Virology Laboratory

The main activities of the virology laboratory include:

Understanding the ecology and emergence of known and novel viruses in Lao PDR;
Developing countermeasures to diagnose, prevent, or control viral infections;
Training, education, and capacity building for scientists and technicians from Lao and regional partners to adapt and establish novel, cutting-edge technologies for outbreak response;
Providing diagnostic and sequencing support to public health surveillance activities, including for arboviruses, respiratory viruses, or other (re)-emerging pathogens, to support Lao partners in outbreak investigations.

All Research

Our Team

Executive summary

During the 21st century, the world experienced an increasing occurrence of zoonotic disease outbreaks caused by novel or neglected emerging viruses, such as SARS, H1N1 “swine” flu, MERS, Ebola virus disease, Zika fever, COVID-19, and mpox. Lower- and middle-income countries, including Lao PDR, have limited resources that can be allocated to medical care or public health. The rapid development of Lao PDR in recent years has resulted in substantial environmental, climate, and land-use changes. This results in a higher than-typical number of interactions between humans, wild animals and their respective environments, and an increased possibility of cross-species transmission as well as outbreak risk. There is extensive trade activity between Lao PDR and neighboring countries, resulting in a high volume of cross-border movement of workers and goods. In addition, wild animals and vectors are not confined by national boundaries. Therefore, the geographical location of Lao PDR, at the heart of the Greater Mekong Subregion (GMS), means that outbreaks in Lao PDR have a high risk of negatively impacting its neighbors.

The Virology Laboratory at the Institut Pasteur du Laos (IPL) aims to build and reinforce laboratory capacity with Lao and regional partners through regular training workshops and educational courses. The Virology Laboratory provides public health services to support Lao national institutes and hospitals with diagnostic and sequencing services against a number of priority pathogens, such as Dengue, Chikungunya, Zika, avian influenza, and SARS coronaviruses. Through its research activities, the Virology Laboratory strives to characterize the prevalence, maintenance, and transmission of known and unknown viruses in humans, animals, and the environment of Lao PDR, studying associated factors influencing spillover risk, and providing countermeasure options, such as the rational design, validation, and implementation of cutting-edge diagnostic assays.

In 2025, the Virology Laboratory was involved with the following projects and activities:

Reinforced Collaboration for the Investigation and Response to Emerging Viral Pathogens of Security Concern (Global Affairs Canada, National Microbiology Lab of Canada)

In collaboration with the National Microbiology Laboratory in Canada, we reinforced the biosafety and biosecurity of the BSL-2/3 laboratory, as well as field safety, through standardized operating procedures (SOPs) and the creation of a dedicated biosafety office, establishing an inventory of natural bat and rodent reservoirs for detection of SARS-like-CoVs and other putative zoonotic viral pathogens, and studying interspecies spill-over of these putative zoonotic viral pathogens.

Genomic surveillance of avian influenza viruses in Lao PDR (International Pathogen Surveillance Network “IPSN” project and Fonds Equipe France-Rapide “Flu-LAO” project)

In collaboration with the National Animal Health Laboratory and the Department of Agriculture and Forestry in Vientiane Capital, Luang Prabang and Champasack, these projects established monthly surveillance efforts in Northern, Central and Southern Lao PDR, to identify, sequence, and assess the prevalence of circulating avian influenza viruses in live bird markets and animal farms through animal and environmental sampling.

Innovative platform for molecular and serological diagnostics (Fonds Equipe France “PIMES” project)

In collaboration with Institut Pasteur de Paris, the project focuses on establishing a platform for the identification of novel/neglected pathogens, the development of specific molecular and serological assays, and the use of these tools to detect acute infections and to study the prevalence of these infections in human and animal populations. The project includes a capacity-building component for Lao and regional partners on the training of bioinformatic tools used for novel pathogen discovery and in silico antigen design, as well as the development of molecular RPA/LAMP and serological LIPS assays to be used alongside gold-standard diagnostic methods.

Uncovering hidden pathogens: Virome characterization of bat-infesting arthropods in Lao PDR (Institut Pasteur du Laos Foundation, Young Researchers Grant Challenge 2024)

In collaboration with the Entomology Laboratory at IPL, the project focuses on applying the metagenomic and metatranscriptomic approaches to assess the prevalence of putative viral pathogens in the viromes of bat-infesting arthropods collected from bats in Lao PDR, and to investigate the host-vector-pathogen relationship, to further understanding of the maintenance and transmission of viruses amongst host species in nature.

