The genomic landscape of swine influenza A viruses in Southeast Asia.

Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza A virus (swIAV). Effective surveillance is essential to uncover emerging virus strains; however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. More than 4,000 nasal swabs were collected from pigs in Cambodia, yielding 72 IAV-positive samples by RT-qPCR and 45 genomic sequences. We unmasked the cocirculation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swIAV reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two and 15 B.P., indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.

Detection of Clade 2.3.4.4b Avian Influenza A(H5N8) Virus in Cambodia, 2021.

In late 2021, highly pathogenic avian influenza A(H5N8) clade 2.3.4.4b viruses were detected in domestic ducks in poultry markets in Cambodia. Surveillance, biosafety, and biosecurity efforts should be bolstered along the poultry value chain to limit spread and infection risk at the animal-human interface.

Abattoir-based serological surveillance for transboundary and zoonotic diseases in cattle and swine in Cambodia: a pilot study in Phnom Penh province during 2019 and 2020.

A pilot animal disease surveillance program was implemented at four abattoirs in Phnom Penh, Cambodia, between October 2019 and January 2020. A total of 1141 samples were collected from 477 cattle and 664 swine. Serological testing was performed using commercial antibody ELISA kits for zoonotic and high-impact animal diseases, namely brucellosis, Q fever, classical swine fever (CSF), porcine reproductive and respiratory syndrome (PRRS) and African swine fever (ASF). Only two samples tested positive for Brucella antibodies (0.2%, 95% CI 0.4-0.6, n = 1141). The seroprevalence of Q fever was 0.8% (95% CI 0.3-2.1, n = 477) in the cattle samples, while CSF, PRRS and ASF in pigs were 55.4% (95% CI 51.6-59.2, n = 655), 81.2% (95% CI 78.1-84.0, n = 655) and 2.6% (95% CI 1.6-4.1, n = 664), respectively. All 38 doubtful and 17 positive ASF antibody ELISA samples were negative when tested by real-time PCR. Univariate analyses demonstrated that the factor significantly associated with positive results of ASF was the abattoir location (p-value = 0.002). Based on logistic regression models, significant risk factors for CSF were province of origin (p-value = 1.7 × 10-6), abattoir (p-value = 3.6 × 10-11) and PRRS positivity (p-value = 0.004), and for PRRS were province of origin (p-value = 0.0004) and CSF positivity (p-value = 0.001). In conclusion, the seroprevalences of zoonotic diseases in this study were very low. The high prevalence of CSF and PRRS antibodies were most likely the result of vaccination. All ASF seropositive pigs, including those that gave equivocal results, originated from large-scale Cambodian-based commercial farms, as well as Thailand, which raises questions about possible illegal vaccination or low-pathogenicity ASF variants. The pilot abattoir serological surveillance program described here has the potential to provide a sentinel for incursions of novel and endemic pathogens, although further work is required to demonstrate its capacity to provide information on the longitudinal disease trends.

Detection of Low Pathogenicity Influenza A(H7N3) Virus during Duck Mortality Event, Cambodia, 2017.

In January 2017, an estimated 3,700 (93%) of 4,000 Khaki Campbell ducks (Anas platyrhynchos domesticus) died in Kampong Thom Province, Cambodia. We detected low pathogenicity avian influenza A(H7N3) virus and anatid herpesvirus 1 (duck plague) in the affected flock; however, the exact cause of the mortality event remains unclear.

Co-circulation of Influenza A H5, H7, and H9 Viruses and Co-infected Poultry in Live Bird Markets, Cambodia.

Longitudinal surveillance of 2 live bird markets in Cambodia revealed year-round, high co-circulation of H5, H7, and H9 influenza viruses. We detected influenza A viruses in 51.3% of ducks and 39.6% of chickens, and co-infections, mainly by H5 and H9 viruses, in 0.8% of ducks and 4.5% of chickens.

Seroprevalence of foot-and-mouth disease in the southern provinces of Cambodia.

A serological surveillance study was conducted between March and June 2006 in the southern provinces of Cambodia to determine the prevalence and distribution of foot-and-mouth disease. Cattle and buffalo originating from eight provinces and 69 villages were sampled. The results revealed that the village level prevalence of foot-and-mouth disease (FMD) in the southern provinces of Cambodia was 87% with an overall individual animal prevalence of 30%. Three serotypes: O, A and Asia 1 were detected in this region with a prevalence of 28.5, 9.5 and 9.3%, respectively. However, as the antibody level to FMDV serotypes A and Asia 1 were generally low, it is likely that serotype O is responsible for most of the recent outbreaks of FMD in Cambodia. Seropositive animals were older than seronegative animals, especially with serotype O.

