Two decades of one health surveillance of Nipah virus in Thailand

BACKGROUND

Nipah virus (NiV) infection causes encephalitis and has > 75% mortality rate, making it a WHO priority pathogen due to its pandemic potential. There have been NiV outbreak(s) in Malaysia, India, Bangladesh, and southern Philippines. NiV naturally circulates among fruit bats of the genus Pteropus and has been detected widely across Southeast and South Asia. Both Malaysian and Bangladeshi NiV strains have been found in fruit bats in Thailand. This study summarizes 20 years of pre-emptive One Health surveillance of NiV in Thailand, including triangulated surveillance of bats, and humans and pigs in the vicinity of roosts inhabited by NiV-infected bats.

METHODS

Samples were collected periodically and tested for NiV from bats, pigs and healthy human volunteers from Wat Luang village, Chonburi province, home to the biggest P. lylei roosts in Thailand, and other provinces since 2001. Archived cerebrospinal fluid specimens from encephalitis patients between 2001 and 2012 were also tested for NiV. NiV RNA was detected using nested reverse transcription polymerase chain reaction (RT-PCR). NiV antibodies were detected using enzyme-linked immunosorbent assay or multiplex microsphere immunoassay.

RESULTS

NiV RNA (mainly Bangladesh strain) was detected every year in fruit bats by RT-PCR from 2002 to 2020. The whole genome sequence of NiV directly sequenced from bat urine in 2017 shared 99.17% identity to NiV from a Bangladeshi patient in 2004. No NiV-specific IgG antibodies or RNA have been found in healthy volunteers, encephalitis patients, or pigs to date. During the sample collection trips, 100 community members were trained on how to live safely with bats.

CONCLUSIONS

High identity shared between the NiV genome from Thai bats and the Bangladeshi patient highlights the outbreak potential of NiV in Thailand. Results from NiV cross-sectoral surveillance were conveyed to national authorities and villagers which led to preventive control measures, increased surveillance of pigs and humans in vicinity of known NiV-infected roosts, and increased vigilance and reduced risk behaviors at the community level. This proactive One Health approach to NiV surveillance is a success story; that increased collaboration between the human, animal, and wildlife sectors is imperative to staying ahead of a zoonotic disease outbreak.

A spatial assessment of Nipah virus transmission in Thailand pig farms using multi-criteria decision analysis

BACKGROUND

Thailand's Central Plain is identified as a contact zone between pigs and flying foxes, representing a potential zoonotic risk. Nipah virus (NiV) has been reported in flying foxes in Thailand, but it has never been found in pigs or humans. An assessment of the suitability of NiV transmission at the spatial and farm level would be useful for disease surveillance and prevention. Multi-criteria decision analysis (MCDA), a knowledge-driven model, was used to map contact zones between local epizootic risk factors as well as to quantify the suitability of NiV transmission at the pixel and farm level.

RESULTS

Spatial risk factors of NiV transmission in pigs were identified by experts as being of three types, including i) natural host factors (bat preferred areas and distance to the nearest bat colony), ii) intermediate host factors (pig population density), and iii) environmental factors (distance to the nearest forest, distance to the nearest orchard, distance to the nearest water body, and human population density). The resulting high suitable areas were concentrated around the bat colonies in three provinces in the East of Thailand, including Chacheongsao, Chonburi, and Nakhonnayok. The suitability of NiV transmission in pig farms in the study area was quantified as ranging from very low to medium suitability.

CONCLUSIONS

We believe that risk-based surveillance in the identified priority areas may increase the chances of finding out NiV and other bat-borne pathogens and thereby optimize the allocation of financial resources for disease surveillance. In the long run, improvements of biosecurity in those priority areas may also contribute to preventing the spread of potential emergence of NiV and other bat-borne pathogens.

Genetic variations of nucleoprotein gene of influenza A viruses isolated from swine in Thailand

Background

Influenza A virus causes severe disease in both humans and animals and thus, has a considerably impact on economy and public health. In this study, the genetic variations of the nucleoprotein (NP) gene of influenza viruses recovered from swine in Thailand were determined.