Diagnostic services for public health

To support public health activities in Lao PDR, the Virology Laboratory provides diagnostic services on request from various Lao-based partners for diagnostics against certain pathogens of interest, such as PCR-confirmation of arboviruses or respiratory pathogens, and whole-genome sequencing of SARS-CoV-2 and avian influenza viruses.

Plain language summary

Lao PDR is geographically located at the center of the Greater Mekong Subregion and has recently undergone rapid environmental changes. Wild animals are increasingly encroaching into areas inhabited by humans, and more frequent contact between these two populations results in a higher chance of disease spread. Providing quality healthcare in Lao PDR is challenging because of limited infrastructure and capacity. The Virology Laboratory at the Institut Pasteur du Laos focuses on addressing these issues through public health services to support healthcare professionals in making accurate diagnoses and to advise public health officials in policymaking, training, and education of researchers to elevate their abilities and competence, as well as research to understand the current up-to-date situation of infectious diseases in Lao PDR and provide evidence-based solutions to improving outbreak preparedness.

Projects

CAN2

Reinforced Collaboration for the Investigation and Response to Emerging Viral Pathogens of Security Concern

Reinforced Collaboration for the Investigation and Response to Emerging Viral Pathogens of Security Concern (Global Affairs Canada, National Microbiology Lab of Canada).

National Microbiology Laboratory, Canada
Faculty of Environmental Sciences, National University of Laos, Lao PDR
National Animal Health Laboratory, Ministry of Agriculture and Forestry, Lao PDR

Global Affairs Canada, Canada

The project aims to accomplish the following expected results:

Enhanced capacity in Lao PDR to monitor for, rapidly detect, and effectively respond to disease events involving especially dangerous pathogens of bioterrorism and bioweapons concern.
Increased knowledge and awareness among local scientists/community on zoonotic viral pathogens and their safe acquisition, handling, storage, and cataloguing of biological samples.
Increased biosafety and biosecurity skills, awareness, and application at IPL through the creation of a dedicated biosafety office. • Strengthened detection, diagnosis, science, and response to emerging viral pathogens by Lao scientists, technicians, and other national stakeholders; and ultimately. • Reduced risks and threats from emerging infectious zoonotic diseases in Lao PDR and globally

Southeast Asia is well-known as a hotspot for emerging viral diseases, which have included Severe Acute Respiratory Syndrome Coronavirus Infection (SARSCoV), Avian Influenza H5N1, Nipah, and COVID-19. These viruses are believed to have originated in animals before being transmitted to humans, either directly or through an intermediate host.

Lao PDR, a landlocked country in Southeast Asia, is situated in a region recognized as a hotspot for emerging infectious diseases (EIDs) (Jones K.E., et al. 2008). However, Lao PDR currently lacks a robust EIDs surveillance system and has limited laboratory capacity for the rapid detection of novel emerging viral pathogens. Consequently, it is imperative to establish and reinforce local capabilities for the safe investigation and response to emerging zoonotic viral diseases.

The project, “Reinforced Collaboration for the Investigation and Response to Emerging Viral Pathogens of Security Concern,” is a scientific collaborative effort between the Institut Pasteur du Laos (IPL) in Lao PDR and the National Microbiology Laboratory (NML) in Canada, funded by Global Affairs Canada (GAC). Following the completion of the initial pilot phase, the project is dedicated to further enhancing sustainable local capacities in Lao PDR for the safe investigation and response to emerging viral pathogens with pandemic potential, thus reducing the biological threats and strengthening the scientific cooperation between Canada and Lao PDR.

To implement the One Health approach, IPL, representing the human health sector, has established collaborative partnerships with local entities in both the animal and environmental sectors, including the Faculty of Environmental Sciences (FES) at the National University of Laos and the National Animal Health Laboratory (NAHL) under the Ministry of Agriculture and Forestry. These multi-sectoral partnerships play a vital role in ensuring the widespread delivery of positive changes in capacity and performance, practices or behaviour to a wide range of intermediaries and beneficiaries. Figure 1: Collaboration and conceptual framework.

Biosafety and biosecurity. Several activities have been implemented to increase the biosafety and biosecurity level of the institute. These include the nomination of a new scientist as Deputy Biosafety Officer to support the activities related to biosafety and biosecurity, the enrollment of a team member in Certificate of Advanced Studies (CAS) in Biobanking program, the installment of a new autoclave to maintain proper safety and waste management standards, and installation of improved Closed-Circuit Television (CCTV) cameras to expand the coverage area of surveillance.

