material in the lumens. Histopathological examination showed epithelial sloughing, syncytium formation, heterophilic exudation, and development of eosinophilic intranuclear inclusion bodies. Infectious laryngotracheitis virus (ILTV) antigen was detected in the tracheal epithelium, infiltrated inflammatory cells, and syncytial cells, using immunohistochemistry. PCR targeting a portion of the thymidine kinase gene was further utilized to confirm the presence of ILTV DNA. The complete coding sequences of three envelope glycoprotein genes, gG, gD, and gJ, and a partial sequence of the infected cell polypeptide 4 (ICP4) gene from samples representing all of the farms and disease outbreaks were determined. Five prototype strains with unique sequences were chosen for detailed molecular characterization. Sequence comparisons and phylogenetic analysis of the partial ICP4 gene revealed that two strains were chicken embryo origin (CEO)-vaccine-like strains, and three were tissue culture origin (TCO)-vaccine-like strains. Analysis of the gJ gene sequence indicated that all of the strains were CEO vaccine-like strains. It was predicted that the latter three strains were recombinants of CEO- and TCO-vaccine-like strains. In conclusion, immunohistochemistry coupled with multi-genomic PCR sequencing proved to be efficient for identification and typing of ILTV strains during disease outbreaks. Both CEO-vaccine-like and recombinant virus strains were circulating in Egypt during the 2018 and 2019 outbreaks.

Phylogenetic Evidence of a Close Relationship between the Peruvian Strain Vfar-043 and Two U.S. Origin Iltv Field Strains

Infectious laryngotracheitis virus (ILTV) is the causative agent of an acute respiratory avian disease known as infectious laryngotracheitis (ILT), which has been associated with economic losses in poultry. The presence of ILTV has been widely reported in South American countries; however, only one full genomic sequence (VFAR-043 strain) has been recently published, from an outbreak in Peru. The aim of this study was to determine the genetic relationship of the Peruvian strain with other ILTV strains from different geographic regions. The phylogenetic analyses revealed a close relationship between VFAR-043 and two U.S. origin strains (1874C5 and J2) using only the whole genome, Unique Long (UL), and Unique Short (US) genomic regions. Then these three genomic sequences were compared to evaluate their genetic variations using the USDAref as a reference strain. Genetic variations such as synonymous and nonsynonymous single-nucleotide polymorphisms, insertions, deletions, and nucleotide-codon variations were identified among these three strains. Moreover, the phylogenetic tree analysis using gene sequences of the US5 and ICP4 coding regions from South American isolates showed that VFAR-043 does not have a close relationship with either the Argentinian (US5) or Brazilian (ICP4) reported sequences. However, a close relationship was observed between VFAR-043 and another Peruvian isolate (USP-81) when the ICP4 gene sequence was analyzed. All these results suggest that VFAR-043 together with 1874C5 and J2 are closely related. These findings contribute to our understanding of the epidemiology of ILTV in South America.

Evaluation of vaccination against infectious laryngotracheitis (ILT) with recombinant herpesvirus of turkey (rHVT-LT) and chicken embryo origin (CEO) vaccines applied alone or in combination

The chicken embryo origin (CEO) infectious laryngotracheitis (ILT) live attenuated vaccines, although capable of protecting against disease and reducing challenge virus replication, can regain virulence. Recombinant ILT vaccines do not regain virulence but are partially successful at blocking challenge virus replication. The objective of this study was to evaluate the effect of rHVT-LT vaccination on CEO replication and how this vaccination strategy enhances protection and limits challenge virus transmission to naïve contact chickens. The rHVT-LT vaccine was administered at 1 day of age subcutaneously and the CEO vaccine was administered at 6 weeks of age via eye-drop or drinking water. CEO vaccine replication post vaccination, challenge virus replication and transmission post challenge were evaluated. After vaccination, only the group that received the CEO via eye-drop developed transient conjunctivitis. A significant decrease in CEO replication was detected for the rHVT-LT + CEO groups as compared to groups that received CEO alone. After challenge, reduction in clinical signs and challenge virus replication were observed in all vaccinated groups. However, among the vaccinated groups, the rHVT-LT group presented higher clinical signs and challenge virus replication. Transmission of the challenge virus to naïve contact chickens was only observed in the rHVT-LT vaccinated group of chickens. Overall, this study found that priming with rHVT-LT reduced CEO virus replication and the addition of a CEO vaccination provided a more robust protection than rHVT alone. Therefore, rHVT-LT + CEO vaccination strategy constitutes an alternative approach to gain better control of the disease.