Results

Twelve influenza A virus specimens were isolated from Thai swine. All samples were subjected to nucleotide sequencing of the complete NP gene. Phylogenetic analysis was conducted by comparing the NP gene of swine influenza viruses with that of seasonal and pandemic human viruses and highly pathogenic avian viruses from Thailand (n = 77). Phylogenetic analysis showed that the NP gene from different host species clustered in distinct host specific lineages. The NP gene of swine influenza viruses clustered in either Eurasian swine or Classical swine lineages. Genetic analysis of the NP gene suggested that swine influenza viruses circulating in Thailand display 4 amino acids unique to Eurasian and Classical swine lineages. In addition, the result showed 1 and 5 amino acids unique to avian and human lineages, respectively. Furthermore, nucleotide substitution rates showed that the NP gene is highly conserved especially in avian influenza viruses.

Conclusion

The NP gene sequence of influenza A in Thailand is highly conserved within host-specific lineages and shows amino acids potentially unique to distinct NP lineages. This information can be used to investigate potential interspecies transmission of influenza A viruses. In addition, the genetic variations of the NP gene will be useful for monitoring the viruses and preparing effective prevention and control strategies for potentially pandemic influenza outbreaks.

Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand

Background  Recent studies have revealed the existence of genetic diversity in swine influenza viruses (SIVs) in the world. In Thailand, there has been a little information on the molecular characteristics of the SIVs since the first isolation of viruses of H1N1 and H3N2 subtypes in the late 1970s. Our previous study demonstrated that Thai H1N1 SIVs possessed the classical swine H1 and avian‐like swine N1 genes (Takemae et al., Proceedings of the Options for the Control of Influenza VI.2007;350–353).

Objectives  In the present study, we genetically characterized 12 SIVs including those of H1N1, H1N2 and H3N2 subtypes isolated between 2000 and 2005.

Methods  We determined the entire nucleotide sequences of the eight gene segments of those isolates.

Results  Phylogenetic analysis revealed the existence of nine distinct genotypes amongst the Thai SIVs. These genotypes arose from multiple introductions of classical swine, avian‐like swine and human viruses. The existence of two distinct sublineages within classical swine H1 and NS, avian‐like swine PA and M and human H3 and N2 genes of the Thai SIVs suggested that introduction of viruses of classical swine, avian‐like swine and human origins occurred twice respectively into the Thai pig population. The predominance of avian‐like swine genes amongst the Thai SIVs was evident. In particular, three polymerase (PB1, PB2 and PA) and matrix genes of avian‐like swine origin were retained in all the Thai SIVs examined.

Conclusions  These observations may suggest that genes of avian‐like swine lineages have some advantages to be maintained in pigs as seen in the SIVs established through multiple introductions in other regions.

Qualitative detection of avian influenza A (H5N1) viruses: a comparative evaluation of four real-time nucleic acid amplification methods

The aim of this study was to determine the performance of real-time amplification based methods - NASBA, TaqMan, RT-FRET, and RT-PCR LUXtrade mark formats - for the detection of influenza A (H5N1) virus RNA. In an analysis of 54 samples obtained from a range of animal species in Thailand during the period 2003-2006, results showed that the NASBA (H5=98.2%, N1=96.3%), TaqMan (H5=98.2%, N1=96.3%) and FRET (H5=98.2%, N1=96.3%) had significantly higher rates of positive detection than LUX (H5=94.4%, N1=50.0%; P<0.001) for influenza A, H5 and N1 isolates. There were no false-positive results from any methods used in the negative-control group of samples. The limits of analytical detection were at least 10copies/reaction in real-time NASBA and LUX assays, while FRET and TaqMan assay appeared to be less sensitive at > or =100copies/reaction. The assays were relatively specific without cross-reactivity to a number of other influenza strains or viral pathogens. In conclusion, our study demonstrated that real-time NASBA, TaqMan and FRET assays can be used to detect influenza A (H5N1) from a wide range of hosts, and be specific for H5N1 samples obtained during different outbreaks (2003-2006). All assays provided the benefit of rapid influenza H5N1 identification for early diagnosis, in the range of hours, and they are well suited to high throughput analyses.