The Importance and Challenges of Implementing and Maintaining Biorepositories for High-Consequence Veterinary and One Health Pathogens in South-East Asia.

Introduction: Emerging infectious diseases pose a threat to public health and the economy, especially in developing countries. Southeast Asian veterinary laboratories handle numerous high-risk pathogens, making pathogen accountability crucial for safe handling and storage. Methods: Thirteen veterinary laboratories in Cambodia (n = 1), Lao People's Democratic Republic (n = 1), and Thailand (n = 11) participated in a study conducted between 2019 and 2020. Data were collected using a questionnaire, group discussions, and interviews. Conclusion: Significant gaps in biosecurity and biorepository management were recognized and discussed in the context of regional biosafety and biosecurity. Laboratories could use the findings and recommendations of the study to develop or improve their pathogen inventory and biosecurity systems. Governments play a significant role in setting standards and regulations and providing necessary support for laboratories to maintain inventory controls sustainably and have a very important role to play in ensuring biosafety and biosecurity compliance.

Detection and phylogenetic analysis of contemporary H14N2 Avian influenza A virus in domestic ducks in Southeast Asia (Cambodia).

Avian influenza virus (AIV) in Asia is a complex system with numerous subtypes and a highly porous wild birds-poultry interface. Certain AIV subtypes, such as H14, are underrepresented in current surveillance efforts, leaving gaps in our understanding of their ecology and evolution. The detection of rare subtype H14 in domestic ducks in Southeast Asia comprises a geographic region and domestic bird population previously unassociated with this subtype. These H14 viruses have a complex evolutionary history involving gene reassortment events. They share sequence similarity to AIVs endemic in Cambodian ducks, and Eurasian low pathogenicity and high pathogenicity H5Nx AIVs. The detection of these H14 viruses in Southeast Asian domestic poultry further advances our knowledge of the ecology and evolution of this subtype and reinforces the need for continued, longitudinal, active surveillance in domestic and wild birds. Additionally, in vivo and in vitro risk assessment should encompass rare AIV subtypes, as they have the potential to establish in poultry systems.

Access to food markets, household wealth and child nutrition in rural Cambodia: Findings from nationally representative data.

Access to informal fresh food markets plays a vital role in household food security and dietary quality in transitioning rural economies. However, it is not well understood if market access also improves child nutrition and if the improvement applies to all socioeconomic groups. In this secondary research study, we combined a national listing of food markets (n = 503) with a national household survey to examine the associations of market access with diet and height across wealth groups in children aged 6 to 23 months in rural Cambodia. All children under two years of age with dietary data (n = 1537) or anthropometry data (n = 989) were selected from the household survey. Food markets were geocoded using Google Maps or villages' geographical coordinates publicly available in the Open Development Mekong data platform. Regression calibration was then used to estimate household distance to the nearest market. Descriptive results indicated a highly uneven distribution of food markets with median household distance to the nearest markets ranging between 4 km (IQR: 3-8 km) in the lowland areas and 9 km (IQR: 4-17 km) in the highland areas. Results from the multivariate linear regressions showed that distance to the nearest market was modestly associated with child dietary diversity score (ß: -0.17; 95% CI: -0.29, -0.05) but it was not related to child height-for-age z-score, and that household wealth did not modify the associations between distance to markets and child dietary diversity score. These findings suggest that improving access to food markets alone might not lead to meaningful improvement in child diet. Detailed surveys on household food acquisition are needed to clarify the role of food markets relative to other food sources such as subsistence fisheries, subsistence gardening and mobile food traders.

Risk mapping using serologic surveillance for selected One Health and transboundary diseases in Cambodian goats.