Figure 2: Biosafety/biosecurity-related activities.

Expanded coverage area of a CCTV system
The installment ofa new autoclave

Local capacity building.

Several Standard Operating Procedures (SOPs) were revised and improved, sample inactivation workflow for swab and tissue was adjusted according to the new BSL-2 laboratory. The screening protocols of 4 viral groups (coronaviruses, hantaviruses, paramyxoviruses, and flaviviruses) were updated to include the procedure for heatsealing plates. Multiple on-site visits were organized to strengthen the skills of Lao scientists and researchers. This included two NML scientists’ visits to IPL, where training was provided on bioinformatics and ELISA techniques.

Field missions.

The field missions for the year 2025 were conducted in 3 sites, including Kasi district, Vientiane province; Khounkham district, Khammouane province; and Viengthong district, Bolikhamxay province. As of now, a total of 14,291 biological samples were collected. These samples included anal, saliva, and urine swabs, ectoparasites, as well as blood and tissues obtained from bats, rodents, and small mammals. The collection methods involved both livecapture techniques and surveys conducted at local wet markets. Additionally, bat guano (labelled as environmental samples) was collected using plastic sheets.

Figure 3: Number of biological samples collected.

IPSN

Genomic surveillance of avian influenza viruses in Lao PDR

National Animal Health Laboratory (NAHL), Ministry of Agriculture and Forestry, Lao PDR
Department of Forestry and Agriculture in Vientiane Capital, Luang Prabang and Champasack, Lao PDR
French National Research Institute for Sustainable Development (IRD), Lao PDR

International Pathogen Surveillance Network, World Health Organization
Fonds Equipe France-Rapide, Ministry of Foreign Affairs, France

To establish a pilot genomic surveillance program for avian influenza viruses (AIVs) in Live Bird Markets (LBMs), based on environmental and animal sampling. To generate whole genome sequences of AIVs sampled from LBMs, to identify risk factors that contribute to increased AIVs prevalence and spillover, and to detect molecular markers linked with higher virulence or transmission in humans, or antiviral resistance.

Avian influenza viruses (AIVs) cause severe respiratory illness with high fatality rates in humans. LBMs are known to facilitate the recombination and transmission of AIVs with pandemic potential. Lao PDR shares borders with China, Vietnam, Cambodia, Myanmar, and Thailand, countries that have previously reported AIV outbreaks. In 2024, Vietnam and Cambodia reported human infections with H5. There is a knowledge gap on AIVs circulating in Lao PDR. To address this, IPL established a pilot genomic surveillance program to characterize circulating AIVs from LBMs in three Laotian regions: North (Luang Prabang), Central (Vientiane Capital), and South (Champasack).

Samples from the environment and poultry were collected and screened, and subtyped for AIV. Positive samples with high viral loads were directly sequenced to generate whole-genome sequences. Samples with low viral loads were amplified in specific pathogen-free (SPF) embryonated eggs under Biosafety Level (BSL)-3 conditions before direct sequencing. Phylogenetic and mutation analysis were performed with whole-genome sequences, and mutations in genomes contributing to enhanced replication, transmissibility, virulence, virion stability, or drug resistance were identified.

A total of 2054 samples have been collected from November 2024 to October 2025, in which 607 AIV-positive samples were detected (29.6%), with H5Nx (n=417), H9Nx (n=92), HxNx (n=78), and co-occurring H5Nx/N9Nx (n=24) as the identified subtypes. It was found that ducks had higher AIV-positive rates compared to chickens, and environmental samples had higher positive rates compared to animal samples across all three locations. Additionally, water and slaughtering equipment typically showed the highest AIV-positive rates (Figure 4). The whole-length genome sequence was obtained via direct sequencing for 58 samples, and 35 whole-length genome sequences were obtained after amplification in SPF-eggs for 35 samples.

Figure 4. AIV prevalence in various sample types collected from LBMs from Luang Prabang (left), Vientiane Capital (center) and Champasack (right).

Phylogenetic analysis of complete and partial sequences of the H5N1 samples revealed that these viruses clustered within Clade 2.3.2.1e (similar to Cambodia and Vietnam) and 2.3.4.4b (worldwide distribution) (Figure 5).