Geographic and Temporal Distribution of Highly Pathogenic Avian Influenza A Virus (H5N1) in Thailand, 2004–2005: An Overview

Outbreaks of H5N1 highly pathogenic avian influenza (HPAI) occurred in various types of domestic poultry in Thailand during 2004-05. H5N1 viruses were also detected in humans and other mammalian species. Infections were mainly detected in backyard chickens and domestic ducks. The geographic distribution of the 2004 outbreaks was widespread throughout Thailand; most outbreaks occurred in the Central Region, the southern part of the Northern Region, and the Eastern Region. In 2005, the H5N1 outbreaks continued and showed a clustered pattern in four provinces in the southern part of the Northern Region and in one province in the Central Region. H5N1 HPAI outbreaks caused serious socioeconomic consequences to the poultry industry, the social community, farmers' livelihood, and human health. After key measures were implemented, the incidence of the outbreaks declined remarkably in 2005.

Factors critical for successful vaccination against classical swine fever in endemic areas

Classical swine fever (CSF) or hog cholera, caused by the classical swine fever virus (CSFV), is one of the most important viral diseases that cause serious economic loss to the swine industry worldwide. During the past 5 years, several techniques for measuring porcine cell-mediated immunity (CMI) were applied, in conjunction with other conventional techniques, to study factors that influence the induction of CSFV-specific immunity. Information, obtained from a series of experiments, demonstrated cell-mediated immune responses in providing protective immunity against CSF infection. Although it has been confirmed that commercially available modified live CSF vaccines are able to induce complete protection in vaccinated pigs, several factors including maternal immunity, the age of primary vaccination, vaccination protocol and complications caused by other pathogens, can greatly affect the effectiveness of CSF vaccines in the field.

The Single-Step Multiplex Reverse Transcription- Polymerase Chain Reaction Assay for Detecting H5 and H7 Avian Influenza A Viruses

Avian influenza (AI) A virus subtypes H5 and H7 cause severe disease in domestic poultry, including chickens and turkeys. Moreover, H5 and H7 AI A viruses can cross the species barrier from poultry to humans. In the present study, we have developed a single-step multiplex reverse transcription-polymerase chain reaction assay (RT-PCR) for detecting H5 and H7 AI A viruses. This assay was applied to the poultry isolates with the aim of establishing a surveillance method to monitor possible transmission to humans. Two subtype-specific primer sets capable of producing PCR products of 157 and 326 base pairs corresponding to AI A virus H5 and H7 subtypes, respectively, were utilized in a one-step and one-tube reaction. The single-step multiplex RT-PCR assay developed in this study was found to be specific for detecting H5 and H7 AI A viruses. No specific amplification bands were detected with total nucleic acids extracted from other influenza hemagglutinin subtypes and other viral pathogens. The sensitivity of this assay was about 10(3) RNA copies/microl. In conclusion, this novel single-step multiplex RT-PCR is a simple assay with high potential for rapid, specific and cost effective laboratory diagnosis of H5 and H7 AI A virus isolates from clinical specimens of poultry.

H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes

A single amino acid substitution, from histidine to tyrosine at position 274 of the neuraminidase gene has converted Oseltamivir sensitive H5N1 influenza A virus into a resistant strain. Currently, Oseltamivir is being stockpiled in many countries potentially affected by the influenza A virus subtype H5N1 epidemic. To identify this change in Oseltamivir-treated patients, a method based on real-time PCR using two labeled TaqMan probes was developed for its rapid detection. In order to validate the method, Oseltamivir specimen from treated (Oseltamivir-resistant strain from a Vietnamese patient, two Oseltamivir-treated tigers) and untreated subjects have been used for this study. The results thus obtained as well as those derived from clone selection and sequencing showed that TaqMan probes could clearly discriminate wild type H274 from the mutant 274Y variant. The sensitivity of this assay was as low as 10 copies/microl and allowed the detection of the mutation in a mixture of wild type and mutant. Overall, the assay based on real-time PCR with two labeled TaqMan probes described here should be useful for detecting Oseltamivir-resistant H274Y H5N1 influenza A virus in many species and various sources of specimens with high sensitivity and specificity. Such studies can address potential differences in the diagnostic outcomes between patients who develop detectable Oseltamivir resistance and those who retain only the wild type strain of H5N1.