In Cambodia, goat production and meat consumption are customary among Muslim communities. Recently, goat meat has gained popularity among Cambodians. Goat farmers use a traditional management system, including grazing, requiring minimal labour. The close proximity between humans and animals could increase the risk of zoonotic disease transmission. A serological survey was undertaken to estimate the prevalence of some priority zoonoses and high-impact animal diseases in the Cambodian goat population. A total of 540 samples were collected from goats in six provinces and analysed with commercially available enzyme-linked immunosorbent assays for Brucella species, Q fever (Coxiella burnetii), Foot and Mouth Disease virus non-structural protein (FMDV NSP) and Peste des Petits Ruminants virus (PPRV). True seroprevalences with a 95% Confidence Interval (CI), taking into account imperfect tests, risk factors and odds ratios (ORs), were calculated to better understand the disease distribution and epidemiology. Independent variables used in statistical modellings included sex, body condition score, age, vaccination history, province and commune, while dependent variables were ELISA test results. The overall true prevalence of antibodies to Brucella spp., C. burnetii, FMDV and PPRV, were 0.1% (95% CI 0.0, 1.0), 7.2% (95% CI 5.3, 9.7), 57.7% (95% CI 53.1, 62.3) and 0.0% (95% CI 0.0, 0.0), respectively. There was no identified risk factor for brucellosis and PPR. The two risk factors for C. burnetii seropositivity were sex (p-value = 0.0005) and commune (p-value <0.0001). However, only the OR of C. burnetii seropositive female goat was significant at 9.7 (95% CI 2.7, 35.5) times higher than male. The risk factors of FMD NSP seropositivity were age (p-value = 0.001) and commune (p-value <0.0001). Only the age 'more than two-year-old' group with a significant OR of 6.2 (95% CI 2.1, 18.4) using the 'up to one-year-old' group as the reference. In summary, Brucella spp. seroprevalence was low, while no evidence of PPRV antibodies was detected in the goat populations. C. burnetii seroprevalence in female goats was significantly higher than for males, and there were significant differences in C. burnetii seroprevalence between communes. The overall FMDV NSP seroprevalence was high, especially in older animals. Vaccination should be advocated to protect animals from FMDV and improve productivity. As the impacts of these zoonoses on human and animal health were still unknown, further investigation of these zoonotic diseases' epidemiology is recommended.

Aerosol exposure of live bird market workers to viable influenza A/H5N1 and A/H9N2 viruses, Cambodia.

Live bird markets (LBMs) have been identified as key factors in the spread, persistence and evolution of avian influenza viruses (AIVs). In addition, these settings have been associated with human infections with AIVs of pandemic concern. Exposure to aerosolised AIVs by workers in a Cambodian LBM was assessed using aerosol impact samplers. LBM vendors were asked to wear an air sampler for 30 min per day for 1 week while continuing their usual activities in the LBM during a period of high AIV circulation (February) and a period of low circulation (May). During the period of high circulation, AIV RNA was detected from 100% of the air samplers using molecular methods and viable AIV (A/H5N1 and/or A/H9N2) was isolated from 50% of air samplers following inoculation into embryonated chicken eggs. In contrast, AIV was not detected by molecular methods or successfully isolated during the period of low circulation. This study demonstrates the increased risk of aerosol exposure of LBM workers to AIVs during periods of high circulation and highlights the need for interventions during these high-risk periods. Novel approaches, such as environmental sampling, should be further explored at key high-risk interfaces as a potentially cost-effective alternative for monitoring pandemic threats.

Case report: Lumpy skin disease in an endangered wild banteng (Bos javanicus) and initiation of a vaccination campaign in domestic livestock in Cambodia.

We describe a case of lumpy skin disease in an endangered banteng in Cambodia and the subsequent initiation of a vaccination campaign in domestic cattle to protect wild bovids from disease transmission at the wildlife-livestock interface. Lumpy skin disease virus (LSDV) was first detected in domestic cattle in Cambodia in June of 2021 and rapidly spread throughout the country. In September 2021, a banteng was seen in Phnom Tnout Phnom Pok wildlife sanctuary with signs of lumpy skin disease. Scab samples were collected and tested positive for LSDV. Monitoring using line transect surveys and camera traps in protected areas with critical banteng and gaur populations was initiated from December 2021-October 2022. A collaborative multisector vaccination campaign to vaccinate domestic livestock in and around priority protected areas with banteng and gaur was launched July 2022 and a total of 20,089 domestic cattle and water buffalo were vaccinated with LumpyvaxTM. No signs of LSDV in banteng or gaur in Cambodia have been observed since this initial case. This report documents the first case of lumpy skin disease in wildlife in Cambodia and proposes a potential intervention to mitigate the challenge of pathogen transmission at the domestic-wildlife interface. While vaccination can support local livestock-based economies and promote biodiversity conservation, it is only a component of an integrated solution and One Health approach to protect endangered species from threats at the wildlife-livestock interface.

Experimental cross-contamination of chicken salad with Salmonella enterica serovars Typhimurium and London during food preparation in Cambodian households.

