Innovative platform for molecular and serological diagnostics (PIMES)
Collaboration
• Institut Pasteur (IP) Paris, France.
Funding
• Ministry of Foreign Affairs, France.
Objectives
1. Laboratory capacity building. To establish a new platform to develop novel serological and molecular diagnostic tools against priority viruses and estimate the presence and circulation of these pathogens in humans and animals.
2. Training. To train a team of young Lao researchers to ensure they acquire the necessary skills to work with these new technologies.
3. Communication. To share the study results with the Lao Ministry of Health, various Lao institutional collaborators, and international public health authorities.
Background
Zoonotic diseases, which are transmitted from animals to humans, pose a significant threat to public health. The COVID-19 pandemic is a recent example that demonstrates on a global level the negative consequences if the causative pathogen cannot be accurately identified and controlled in a timely manner. Factors such as deforestation, climate change, and globalization increase the risk of pathogen spillover to humans. The “One Health” initiative aims to reduce the risk of diseases at the interface between humans, animals, and the environment. PIMES is a project aligned with the “One Health” initiative by improving the capacity to rapidly and accurately identify new viruses circulating in humans and animals.
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.
The milestones and indicators of the project include training local researchers on antigen design in silico, developing and validating molecular assays to detect emerging viruses, establishing a map of pathogen circulation, and assessing the risk of spillover. The results will be shared with national and international health authorities, funders, and other stakeholders in the form of reports and meetings, as well as with the general public through the project webpage.
The steering committee will monitor project progress regularly and facilitate communication among various organizations and authorities. Ultimately, this project aims to improve existing laboratory and research capacity and contribute to rapid outbreak response, leading to effective prevention and control of zoonotic diseases in Lao PDR.
Methodology
Training workshops.
From September 18 to October 4, two workshops were held on bioinformatic analysis and in silico antigen design, as part of knowledge transfer and capacity building. The trainers were experts from IP Paris: bioinformatics (Drs. Thomas BIGOT and Julia KENDE) and antigen design (Drs. Massimiliano BOMONI and Vincent SCHNAPKA).
Invitations to attend were sent to staff researchers at other Lao partner institutes, including the Department of Communicable Disease Control (DCDC) and National Centre for Laboratory and Epidemiology (NCLE), Lao Ministry of Health; the National Animal Health Laboratory (NAHL), Lao Ministry of Agriculture and Forestry; the Lao-Oxford-Mahosot Hospital- Wellcome Trust Research Unit (LOMWRU); and Centre Infectiology Lao-Christophe Merieux (CLIM). Regional invitations were sent to staff from the Institut Pasteur du Cambodge (IPC).
The training consisted of theoretical (classroom) and practical (computer-based) components. The agenda included the following topics for bioinformatics: fundamentals of bioinformatics, next-generation sequencing, and alignments, introduction to databases in bioinformatics, genome assembly, functional and taxonomic annotation, consensus and variant calling, from homology to phylogeny, and summary of concepts for pathogen discovery.
The agenda for in silico antigen design is as follows: identify homolog structures with BLAST, sequence alignment with MAFFT, build homology models of viral protein in complex with receptor/antibody, structural analysis with MDAnalysis, building models of viral proteins with AF2/AF3, look for similar structures in complex with antibodies/receptors, building models of protein complexes with AF3, quality assessment and binding free-energy estimation, structural analysis with MDAnalysis, predicting protein-protein interactions with AI, HADDOCK Tutorial on antibody/antigen.
Results
Over 20 staff members from the IPL, DCDC, NCLE, NAHL, LOMWRU, CILM, and IPC attended the basic bioinformatics and in silico antigen design training sessions (Figure 1A-B).
For the basic bioinformatics session, the hands-on practices were conducted using Galaxy installed on IPL’s in-house server, along with other open-source software, covering a range of bioinformatics tasks. These included quality checks of Illumina and ONT sequence data using FastQC, MultiQC, NanoPlot, and PycoQC; taxonomic classification with Kraken2; de novo assembly using Velvet; genome annotation with Augustus and Prokka; variant calling via GATK; and phylogeny reconstruction using Seaview.
For the in silico antigen design session, the practices involved several approaches, including homolog-based identification using MAFFT and Modeller, AI-based structure prediction and homolog identification using AlphaFold3 and Foldseek, a geometric deep-learning approach with PeSTo and ScanNet, and physics-based docking using HADDOCK. The trainees were provided with the necessary tools and Python scripts to predict the antigenic domain of the BANAL-52 coronavirus and estimate its antigen-antibody binding affinity. Additionally, the trainees were given the task of predicting the antigenic region of the given amino acid sequence by using the acquired skills and presenting the result on the final day.
Lectures were recorded for future training purposes and for reference for trainees who had unforeseen enforced absences, and they were stored on the IPL server. Trainees who successfully completed the training were awarded certificates of completion (Figure 2A-B).
The courses were well-received, with overwhelmingly positive participant feedback and demonstrable improvements in participants’ proficiency in bioinformatics and in silico antigen design.

Figure 1. (A) Basic bioinformatics, (B) in silico antigen design training at IPL.

Figure 2. Certificate presentation ceremony (A) Basic bioinformatics, (B) in silico antigen design training course.