Expression of hemagglutinin protein from the avian influenza virus H5N1 in a baculovirus/insect cell system significantly enhanced by suspension culture

Background

Prevention of a possible avian influenza pandemic necessitates the development of rapid diagnostic tests and the eventual production of a vaccine.

Results

For vaccine production, hemagglutinin (HA1) from avian influenza H5N1 was expressed from a recombinant baculovirus. Recombinant HA1 was expressed in monolayer or suspension culture insect cells by infection with the recombinant baculovirus. The yield of rHA1 from the suspension culture was 68 mg/l, compared to 6 mg/l from the monolayer culture. Immunization of guinea pigs with 50 μg of rHA1 yielded hemagglutinin inhibition and virus neutralization titers of 1:160 after two times vaccination with rHA1 protein.

Conclusion

Thus, the production of rHA1 using an insect suspension cell system provides a promising basis for economical production of a H5 antigen.

The kinetics of cytokine production and CD25 expression by porcine lymphocyte subpopulations following exposure to classical swine fever virus (CSFV)

Surface expression of IL-2R-alpha (CD25) is widely used to identify activated lymphocyte populations, while interferon-gamma (IFN-gamma) levels have been shown to be a good indicator of cell-mediated immunity (CMI) in pigs. To investigate the relationship between these two parameters, we developed an intracellular cytokine-staining assay and studied the kinetics of cytokine (IFN-gamma and interleukin-10, IL-10) production relative to CD25 expression in porcine lymphocyte subpopulations, following immunization with a classical swine fever (CSF) vaccine. The number of activated memory T cells (CD4(+)CD8(+)CD25(+) cells) increased slightly in the peripheral blood mononuclear cell (PBMC) population soon after vaccination, then diminished within a few weeks. The number of activated cytotoxic T cells (CD4(-)CD8(+)CD25(+) cells) peaked approximately 2 weeks after the memory population. Although the number of IFN-gamma producing cells detected in this experiment was relatively low, the CD4(+)CD8(+) T cells were major IFN-gamma producers in the PBMCs throughout the experiment. In another experiment, CSF-vaccinated pigs were challenged with a virulent classical swine fever virus (CSFV), and the kinetics of CD25 expression and cytokine productions were monitored. Following exposure to the virus, the number of IFN-gamma producing cells in the PBMCs increased markedly in both the vaccinated and unvaccinated groups. The CD4(-)CD8(+) cells were major IFN-gamma producing cells in vaccinated pigs, while both CD4(+)CD8(+) and CD4(-)CD8(+) populations contributed to the IFN-gamma production in the control group. Interestingly, the enhanced IFN-gamma production was not associated with the upregulation of CD25 expression following the CSFV challenge. In addition, exposure to the virulent CSFV significantly increased interleukin-10 production by the CD4(-)CD8(+) populations in PBMCs of the unvaccinated pigs. Taken together, our results indicated that CD25 expression and IFN-gamma production were not tightly associated in porcine lymphocytes. In addition, the CD4(-)CD8(+) lymphocytes of the PBMCs played a major role in cytokine productions following the CSFV challenge.

Probable tiger-to-tiger transmission of avian influenza H5N1

During the second outbreak of avian influenza H5N1 in Thailand, probable horizontal transmission among tigers was demonstrated in the tiger zoo. Sequencing and phylogenetic analysis of those viruses showed no differences from the first isolate obtained in January 2004. This finding has implications for influenza virus epidemiology and pathogenicity in mammals.