Non-typhoidal Salmonellae are common foodborne pathogens that can cause gastroenteritis and other illnesses in people. This is the first study to assess the transfer of Salmonella enterica from raw chicken carcasses to ready-to-eat chicken salad in Cambodia. Twelve focus group discussions in four Cambodian provinces collected information on typical household ways of preparing salad. The results informed four laboratory experiments that mimicked household practices, using chicken carcasses inoculated with Salmonella. We developed four scenarios encompassing the range of practices, varying by order of washing (chicken or vegetables first) and change of chopping utensils (same utensils or different). Even though raw carcasses were washed twice, Salmonella was isolated from 32 out of 36 chicken samples (88.9%, 95% CI: 73.0-96.4) and two out of 18 vegetable samples (11.1%, 95% CI: 1.9-36.1). Salmonella was detected on cutting boards (66.7%), knives (50.0%) and hands (22.2%) after one wash; cross-contamination was significantly higher on cutting boards than on knives or hands (p-value < 0.05). The ready-to-eat chicken salad was contaminated in scenario 1 (wash vegetables first, use same utensils), 2 (wash vegetables first, use different utensils) and 3 (wash chicken first, use same utensils) but not 4 (wash chicken first, use different utensils) (77.8%, 11.1%, 22.2% and 0%, respectively). There was significantly higher Salmonella cross-contamination in scenario 1 (wash vegetables first, use same utensils) than in the other three scenarios. These results show how different hygiene practices influence the risk of pathogens contaminating chicken salad. This information could decrease the risk of foodborne disease in Cambodia and provides inputs to a quantitative risk assessment model.

Low Prevalence of Cysticercosis and Trichinella Infection in Pigs in Rural Cambodia.

Cysticercosis and Trichinella spp. infection are parasitic zoonoses prevalent among pigs in Southeast Asia, where pork is the most important source of meat. In rural Cambodia, many pigs are raised extensively in family backyards, and information regarding the prevalence in rural small-scale pig production is very limited. This study was conducted in four provinces in north-eastern Cambodia to determine the seroprevalence of porcine cysticercosis and Trichinella spp. infection in rural villages, and to identify possible risk factors. Only households with less than 10 pigs above three months old were eligible. In total, 139 households participated, and 242 blood samples were collected. Farmers were interviewed about food and hygiene habits, disease knowledge and practices. The serum samples were analysed by ELISA to determine antigens to Taenia spp. cysticerci or antibodies to Trichinella spp. muscle larvae. Positivity among the pigs was 11.2% (95% CI 7.5-15.8) for Taenia spp. cysts and 2.5% (95% CI 0.9-5.4) for Trichinella spp. Cysticerci were more common in the province Preah Vihear (p < 0.001) than in the other provinces. Risk factors associated with porcine cysticercosis were management systems for the pigs and access to human faeces (p < 0.001). Trichinella spp. infection in pigs was more common in the province Ratanakiri (p = 0.001). The main risk factor associated with Trichinella spp. transmission was feeding pigs with food waste (p = 0.048). More men had heard about cysticercosis than women (p = 0.002), and men also consumed undercooked pork meat to a greater extent (p = 0.004). Although the present study is relatively small, several risk factors could be identified for porcine infection with Taenia spp. and Trichinella spp., which can be used to guide future interventions to improve both porcine and human health in these provinces.

Prevalence of Salmonella spp. and Staphylococcus aureus in Chicken Meat and Pork from Cambodian Markets.

Salmonella spp. and Staphylococcus aureus are two of the most common foodborne bacteria in animal-source foods (ASF) that cause illness worldwide. This study aimed to determine the prevalence of Salmonella spp. and S. aureus in chicken meat and pork in markets in Cambodia. Sampling was done in 52 traditional markets and 6 supermarkets in 25 provinces of Cambodia between October 2018 and August 2019. In total, 532 samples were obtained: chicken meat and pork (n = 408, 204 of each), chicken and pork cutting board swabs (n = 124, 62 of each). All samples were analyzed for the presence of Salmonella spp. and S. aureus; colony-forming units per gram (CFU/g) of coagulase-positive Staphylococci (CPS) were counted, and a subset of samples was also analyzed for the most probable number (MPN, n = 136) of Salmonella. The overall prevalence of Salmonella spp. and S. aureus were 42.1% (224/532) and 29.1% (155/532), respectively, with 14.7% (78/532) of samples containing both bacteria. The prevalence of Salmonella spp. in chicken meat was 42.6%, on chicken cutting board it was 41.9%, on pork it was 45.1%, and the pork cutting board 30.6%. Chicken meat had a significantly (p-value < 0.05) higher prevalence of S. aureus, 38.2%, compared to the chicken cutting board, 17.7%, pork 28.9%, and pork cutting board 11.3%. Mean MPN-Salmonella was 10.6 MPN/g in chicken and 11.1 MPN/g in pork samples. Average Log CFU/g of CPS in chicken and pork samples were 2.6 and 2.5, respectively. The results indicate that chicken meat and pork in Cambodia were highly contaminated with Salmonella spp. and S. aureus, posing risks to consumers' health. Urgent interventions are necessary to improve hygiene for safer meat in Cambodian markets.