Figure 5. Phylogenetic tree of the H5Nx hemagglutinin (HA) gene.

Of note, mutation analysis found that all of the H5-subtype sequences contained a polybasic cleavage site in the HA gene and thus highly pathogenic, and 3 of the H5-subtype sequences contained a critical E627K mutation in PB2, suggesting increased virulence in mice and humans. For H9N2, phylogenetic analysis revealed that the AIVs clustered within Clade B.4.7.1 and B4.5 (Figure 6), similar to those found in neighbouring Cambodia and Vietnam. The sequences did not contain a polybasic cleavage site in the HA gene and thus low pathogenic, and the E627K mutation was not detected in H9N2 sequences.

Figure 6. Phylogenetic tree of the H9Nx HA gene.

The identification of the E627K mutation from whole-length genome sequences is concerning and relevant for public health, as the same mutation was found in human cases of H5N1 infection in Cambodia over the past year, suggesting that some of the circulating AIVs in Lao PDR can potentially cause severe disease in humans. This project has been crucial for supporting IPL to establish a next-generation sequencing platform to rapidly sequence potentially novel strains of AIV, and to carry out the required sequence, mutation, and phylogenetic analysis. The SPF-embryonated egg platform provides the ability to isolate AIVs of interest for future studies and to amplify AIV-positive samples to high titers for direct sequencing. This work is instrumental for pandemic preparedness efforts by Lao PDR against the threat of AIVs.

FLULAO

PIMES

Innovative platform for molecular and serological diagnostics

Institut Pasteur de Paris, France

Fonds Equipe France, Ministry of Foreign Affairs, France

To establish a new platform to develop novel serological and molecular diagnostic tools against priority viruses, and to estimate the presence and circulation of these pathogens in humans and animals collected prospectively and retrospectively. To train a team of young Lao researchers to ensure they acquire the necessary skills to work with these new technologies. To share the study results with the Lao Ministry of Health, various Lao institutional collaborators, and international public health authorities.

This project aims to develop cutting-edge, high-performance molecular diagnostic tools to detect new viruses in samples collected from humans and animals of Lao PDR. These tools can theoretically be generated and validated within weeks if the sequence is known, contributing to a rapid response against an emerging outbreak. These tools can also be used to estimate the prevalence of these pathogens in the general population and strengthen surveillance efforts in Lao PDR. The establishment of this novel diagnostic platform will allow local researchers to be trained on the development of these techniques against any known or novel pathogens and constitute an essential link for the successful control and prevention of infectious disease outbreaks.

Novel field-friendly molecular diagnostic assays based on isothermal amplification of nucleic acids (recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification techniques), as well as novel serological assays (luciferase immunoprecipitation system (LIPS)) were developed or will be developed against several target pathogens: Laotian phleboviruses (LPV) 1 and 2, Jingmen tick virus, Wenzhou virus, Loei virus, bat hantavirus, and Tembusu virus. Surveillance studies in humans include the establishment of a fever surveillance site in Vieng Phou Kha, Luang Namtha, as well as seroprevalence sites in 1) Kasi, Vientiane Province, 2) Naxaythong, Vientiane Capital, and 3) Pakse, Champasack Province. Surveillance studies in animals were performed in Vieng Phou Kha, Luang Namtha. Retrospective studies involved screening 1,500 human samples and 600 samples from bats and rodents previously collected through other initiatives and stored at the IPL Biobank.

Using LPV1 and LPV2 as a proof-of-concept:

Development of RPA and LAMP assays and screening of sandflies. The development of molecular assays specific to the RdRp gene of LPV1 and LPV2 was found to be specific (no cross-reactivity between the two pathogens) and sensitive, with a limit of detection of 10 genome copies (Figure 7). These assays were used to screen a total of 157 sandfly samples collected from Vieng Phou Kha. Screening with LAMP-based assays revealed a positive rate of 8 positives (5.1%) and 2 positives (1.3%) against LPV1 and 2, respectively. Screening with RPA-based assays revealed a positive rate of 23 positives (14.6%) and 24 positive (15.3%) against LPV1 and 2, respectively.

Figure 7. Development of LAMP (left) and RPA-based (right) assays against LPV 1 and 2.

Development of LIPS assays. Plasmids designed against the nucleoprotein (NP) of LPV1 and 2 have been developed (Figure 8), and experiments to establish and validate the LIPS-based assay via transfection of 293Expi cell lines are ongoing.