Glycoprotein D peptide-based diagnostic approach for the detection of avian infectious laryngotracheitis antibodies

Infectious laryngotracheitis (ILT) is a highly contagious respiratory disease of chickens, pheasants, and peafowl. It is caused by the alpha herpesvirus, infectious laryngotracheitis virus (ILTV). Glycoprotein D (gD) of ILTV is immunogenic and helps in its binding to the susceptible host cell receptor. In the present study, a recombinant gD protein was expressed in a prokaryotic system to develop a single serum dilution ELISA. In addition, two immunogenic peptides, corresponding to regions 77-89 and 317-328, were identified in gD protein. The peptides were synthesized using solid-phase peptide synthesis, purified using reversed-phase HPLC, and characterized using mass spectrometry. The peptides displayed a good titre and were found to be promising antigens to coat the ELISA plate to detect the ILTV antibodies in the serum sample. The developed ELISA showed 96.9% sensitivity, 87.5% specificity, and 95.3% accuracy as compared to OIE referenced standard indirect ILTV ELISA (whole viral coated). The assay may not differentiate vaccinated from infected birds when the flocks are administered with live attenuated vaccines. However, the assay could be useful to detect the disease condition in birds vaccinated with recombinant vaccine expressing glycoproteins other than gD. The developed ILTV single serum dilution ELISA could be an alternative to the existing diagnostics for the detection of ILTV antibodies.

Co-infections, genetic, and antigenic relatedness of avian influenza H5N8 and H5N1 viruses in domestic and wild birds in Egypt

A total of 50 poultry farms of commercial broilers (N = 39) and commercial layers (N = 11) suffered from respiratory problems and mortality during the period from January 2016 to December 2017 were investigated. Also, samples were collected from quail (N = 4), Bluebird (Sialis, N = 1), and Greenfinch (Chloris chloris, N = 1) for analysis. Respiratory viral pathogens were screened by PCR and positive samples were subjected to virus isolation and genetic identification. Antigenic relatedness of isolated avian influenza (AI) H5 subtype was evaluated using cross-hemagglutination inhibition. Results revealed that the incidence of single virus infections in commercial broilers was 64.1% (25/39), with the highest incidence for ND (33.3%) and H9N2 (20.5%), followed by H5N1 (7.7%) and H5N8 (2.7). Meanwhile, H9N2/ND mixed infection was the most observed case (7.7%). Other mixed infections H5N1/ND, H5N1/H9N2/ND, H5N1/H9N2/ND/IB, H9N2/IB, and H9N2/ILT were also observed (2.6% each). In commercial layers, H5N1 and ILT were the only detected single infections (18.1% each). Mixed H9N2/ND was the most predominant infection in layers (27.3%). Other mixed infections of H9N2/IB, H5N1/H5N8/H9N2, and H9N2/ND/IB were observed in 3 separate farms (9.1% each). The H5N8 virus was detected in one quail farm and 2 out of 3 wild bird's samples. Partial HA gene sequence analysis showed the clustering of the selected AI H5N8 within the 2.3.4.4 clade, while H5N1 clustered with the clade 2.2.1.2. Interestingly, the H5N8 isolated from chickens possessed 6 amino acids substitutions at HA1 compared to those isolated from wild birds with low antigenic relatedness to AI H5N1 clades 2.2.1 or 2.2.1.2. In conclusion, mixed viral infections were observed in both broiler and layer chickens in Egypt. The detected triple H5N1, H9N2, and H5N8 influenza co-infection raises the concern of potential AI epidemic strain emergence. The low genetic and antigenic relatedness between AI H5N1 and H5N8 viruses suggest the need for modification of vaccination strategies of avian influenza in Egypt along with strict biosecurity measures.