Japanese Encephalitis in Small-Scale Pig Farming in Rural Cambodia: Pig Seroprevalence and Farmer Awareness.

Japanese encephalitis (JE) is endemic in Cambodia, but circulation of JE virus (JEV) among domestic pigs has previously only been studied in the southern part of the country. The main purpose of this study was to determine the seroprevalence of JEV antibodies in smallholder pigs held in rural areas of Kampong Thom, Preah Vihear, Ratanakiri, and Stung Treng provinces, northeastern Cambodia. Another purpose was to identify possible associations between serologic status and other factors, such as reproductive disorders, and to investigate the farmers' knowledge of mosquito-borne diseases and use of preventive measures. In October 2019, 139 households were visited throughout the study area, and 242 pigs were sampled for blood. The sera were analysed with ELISA for JEV antibodies. Household representatives were interviewed, and data were recorded for each sampled pig. The apparent seroprevalence was 89.1% in pigs between 3 and 6 months of age, and 100% in pigs over 6 months of age. In total, 93.0% of the pigs tested positive. Province appeared to be the only factor significantly associated with serologic status (p < 0.001). Almost all (97.8%) respondents knew that mosquitos could transmit diseases, and 70.5% had heard of JE. However, only one respondent knew that JEV is transmitted to people through mosquito bites. Very few respondents knew that pigs can become infected with JEV, and no one knew that mosquitos transmit the virus. All families used some sort of mosquito protection for themselves, but only 15.1% protected their pigs from mosquito bites. The children were vaccinated against JE in 93 households, while adults only were vaccinated in eight households. The results suggest that JEV transmission is intense in northeastern Cambodia, and that people's knowledge about the transmission route of JEV and the role of pigs in the transmission cycle is low. Fortunately, people are well aware of mosquito-borne diseases in general and use mosquito protection, and many children are vaccinated against JE. Nonetheless, it is important that national vaccination is continued, and that people-especially in rural areas where pigs are commonly kept-are educated on the ecology and transmission of JEV.

Identification of the O/ME-SA/Ind-2001e Sublineage of Foot-and-Mouth Disease Virus in Cambodia.

Foot-and-mouth (FMD) is endemic in Cambodia with numerous outbreaks in cattle, pigs and other susceptible animal species reported every year. Historically, these outbreaks were caused by the FMD virus (FMDV) of serotype O PanAsia and Mya-98 lineages and serotype A Sea-97 lineage. However, the trans-pool movement of FMDV between inter-pool regions or countries throughout FMD endemic regions has raised concerns regarding infection with the new genotype or serotype of FMDV in Cambodia. In this study, 19 sequences of VP1 coding region obtained from 33 clinical samples collected from FMDV-affected cattle farms in Cambodia during January to March 2019 were genetically characterized to identify the genotypes/lineages of FMDV. Phylogenetic analysis of VP1 coding sequences revealed that recent field viruses belonged to O/ME-SA/Ind-2001e (15.8%), O/ME-SA/PanAsia (52.7%), and A/ASIA/Sea-97 (31.5%). Besides, the field viruses of O/ME-SA/Ind-2001e in Cambodia showed 93.5-96.8% identity with the VP1 coding sequences of the same sublineage viruses from pool 1 and 2 surrounding Cambodia. This is the first report of O/ME-SA/Ind-2001e infection in Cambodia, suggesting that the trans-pool movement of the new genotype should be closely monitored for efficient control of FMD.

Pathogenesis and genetic characteristics of a novel reassortant low pathogenic avian influenza A(H7N6) virus isolated in Cambodia in 2019.