Figure 8. Plasmid constructs containing the nucleoprotein gene of LPV1 and 2.

Prospective studies in humans. An inclusion study based on residents from three villages (Nam O, Nam Eng and Phou Lan) in Vieng Phou Kha was carried out in June 2025, in which 517 participants were enrolled for seroprevalence studies (Figure 9) and are currently monitored regularly for symptoms of fever. A further 83 and 113 participants were enrolled from Naxaythong and Kasi, respectively, for seroprevalence studies.

Figure 9. Clinical monitoring and laboratory analysis of collected samples.

Prospective studies in animals. Trapping and sampling of wild bats, rodents and their ectoparasites from caves and other sites in Vieng Phou Kha was carried out in July 2025 (Figure 10), in which 761 samples were collected for analysis.

Figure 10. Bat capture (left) and sampling (right).

Retrospective studies in humans and animals. Currently, a total of 1377 human sera samples and 600 bat and rodent samples were identified from the IPL Biobank for ongoing screening studies.

Workshops. Two workshops were held in 2025 to transfer critical skills to Lao researchers for capacity building purposes. The first, a workshop titled “Loop-Mediated Isothermal Amplification (LAMP) and Recombinase-Based Isothermal Amplification (RPA/RAA)” was held in March 2025. The workshop participants included 24 trainees from IPL, NAHL, NCLE, Lao TPHI, CLIM (all Lao PDR), as well as IPC (Cambodia). During this training, the participants gained foundational knowledge of LAMP and RPA/RAA principles and applications; developed skills in reaction setup, primer design, and assay sensitivity testing; learned data analysis techniques, including copy number calculations and limit of detection (LOD) testing; learned about assay validation focusing on sensitivity and specificity; developed SOPs for LAMP and RPA assays and learned about current trends in diagnostic methodologies (Figure 11).

Figure 11. Lecture and laboratory components of the LAMP and RPA workshop.

The second workshop, titled “Advanced bioinformatics”, was held in September 2025. The workshop participants included 16 trainees from IPL, NAHL, NCLE, Lao TPHI, CLIM (all Lao PDR), as well as IPC (Cambodia). During this training, the participants reinforced their basic knowledge in bioinformatics, such as sequence homology, Galaxy tools and workflows, and long-read sequencing, as well as gaining advanced knowledge, including molecular phylogenetics, Bayesian methods, Pathogen discovery methods, Python programming for bioinformatics, and pipeline construction using command line and Python with Snakemake (Figure 12).

Figure 12. Lecture and hands-on components of the Advanced Bioinformatics Workshop.

The novel diagnostics development, the prospective and retrospective studies are still in progress with Jingmen tick virus, Wenzhou virus, Loei virus, bat hantavirus, and Tembusu virus. The workshops held in 2024 (see previous year’s activity report) and 2025 have been a crucial activity for capacity building for local Lao researchers to rapidly develop and validate assays against selected pathogens of interest, and the surveillance and screening activities in human and animal populations over the next year will provide a clearer picture of past and present disease burden in Lao PDR.

ECOMORE

YRGC 2024

Uncovering Hidden Pathogens: Virome characterization of bat-infesting arthropods in Lao PDR

Entomology Laboratory, Institut Pasteur du Laos

Young Researcher’s Grant Challenge 2024, Foundation lnstitut Pasteur du Laos

This project aims to achieve the following expected outcomes:

The identification of novel/known viral pathogens: Utilizing the metatranscriptomic approach, this study aims to uncover both known and potentially novel viral pathogens harbored by bat-infecting hematophagous arthropods (BIHA). These findings could highlight viruses with zoonotic significance.
Characterization of viral diversity and abundance: By analyzing the viral communities within BIHA, this research will provide comprehensive insights into the diversity and prevalence of viruses carried by these arthropods in bat populations.
Contribution to further studies: Genomic prevalence of putative viruses and related results from this proposed research will serve as background evidence for future studies.

Arthropoda, the largest phylum in the animal kingdom, constitutes the majority of global animal biomass. Numerous arthropod species serve as vectors for diverse viruses, for example, dengue, Japanese encephalitis, West Nile, and Chikungunya transmitted by mosquitoes; Crimean-Congo hemorrhagic fever transmitted by ticks; and Toscana virus transmitted by sandflies. Likewise, bats, which constitute the second most specious mammal order, host a multitude of viruses with some of which have spilled over to humans, leading to disease outbreaks, epidemics, or pandemics, including SARS, Ebola, Nipah viruses, etc. Importantly, several arthropod species infest bats, such as bat flies, ticks, mites, and fleas, and these have been shown to harbor viruses from families including Flaviviridae, Rhabdoviridae, Reoviridae, and Peribunyaviridae. Moreover, beyond viral sequence detection, infectious viruses have also been isolated from BIHA, thereby highlighting their potential role in viral maintenance and transmission.