Investigation of infectious laryngotracheitis outbreaks in Namibia in 2018

Between July and August 2018, two outbreaks of infectious laryngotracheitis caused the death of over 116,000 commercial poultry (layers and broilers) near the city of Windhoek, Namibia. A third outbreak occurred in September 2018 in the north of the country approximately 800 km from the original outbreaks. Sample collection and molecular epidemiological analyses revealed that the outbreaks were most likely caused by poor vaccination practices leading to the reversion to virulence of an ILT vaccine strain. The analyses also indicate that inaccurate declarations were made by one of the farms involved and that illegal movement of animals most likely occurred.

Retrospective analysis of infectious laryngotracheitis in backyard chicken flocks in California, 2007-2017, and determination of strain origin by partial ICP4 sequencing

Infectious laryngotracheitis (ILT) can cause severe losses in backyard flocks (BYFs) and commercial poultry. The prevalence of ILT, the circulating strains of ILT virus (ILTV) in BYFs, and the correlation of disease in BYF and commercial operations, is largely unknown. Of 8,656 BYF submissions, 88 cases of ILT were diagnosed at the California Animal Health and Food Safety Laboratory System in 2007-2017. ILT diagnosis by year varied from 0.19% to 1.7% of the total BYF submissions, with the highest number of cases submitted from Amador and Riverside counties. Moderate tracheitis, conjunctivitis, and occluded tracheal lumen were commonly reported gross anatomic lesions. Microscopically, inflammation and edema were observed in the trachea, lung, and conjunctiva; 62 (70%) cases had intranuclear inclusion bodies (INIBs), with 10 cases containing INIBs only in conjunctival sections. To analyze the circulating ILTV strains and to differentiate between field and vaccine strains of ILTV, real-time PCR and sequencing of 996 base pairs of the infected-cell polypeptide 4 ( ICP4) gene was performed on 15 ILTV-positive tracheal samples and compared to reference field and vaccine ILTV ICP4 sequences in GenBank. Fourteen strains were identical or closely related to the chicken embryo origin live virus vaccine strains, and one strain was closely related to a Chinese isolate, the USDA reference strain, and a vaccine strain. The presence of ILT in BYFs in counties with high commercial poultry concentrations demonstrates a risk for disease transmission and emphasizes the importance of continued surveillance and improved biosecurity in BYFs.

MinION sequencing to genotype US strains of infectious laryngotracheitis virus

Over the last decade the US broiler industry has fought long-lasting outbreaks of infectious laryngotracheitis (ILTV). Previously, nine genotypes (I-IX) of ILTVs have been recognized using the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method with three viral alleles (gB, gM and UL47/gG). In this study, the genotyping system was simplified to six genotypes by amplicon sequencing and examining discriminating single nucleotide polymorphisms (SNPs) within these open reading frames. Using phylogenomic analysis of 27 full genomes of ILTV, a single allele (ORF A/ORF B) was identified containing SNPs that could differentiate ILTVs into genotypes congruent with the phylogenetic partitioning. The allelic variations allowed for the cataloging of the 27 strains into 5 genotypes: vaccinal TCO, vaccinal CEO, virulent CEO-like, virulent US and virulent US backyard flocks from 1980 to 1990, correlating with the PCR-RFLP genotypes I/ II/ III (TCO), IV (CEO), V (virulent CEO-like), VI (virulent US) and VII/VIII/IX (virulent US backyard flock isolates). With the unique capabilities of third generation sequencing, we investigated the application of Oxford Nanopore MinION technology for rapid sequencing of the amplicons generated in the single-allele assay. This technology was an improvement over Sanger-based sequencing of the single allele amplicons due to a booster amplification step in the MinION sequencing protocol. Overall, there was a 90% correlation between the genotyping results of the single-allele assay and the multi-allele assay. Surveillance of emerging ILTV strains could greatly benefit from real-time amplicon sequencing using the single-allele assay and MinION sequencing. RESEARCH HIGHLIGHTS A multi-allelic assay identified nine ILTV genotypes circulating in the US Single-allele genotyping is congruent with whole genome phylogenetic partitioning US ILTV strains can be grouped into five genotypes using the single-allele assay The single-allele assay can be done using MinION sequencing of barcoded amplicons.