Genetics and geographical variation of porcine reproductive and respiratory syndrome virus (PRRSV) in Thailand

The Thai isolates of porcine reproductive and respiratory syndrome virus (PRRSV) were obtained from the Chulalongkorn University-Veterinary Diagnostic Laboratory (CU-VDL). Virus isolation was confirmed by immunoperoxidase monolayer assay (IPMA) using SDOW-17. The virus genotype was determined using nested multiplex RT-PCR (nm RT-PCR) of ORF 1b. The nm RT-PCR was able to detect at least 10TCID50/ml of PRRSV. Of 137 Thai isolates, 66.42% belonged to the European (EU) genotype and 33.58% to the North American (US) genotype. ORF5 products of the eight US strains (00CS1, 01NP1, 01UD6, 02CB13, 02KK1, 02PB1, 02SP2 and 02SP3) and the six EU strains (01CB1, 01RB1, 02BR1, 02CB12, 02SB2 and 03RB1) were sequenced for genetic variation analysis. The US strains of the Thai isolates are clustered within the same group and are more closely related to the IAF-EXP91 from Canada (89-90% nucleotide identity), whereas the EU strains were very similar to the EU prototype, Lelystad virus (87-97.5% nucleotide identity). The ORF5 nucleotide identities within the US genotype tested in this study compared to the US prototype, VR-2332 varied from 83.7 to 85.2%, whereas 83.5-85.5% amino acid identities were found. Based on the phylogenetic tree, each pair of the Thai isolates (01NP1 and 02KK1, 00CS1 and 01UD6, and 01CB1 and 01RB1) was identical despite they were collected from different provinces. Therefore, there was no geographic influence on the spreading of PRRSV in Thailand. Interestingly, 02CB12 (EU genotype) shared over 99% similarity of the ORF5 nucleotide sequence and 98.6% of amino acid identity with the European vaccine, Porcillis (AF378819). However, modified live virus vaccines for PRRSV have not yet been used in the swine population in Thailand. The results suggested that both US and EU genotypes exist in Thailand, genetic variation does occur in both genotypes, and the sources of the viruses appear to be from Canada and Northern Europe, respectively. In addition, the spreading of PRRSV in Thailand might be due to introducing infected replacement pigs or infected semen into the farm.

The influence of maternal immunity on the efficacy of a classical swine fever vaccine against classical swine fever virus, genogroup 2.2, infection

In Thailand, where vaccination is routinely employed, there has been an increased incidence of chronic classical swine fever (CSF) outbreaks during the past decade. The major causative virus has been identified to be the moderate virulence, classical swine fever virus (CSFV) of the genogroup 2.2. An investigation was made into the efficacy of a CSF vaccine against this genogroup 2.2 challenge. Five-week-old pigs, grouped by their level of passive antibody titer were immunized with lapinized Chinese-strain CSF vaccine and challenged with CSFV genogroup 2.2, 13 days after vaccination. The group containing passive titers of lower than 64 at the time of immunization, had significantly higher number of CSFV-specific IFN-gamma secreting cells and was completely protected against the challenge. Interestingly, both cellular and antibody responses were inhibited in the pigs with the higher passive titer. Furthermore, following challenge, CSFV could be isolated from 50% of the pigs in this group. It was demonstrated that the CSF vaccine could induce complete protection in pigs, provided that the maternal derived titer at the time of vaccination was lower than 64. The result implied that an increase in CSFV outbreaks might be due to the inappropriate timing of vaccination as well as the nature of the CSFV genogroup 2.2.

The correlation of virus-specific interferon-gamma production and protection against classical swine fever virus infection