In Lao PDR, knowledge of viral pathogens in BIHA remains limited. Institut Pasteur du Laos previously reported the discovery of a nearly complete segmented reovirus in these arthropods, but broader viral diversity is yet to be explored. This project applies a metatranscriptomic approach to investigate the prevalence and diversity of putative viral pathogens in BIHA collected from bats in Lao PDR. The findings will contribute to a better understanding of the role of BIHA in the amplification, maintenance, and transmission of viruses in natural ecosystems.

The proposed study uses the collected BIHA stored in IPL’s biobank as starting materials; these samples have undergone taxonomic identification using both morphological and genetic methods. Samples were categorized and pooled based on location, time of collection, and host species, and subjected to metatranscriptomic sequencing. The sequencing data were processed and analyzed, and the detected viral sequences were validated using polymerase chain reaction (PCR). Comprehensive analyses were conducted by integrating ecological data, host taxonomy, and viral pathogen information to explore relationships among these variables (Figure 13).

Figure 13: A schematic diagram of study design and methodology.

A total of 1,378 ectoparasite samples were analyzed and distributed across several families (Figure 14). The majority of samples belonged to the families Streblidae (768 samples) and Nycteribiidae (430 samples), together accounting for nearly 87% of the total. Smaller proportions were observed in Tenuipalpidae (77 samples), Mites (68 samples), and Acaridae (22 samples), while Anisolabididae (7 samples), Ixodidae (4 samples), and Pulicidae (2 samples) were minimally represented. These BIHA were extracted and pooled into 60 pools based on bat host and ectoparasite taxonomic classifications. The next-generation sequencing (NGS) libraries of the extracted RNA were then prepared and subjected to deep sequencing.

The obtained sequencing data yielded a total of 1,538 gigabases (GB). These data were analyzed on IPL’s in-house bioinformatic server using open-source pipelines. The initial analysis revealed viral contigs in different families including Iflaviridae, Orthomyxoviridae, Rhabdoviridae, Chuviridae, Partitiviridae, Retroviridae, Solemoviridae, Aliusviridae, Parvoviridae and unclassified families in the order Bunyavirales, Picornavirales, Mononegavirales.

Figure 14: Taxonomic classification of BIHA.

The study leverages IPL’s existing resources to broaden its scope and impact. The baseline analysis of the project showed the diversity of viral sequences identified. Looking ahead, more in-depth analyses are required to further characterize the detected viruses at the genomic and functional levels, including phylogenetic analysis, genome completeness assessment, and identification of potential novel lineages. Additionally, integrating ecological and epidemiological data will be critical to unravel the complex host-vector-pathogen relationships.

Public Health

Public Health surveillance activities

National Centre for Laboratory and Epidemiology (NCLE), Ministry of Health, Lao PDR
Department of Communicable Diseases Control (DCDC), Ministry of Health, Lao PDR
National Animal Health Laboratory (NAHL), Ministry of Agriculture and Forestry, Lao PDR
103 Hospital and Settahirath Hospital, Lao PDR

N/A

One of the mandates of IPL is to provide support to frontline Lao institutions responsible for outbreak response in animals and humans. As part of the disease control and prevention strategy, IPL provides PCR-based diagnostics and sequencing support to other public health partners. In 2025, IPL performed the following public health activities: 1) PCR-based diagnostics against arbovirus infections, 2) PCR-based diagnostics against respiratory syncytial virus (RSV), 3) variant identification of SARS-CoV-2 via next-generation sequencing (NGS), and 4) PCR-based diagnostics and sequencing against avian influenza viruses, as well as subsequent phylogenetic and mutation analyses of whole-length genome sequences.

PCR-based diagnostics against arbovirus infections. In 2025, a total of 129 samples from patients were received from 103 hospital and Settahirath Hospital. The results showed that 80 samples tested positive for Dengue virus (DENV), with 73 and 7 samples identified to be DENV-1 and 2, respectively. Infections with Chikungunya and Zika viruses were not observed.