Development and application of high-resolution melting analysis for the classification of infectious laryngotracheitis virus strains and detection of recombinant progeny

Live attenuated vaccines against infectious laryngotracheitis virus (ILTV) are widely used in the poultry industry to control disease and help prevent economic losses. Molecular epidemiological studies of currently circulating strains of ILTV within poultry flocks in Australia have demonstrated the presence of highly virulent viruses generated by genomic recombination events between vaccine strains. In this study, high-resolution melting (HRM) analysis was used to develop a tool to classify ILTV isolates and to investigate ILTV recombination. The assay was applied to plaque-purified progeny viruses generated after co-infection of chicken embryo kidney (CEK) monolayers with the A20 and Serva ILT vaccine strains and also to viruses isolated from field samples. The results showed that the HRM analysis is a suitable tool for the classification of ILTV isolates and can be used to detect recombination between ILTV vaccine strains in vitro. This method can be used to classify a broad range of ILTV strains to facilitate the classification and genotyping of ILTV and help to further understand recombination in these viruses.

Occurrence of infectious laryngotracheitis outbreaks in commercial layer hens detected by ELISA

Infectious laryngotracheitis (ILT) is an acute respiratory disease of chickens and a cause of great economic loss in commercial layers. The aims of this study were to investigate the prevalence of ILT in the field outbreaks and to compare the characteristics of ILT-infected and free flocks of commercial layers. A total of 625 blood serum samples were collected from 25 different layer flocks. The presence of antibodies against infectious laryngotracheitis virus (ILTV) in each sample was determined by ELISA. Of the 625 serum samples, 266 (42.56%) were found to be positive for ILTV antibodies. A total of 16 (64%) flocks were detected ILT positive by ELISA method. The mortality of infected flocks was statistically higher (P < 0.05) than uninfected flocks. The egg production of positive flocks was lower than that of the free flocks, but this difference was not statistically significant. The average live weight of hens in infected flocks was lower (P > 0.05) than hens in free flocks. In conclusion, the results of this study indicated a high prevalence of ILT infection in the commercial layer flocks in Konya region, Turkey. In outbreaks, ILT significantly increased the mortality rate and decreased the average live weight in layer hens.

Genotyping of infectious laryngotracheitis virus using allelic variations from multiple genomic regions

Live attenuated vaccines are extensively used worldwide to control the outbreak of infectious laryngotracheitis. Virulent field strains showing close genetic relationship with the infectious laryngotracheitis virus (ILTV) vaccines of chicken embryo origin have been detected in the poultry industry. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, a reliable molecular epidemiological method, of multiple genomic regions was performed. The PCR-RFLP is a time-consuming method that requires considerable amount of intact viral genomic DNA to amplify genomic regions greater than 4 kb. In this study, six variable genomic regions were selected and amplified for sequencing. The multi-allelic PCR-sequence genotyping showed better discrimination power than that of previous PCR-sequencing schemes using single or two target regions. The allelic variation patterns yielded 16 strains of ILTV classified into 14 different genotypes. Three Korean field strains, 550/05/Ko, 0010/05/Ko and 40032/08/Ko, were found to have the same genotype as the commercial vaccine strain, Laryngo Vac (Zoetis, Florham Park, NJ, USA). Three other Korean field strains, 40798/10/Ko, 12/07/Ko, and 30678/14/Ko, showed recombined allelic patterns. The multi-allelic PCR-sequencing method was proved to be an efficient and practical procedure to classify the different strains of ILTV. The method could serve as an alternate diagnostic and differentiating tool for the classification of ILTV, and contribute to understanding of the epidemiology of the disease at a global level.

Full Genome Sequence-Based Comparative Study of Wild-Type and Vaccine Strains of Infectious Laryngotracheitis Virus from Italy