The level of antigen-specific interferon-gamma (IFN-gamma) production can be used as an indicator of cellular immunity. In this study, we investigated the role of cellular immune response in protection against classical swine fever virus (CSFV). Pigs were vaccinated once with CSFV vaccine and challenged 6 days post-vaccination (dpv). Vaccinated animals had significantly higher CSFV-specific IFN-gamma secreting cells than the unvaccinated pigs (p<0.05) at the time of challenge and were protected against CSFV infection, whereas the control pigs died within 14 days post-infection (dpi). In the second experiment, pigs were vaccinated once with either CSFV vaccine or CSFV vaccine combined with Aujeszky's disease (AD) vaccine and challenged at 140 dpv. All vaccinated pigs developed both CSFV-specific, cellular and antibody responses and were protected against CSFV infection. However, differences in cellular, but not antibody, responses were observed in the two vaccinated groups. The group vaccinated with CSFV vaccine developed a significantly higher number of CSFV-specific, IFN-gamma secreting cells (p<0.05), exhibited a shorter fever period and less pathological changes, when compared with the group vaccinated with the combined vaccine. The kinetics of IFN-gamma production, following challenge in the two vaccinated groups, were also different. Taken together, our results indicated that CSFV-specific, IFN-gamma production could be detected early after antigen exposure and correlated with protection against CSFV challenge. Our findings highlight the role of cellular immune responses in porcine anti-viral immunity.

Sequence analysis of E2 glycoprotein genes of classical swine fever viruses: identification of a novel genogroup in Thailand

Thirty classical swine fever viruses (CSFV) isolated in Thailand between 1988 and 1996 were characterised by genetic sequence analysis of a part of their E2 coding regions, comparing the new data with that for representative reference viruses from other countries and continents. Thai isolates were divided into three distinct genogroups, indicating multiple origins for the outbreaks. Eighteen isolates from 1988-1995 form a new genogroup not previously described from any other geographical region. Eleven isolates from 1988-1995 are in the same genogroup as old US and European strains represented by reference strains Alfort 187 and Brescia. The viruses of this group seem to have died out in Europe but still persist in Thailand. One recent isolate from 1996 represents another previously described genogroup being closely related to Italian viruses isolated in the same year.

Genetic grouping of classical swine fever virus by restriction fragment length polymorphism of the E2 gene

A method for genetic grouping of classical swine fever viruses (CSFV) was developed based on the restriction fragment length polymorphism (RFLP) revealed by AvaII, BanII and PvuII digestion of RT-PCR amplified segments of the E2 gene. From inspection of the genetic sequences of Thai isolates and reference strains, the RFLP method was designed to be capable of differentiating all known genogroups and subgenogroups suggested by phylogenetic analysis of the CSFV E2 gene. The method was applied to 60 CSFV samples which included three genogroups and seven subgenogroups. Unlike previously described RFLP methods, the agarose gel patterns obtained from these samples were completely in agreement with the predicted RFLP patterns and enabled accurate genetic grouping of CSFV at the subgenogroup level. The simplicity of this method allows rapid CSFV genogrouping at diagnostic laboratories without sequencing facilities and provides a useful method for diagnosis as well as epidemiological investigation and control of classical swine fever outbreaks.

Genetic heterogeneity of porcine and ruminant pestiviruses mainly isolated in Japan

The genetic variability of porcine and ruminant pestiviruses was studied by comparative nucleotide sequence analysis of 73 isolates (42 porcine and 31 ruminant), including 65 Japanese isolates (35 porcine and 30 ruminant). The 5'-untranslated region (UTR) amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) was determined by direct sequencing and phylogenetic analysis was performed from the nucleotide sequence data. Most porcine isolates were divided into two major subgroups, classical swine fever virus (CSFV) subgroup 1 (CSFV-1, represented by Brecia strain) and subgroup 2 (CSFV-2, represented by Alfort strain). However, the Japanese Kanagawa/74, Okinawa/86, Okinawa/86-2 and Thai CBR/93 strains were the most distinct variants and these were assigned to another new disparate subgroup, CSFV-3 (represented by p97 strain). Most ruminant isolates were classified as the bovine viral diarrhoea virus (BVDV) genotype-I (BVDV-I) and subdivided into two subgroups, BVDV-Ia (represented by the NADL strain) and Ib (represented by the Osloss strain). Two bovine isolates (MS-1 and SY-89) and a contaminating strain (V/FLL) from an ovine cell line were classified as BVDV genotype-II (BVDV-II) on genetic characteristics. These data suggested that the detection and phylogenetic analysis of 5'-UTRs are useful for the rapid characterization of field isolates.