PCR-based diagnostic tests against RSV. In 2025, a total of 9 samples from patients were received from NCLE. The results showed that 7 samples tested positive for RSV, and the other 2 samples also tested negative for influenza A/B and SARS-CoV-2.

Variant identification of SARS-CoV-2 via NGS. In 2025, a total of 47 SARS-CoV-2 positive samples from patients were received from NCLE. The results showed that 4 samples belonged to variant BA.2.86, 26 samples belonged to variant XDV, one to variant XEC, and one to variant XFG. Five samples were not successfully sequenced due to a low viral load, leading to insufficient sequence coverage to conclusively identify the variant.

PCR diagnostics and whole-length genome sequencing of avian influenza viruses. In 2025, a total of 22 samples from chickens, ducks, geese, ostriches, civet cats, and the environment were received from NAHL. The results showed that all of the samples tested positive for AIV, and subtyping results were as follows: H5Nx (n=6), H9Nx (n=9), or co-occurring H5Nx/H9Nx (n=7). Phylogenetic analysis showed that the H5-subtype viruses were highly pathogenic and belonged to Clade 2.3.2.1e, and H9N2 viruses were low pathogenic and belonged to the Y280/G9-like Clade. The E627K mutation was observed in a subset of H5-subtype viruses but not in H9-subtype viruses.

Discussion, conclusions and perspectives:

Reports on these findings were shared in a timely manner with the relevant partners to support informed decision-making and strategic planning. The services provided by the Virology Laboratory constitute a key contribution to Lao human and animal health, and underscore the commitment of IPL towards fellow Lao institutions in ongoing disease control and prevention efforts in Lao PDR.

Publications in 2025

Detection of Batborne Hantaviruses, Laos, 2023–2024.

Vanhnollat C, Somlor S, Dimitrova K, Medina S, Vongphayloth K, Vungkyly V, Vachouaxiong L, Douangboubpha B, Sanamxay D, Xayaphet V, Paphaphanh P, Theppangna W, Audet J, Buchy P, Safronetz D. Detection of Batborne Hantaviruses, Laos, 2023-2024. Emerg Infect Dis. 2025 Apr;31(4):814-819. doi: 10.3201/eid3104.241720. PMID: 40133083; PMCID: PMC11950268.

Molecular Epidemiology of Dengue Viruses in Lao People’s Democratic Republic, 2020–2023.

Troupin C, Intavong K, Somlor S, Viengphouthong S, Keosenhom S, Chindavong TA, Bounmany P, Vachouaxiong L, Xaybounsou T, Vanhnollat C, Khattignavong P, Phonekeo D, Khamphaphongphane B, Xangsayarath P, Lacoste V, Buchy P, Wong G. Molecular Epidemiology of Dengue Viruses in Lao People’s Democratic Republic, 2020-2023. Microorganisms. 2025 Feb 1;13(2):318. doi: 10.3390/microorganisms13020318. PMID: 40005687; PMCID: PMC11857872.

Circulation of Two Distinct Phylogenetic Subclades of Rabies Viruses in Lao PDR.

Troupin C, Intavong K, Chindavong TA, Keosenhom S, Viengphouthong S, Xaybounsou T, Vanhnollat C, Theppangna W, Phommachanh P, Buchy P, Wong G. Circulation of Two Distinct Phylogenetic Subclades of Rabies Viruses in Lao PDR. Zoonoses Public Health. 2025 Nov 4. doi: 10.1111/zph.70021. Epub ahead of print. PMID: 41185906.

Dengue dynamics beyond biological factors: Revealing the nexus between urbanisation planning, and mobilities in Vientiane, Lao PDR.

Telle O, Grandadam M, Philippon D, Calvez E, Pommelet V, Marcombe S, Béraud J, Somlor S, Choisy M. Dengue dynamics beyond biological factors: Revealing the nexus between urbanisation planning, and mobilities in Vientiane, Lao PDR. PLoS Negl Trop Dis. 2025 Jun 16;19(6):e0011990. doi: 10.1371/journal.pntd.0011990. PMID: 40523038; PMCID: PMC12169584.