Infectious laryngotracheitis (ILT) is an acute and highly contagious respiratory disease of chickens caused by an alphaherpesvirus, infectious laryngotracheitis virus (ILTV). Recently, full genome sequences of wild-type and vaccine strains have been determined worldwide, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. Genomes of three ILTV field isolates from outbreaks occurred in Italy in 1980, 2007 and 2011, and two commercial chicken embryo origin (CEO) vaccines were sequenced using the 454 Life Sciences technology. The comparison with the Serva genome showed that 35 open reading frames (ORFs) differed across the five genomes. Overall, 54 single nucleotide polymorphisms (SNPs) and 27 amino acid differences in 19 ORFs and two insertions in the UL52 and ORFC genes were identified. Similarity among the field strains and between the field and the vaccine strains ranged from 99.96% to 99.99%. Phylogenetic analysis revealed a close relationship among them, as well. This study generated data on genomic variation among Italian ILTV strains revealing that, even though the genetic variability of the genome is well conserved across time and between wild-type and vaccine strains, some mutations may help in differentiating among them and may be involved in ILTV virulence/attenuation. The results of this study can contribute to the understanding of the molecular bases of ILTV pathogenicity and provide genetic markers to differentiate between wild-type and vaccine strains.

Persistence of the tissue culture origin vaccine for infectious laryngotracheitis virus in commercial chicken flocks in Brazil

Infectious laryngotracheitis (ILT) is a respiratory disease of great importance that causes serious economic losses in the poultry industry. Its control is based on biosecurity procedures and vaccination programs that use live attenuated vaccines such as tissue culture origin (TCO), chicken embryo origin (CEO), and vectored vaccines. However, problems have been reported, such as the reversion of virulence, virus latency, and field virus outbreaks. Several molecular techniques have been developed to differentiate between the field and vaccine strains. This study was conducted to determine the presence of infectious laryngotracheitis virus (ILTV) in Brazil from 2012 to 2014. PCR-RFLP (restriction fragment length polymorphism) was used to detect and differentiate ILTV strains; DNA sequencing and predictive RFLP analysis were also used for this purpose. Molecular analysis detected the presence of ILTV in 15 samples that were characterized as strains of TCO vaccine origin. This study showed that the ILTV TCO vaccine strain has been circulating in commercial chicken flocks in Brazil since its introduction during the 2002 outbreak.

Characterization of field strains of infectious laryngotracheitis virus in China by restriction fragment length polymorphism and sequence analysis

Nineteen strains of infectious laryngotracheitis virus (ILTV; Gallid herpesvirus 1) were isolated from dead or diseased birds in chicken flocks from different areas of China between 2010 and 2014 and used to investigate ILTV epidemiology. These strains were characterized using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns and sequence analysis of the thymidine kinase (TK) gene. PCR-RFLP analysis showed that the TK gene generated 2 patterns when digested with restriction endonuclease enzymes. Pattern A corresponded to 2 virulent field strains, while pattern B was characteristic of 2 virulent field strains, 15 low pathogenicity field strains, and all vaccine strains. Sequence analysis of the TK gene indicated that the messenger RNA polyadenylation signals could be identified in some isolates where amino acid 252 was threonine, and in those with methionine at that position. The present study has demonstrated that most of the outbreaks of ILT in China were caused either by low virulence strains or by vaccine-related strains, and also emphasizes the importance of reinforcing ILTV surveillance in both vaccinated and nonvaccinated flocks.

Development of reverse transcription recombinase polymerase amplification assay for avian influenza H5N1 HA gene detection

The 2006 outbreaks of H5N1 avian influenza in Egypt interrupted poultry production and caused staggering economic damage. In addition, H5N1 avian influenza viruses represent a significant threat to public health. Therefore, the rapid detection of H5 viruses is very important in order to control the disease. In this study, a qualitative reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of hemagglutinin gene of H5 subtype influenza viruses was developed. The results were compared to the real-time reverse transcription polymerase chain reaction (RT-PCR). An in vitro transcribed RNA standard of 970 nucleotides of the hemagglutinin gene was developed and used to determine the assay sensitivity. The developed H5 RT-RPA assay was able to detect one RNA molecule within 7 min, while in real-time RT-PCR, at least 90 min was required. H5 RT-RPA assay did not detect nucleic acid extracted from H5 negative samples or from other pathogens producing respiratory manifestation in poultry. The clinical performance of the H5 RT-RPA assay was tested in 30 samples collected between 2014 and 2015; the sensitivity of H5 RT-RPA and real-time RT-PCR was 100%. In conclusion, H5 RT-RPA was faster than real-time RT-PCR and easily operable in a portable device. Moreover, it had an equivalent sensitivity and specificity.