The first human case of zoonotic A(H7N4) avian influenza virus (AIV) infection was reported in early 2018 in China. Two months after this case, novel A(H7N4) viruses phylogenetically related to the Jiangsu isolate emerged in ducks from live bird markets in Cambodia. During active surveillance in Cambodia, a novel A(H7N6) reassortant of the zoonotic low pathogenic AIV (LPAIV) A(H7N4) was detected in domestic ducks at a slaughterhouse. Complete genome sequencing and phylogenetic analysis showed that the novel A(H7N6) AIV is a reassortant, in which four gene segments originated from Cambodia A(H7N4) viruses and four gene segments originated from LPAIVs in Eurasia. Animal infection experiments revealed that chickens transmitted the A(H7N6) virus via low-level direct contacts, but ducks did not. Although avian-origin A(H7Nx) LPAIVs do not contain the critical mammalian-adaptive substitution (E627K) in PB2, the lethality and morbidity of the A(H7N6) virus in BALB/c mice were similar to those of A(H7N9) viruses, suggesting potential for interspecies transmission. Our study reports the emergence of a new reassortant of zoonotic A(H7N4) AIVs with novel viral characteristics and emphasizes the need for ongoing surveillance of avian-origin A(H7Nx) viruses.

Detection of African swine fever virus in free-ranging wild boar in Southeast Asia.

African Swine Fever (ASF) is a highly contagious and fatal viral disease affecting both domestic and wild suids. The virus was introduced to Southeast Asia in early 2019 and has since spread rapidly throughout the region. Although significant efforts have been made to track and diagnose the disease in domestic pigs, very little is known about ASF in free-ranging wild boar and their potential role in maintaining the disease within Southeast Asia. Through a collaboration between government and non-government actors in Laos, Viet Nam, and Cambodia, investigations were conducted to (a) characterize the interface between domestic pigs and wild boar, (b) document risk factors for likely ASF spillover into wild boar populations by way of this interface, and (c) determine whether ASF in wild boar could be detected in each country. An extensive overlap between wild boar habitat and domestic pig ranging areas was found around villages bordering forests in all three countries, creating a high-risk interface for viral spillover between domestic pig and wild boar populations. Fifteen and three wild boar carcasses were detected through passive reporting in Laos and Viet Nam, respectively, in 2019 and early 2020. Four of five carcasses screened in Laos and two of three in Viet Nam were confirmed positive for African swine fever virus using real-time PCR. There were no confirmed reports of wild boar carcasses in Cambodia. This is the first confirmation of ASF in wild boar in Southeast Asia, the result of a probable viral spillover from domestic pigs, which highlights the importance of early reporting and monitoring of ASF in wild boar to enable the implementation of appropriate biosecurity measures.

Phylogeographic analysis of H5N1 highly pathogenic avian influenza virus isolated in Cambodia from 2018 to 2019.

Since 2004, several outbreaks of highly pathogenic avian influenza (HPAI) have been reported in Cambodia. Until 2013, all H5N1 viruses identified in Cambodia belonged to clade 1 and its subclades. H5N1 HPAI viruses belonging to clade 2.3.2.1c have been dominant since the beginning of 2014, with various genotypes (KH1-KH5) reported. Here, we isolated nine H5N1 HPAI viruses from domestic poultry farms and slaughterhouses in Cambodia during 2018-2019 and performed phylogenetic analysis of whole genome sequences. All isolates were classified as H5 clade 2.3.2.1c viruses and all harbored multi-basic amino acid sequences (PQRERRRKR/GLF) at the haemagglutinin (HA) cleavage site. Phylogenetic analysis revealed that the H5N1 isolates in this study belonged to the KH2 genotype, the dominant genotype in Cambodia in 2015. Phylogenetic analysis of the HA gene showed that the isolates were divided into two groups (A and B). The results of Bayesian discrete phylogeography analysis revealed that the viral migration pathways from Vietnam to Cambodia (Bayes factor value: 734,039.01; posterior probability: 1.00) and from Cambodia to Vietnam (Bayes factor value: 26,199.95; posterior probability: 1.00) were supported by high statistical values. These well-supported viral migrations between Vietnam and Cambodia demonstrate that viral transmission continued in both directions. Several factors may have contributed to this, including the free-grazing duck system and movement of poultry-related products. Thus, the results emphasize the need for an enhanced international surveillance program to better understand transboundary infection and evolution of H5N1 HPAI viruses, along with implementation of more stringent international trade controls on poultry and poultry products.