Congress

Oral presentations:

- - Wong G. Avian influenza and dengue in Lao PDR during the COVID-19 era. 2nd A*STAR IDL-Pasteur Joint Symposium, 12 to 13 November 2024, Singapore (talk given online).
  - Wong G. An overview of avian influenza viruses in Lao PDR. The Pasteur Network’s Role and Future in Tackling Avian Influenza in the Asia-Pacific, 10 to 12 December 2024, Phnom Penh, Cambodia.
  - Chindavong T. Pilot surveillance of avian influenza viruses in the poultry and environment of live-bird markets in Lao PDR. Symposium and Workshop on Avian Influenza, 10 to 12 Dec 2024, Phnom Penh, Cambodia.
  - Wong G. Environmental genomic surveillance of avian influenza A viruses in high-risk live-bird markets in Laos: an innovative sequencing approach. Emerging Molecular Pathogen Characterization Technologies (EMPaCT)’s Community of Practice: Advancing Genomic Surveillance in the Western Pacific. World Health Organization. 29 May 2025, online.
  - Wong G. Circulation of two distinct phylogenetic subclades of rabies viruses in Lao PDR between 2017-2023. Review Strategic Plan to Control Rabies Virus in Lao PDR. World Health Organization and Department of Communicable Diseases Control. 29 to 30 May 2025, Vientiane, Lao PDR.
  - Wong G. Environmental genomic surveillance of avian influenza A viruses in high-risk live-bird markets in Laos: an innovative sequencing approach. Fourth Meeting of the Western Pacific Region Emerging Molecular Pathogen Characterization Technologies (EMPaCT) Network. 20 to 22 August 2025, online.
  - Wong G. Contributions by the Institut Pasteur du Laos to counter the threat of H5N1 avian flu in Lao PDR. Annual Meeting: Avian Influenza Surveillance and Response in Lao PDR. 10 September 2025, Luang Prabang, Lao PDR.
  - Wong G. Implications of the catalytic grant fund in Lao PDR. Country Scale-up Accelerator: Leveraging Global and Regional Initiatives to Advance Genomic Surveillance: Perspectives from the Western Pacific. 18 September 2025, online.
  - Vanhnollat C. Progress of CAN2 project. MBT2025 meeting. 30 September to 02 October 2025, Vientiane, Lao PDR.
  - Vanhnollat C. Uncovering Zoonotic Viruses at the Human-Wildlife Interface. “40 under 40” session, PNAM 2025. 21 to 23 October 2025, Ho Chi Minh City, Vietnam.
  - Wong G. Environmental genomic surveillance of avian Influenza A viruses in high-risk live-bird markets in Laos: an innovative sequencing approach. PHA4GE and IPSN Global Partners Forum. 27 to 29 October 2025, Cape Town, South Africa.

Posters:

- - Wong G, Troupin C, Somlor S, Chindavong T, Intavong K, Bounmany P, Viengphouthong S, Keosenhom S, Vachouaxiong L, Vanhnollat C. Surveillance of avian influenza viruses in live bird markets of Lao PDR, 2024-2025. Pasteur Network Annual Meeting. 21 to 23 October 2025, Ho Chi Minh City, Vietnam.

Congress attendance:

- Wong G. The 2025 ASEAN Animal Health Laboratory Technical Advisory Group (Lab-TAG) meeting: Food and Agriculture Organization of the United Nations. 06 to 09 May 2025, Vientiane, Lao PDR.
- Somlor S. MBT2025 meeting. 30 September to 02 October, 2025, Vientiane, Lao PDR.

Training activities

Trainings given by the team:

Wong G., T Chindavong. Trainer for RPA and LAMP workshop, Institut Pasteur du Laos, 03 to 14 March 2025.
Wong G., Chindavong T., Intavong K., Somlor S., Bounmany P., Viengphouthong S. Trainer for IPSN and Flu-LAO workshop, Institut Pasteur du Laos, 29 September to 03 October 2025.

Trainings undertaken by the team:

Chindavong T., Viengphouthong S., Bounmany P., Keosenhom S. ELISA training, Institut Pasteur du Laos, Vientiane, Lao PDR, 31 October 2024 to 05 November 2024
Intavong K. Biobank online course, University of Geneva, Switzerland, January 2025 to December 2025.
Vanhnollat C. Training in genomic sequencing of emerging high threat pathogens, Centre for Pathogen Genomics, Melbourne, Australia, 16 to 20 June 2025.
Vanhnollat C. Emerging Viral Infections, HKU-Pasteur Research Pole, Hong Kong, China, 14 to 18 July 2025.
Chindavong T. Dynameid online course, University of Montpellier, October 2025 to November 2026.