Persistence and spreading of field and vaccine strains of infectious laryngotracheitis virus (ILTV) in vaccinated and unvaccinated geographic regions, in Brazil

Infectious laryngotracheitis (ILT) is a highly infectious respiratory disease that causes morbidity and mortality in commercial chickens. Despite the use of attenuated vaccines, ILT outbreaks have been described in broiler and long-lived birds. Molecular approaches, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing, are used to characterize ILT viruses (ILTVs) detected in vaccinated and unvaccinated geographical regions. As part of an ILT control program implemented in a region of commercial layer production, samples of conjunctiva, trachea, and trigeminal ganglia were collected from chickens in a vaccinated and quarantined region over a period of 8 years after initiation of vaccination. To determine the origin of new ILT outbreaks in unvaccinated regions, samples collected from ill chickens were also analyzed. Chicken embryo origin (CEO) vaccine viruses and the Bastos field strain were detected circulating in healthy chickens in the vaccinated region. CEO strains and field viruses molecularly related to the Bastos strain were also detected outside of the quarantined region in chickens showing clinical signs of ILT. This study reveals the persistence and circulation of a wild field strain, despite the intensive use of tissue culture origin (TCO) and CEO vaccines in a quarantined region. Spreading of CEO viruses to unvaccinated regions and the capacity of this virus to establish latent infections and cause severe outbreaks were also observed.

Molecular characterization of infectious laryngotracheitis virus in naturally infected egg layer chickens in a multi-age flock in Brazil

The virus responsible for an outbreak of infectious laryngotracheitis (ILT) in a multi-age flock of egg layer chickens under quarantine in Brazil was characterized. Layer chickens from this area with circulating gallid herpesvirus 1 (GaHV 1) were evaluated using histopathology and molecular characterization techniques based on sequences of infected-cell polypeptide 4 (ICP4) and thymidine kinase (TK) genes. The infected chickens that were analyzed were PCR-positive for GaHV-1 in the trachea and negative in most trigeminal ganglia. The lack of ILT lesions in the conjunctiva and respiratory tissues, combined with detection of viral DNA in the trachea, was found to be associated with latent infection. The sequences from five farms obtained in the present study were identical, and there were no deletions within the 272- to 283-bp region of the ICP4 gene, as observed in the sequences of vaccine strains (CEO and TCO). The lack of a deletion in the ICP4 fragment analyzed in this study indicates that the chickens were infected with a field virus. The absence of the T252M mutation in a fragment of the TK gene, in addition to the low mortality rate observed, suggests that the outbreak in the state of Minas Gerais was not caused by a highly virulent strain but rather by a field virus of lower virulence. In addition, using phylogenetic reconstructions, it was found that this field strain was grouped together in a separate branch, apart from the previously characterized Brazilian strains. The introduction of vectored vaccines apparently has been effective in reducing clinical disease and lesions, and preventing new outbreaks of disease.

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.

Prevalence and differentiation of diseases in Maryland backyard flocks

Several epidemiologic surveillance studies have implicated backyard flocks as a reservoir for poultry diseases; however, much debate still exists over the risk these small flocks pose. To evaluate this concern, the prevalence of Newcastle disease (ND), infectious laryngotracheitis (ILT), Mycoplasma gallisepticum (MG), and Salmonella was determined in 39 Maryland backyard flocks. Serum, tracheal, and cloacal swabs were randomly collected from 262 birds throughout nine counties in Maryland. Through PCR and ELISA analysis, disease prevalence and seroprevalence were determined in flocks, respectively, for the following: ND (0%, 23%); ILT (26%, 77%); MG (3%, 13%); and Salmonella (0%, not done). Vaccine status could not be accurately confirmed. Premise positives were further differentiated and identified by partial nucleotide sequencing. Screening of the 10 ILT premise positives showed that most were live attenuated vaccines: eight matched a tissue culture origin vaccine, one matched a chicken embryo origin (CEO) vaccine, and one was CEO related. The single MG-positive flock, also positive for the CEO-related sequence, was identified as the infectious S6 strain. The prevalence rates for these economically important poultry diseases ranged from none to relatively low, with the vast majority of sampled flocks presenting no clinical signs.

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.