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The dissemination workshop of Epidemic Intelligence consortium project, jointly funded by Foreign Commonwealth and Development Office and Wellcome Trust, was organized in Kathmandu on 15^th March 2023, with the participation of government and non-government stakeholders from the ministry of health and population and project districts, consortium partners, civil society organizations and BNMT team members. In the program, project overview, achievements, challenges and recommendations of the project along with the findings of the COVID19 sequencing were shared among audiences by BNMT Executive Director Raghu Dhital, Principal Investigator Dr Maxine Caws, and research team members of partner organization Center for Molecular Dynamics-Nepal, Laboratory Manager and molecular genetics researcher, Rajindra Napit and Bioinformatics Specialist, Prajwol Manandhar.

The project conducted large scale pathogen sequencing in Nepal, successfully collecting and sequencing 1900 samples from three locations spanning Nepal: Bheri Hospital in Nepalgunj (Far West), Koshi Hospital, Biratnagar (Eastern Nepal), and Sukraraj Tropical Infectious Diseases Hospital in the capital city, Kathmandu (central region). Moreover, we followed up the participants at three and six months to understand the frequency and symptoms of long-term complications of COVID-19 illness (known as Long COVID) in the patients. The key findings of the project showed that Nepal had experienced three major waves of COVID-19. The first was caused by Beta variant, the second by Delta, the third by Delta and Omicron co-circulating. Tracking of COVID-19 variants showed successive waves caused by different variants, with multiple omicron sub-variants now circulating in Nepal. Similarly, the evaluation of cohort for long COVID showed diabetes and hypertension were strong risk factors.

The project significantly accelerated the genomics capacity for infectious diseases in Nepal, also supporting capacity development in laboratories trying to build sequencing skills base. It established a sequencing professionals network for Nepali scientists and delivered a bioinformatics training course for labs across Nepal with University of Melbourne.

The project was well appreciated by the stakeholders as a big achievement in molecular research and an innovative consortium model in COVID19 research that would inform future genomics study in Nepal addressing other infectious diseases including dengue, tuberculosis and antimicrobial resistance.

“Pathogen Genomics and Bioinformatics for Public Health Workshop 2023” was conducted from 16^th to 20^th January, 2023 in Kathmandu by Epidemic Inteliigence project partner Center for Molecular Dynamics Nepal (CMDN) on behalf of the project consortium, Birat Nepal Medical Trust (BNMT), Nepal Health Research Council (NHRC), and Oxford University Clinical Research Unit (OUCRU), funded by the Wellcome Trust and Foreign Commonwealth and Development Office (FCDO) UK. Bioinformatics experts from Doherty Institute, University of Melbourne, Australia, designed the course module and provided interactive and fruitful training to the participants who came from numerous research institutions and laboratories all over Nepal.

The main purpose of the workshop was to enhance the sequence analysis capacity of researchers working on sequencing and genomics projects as well as familiarize them with the bioinformatics tools and environment. The program was divided into two parts: theoretical and practical sessions focusing on the introduction of sequencing and bioinformatics, data visualization, bacterial and viral genomics, and their interpretation for the public health using various case studies. Constructive discussions on the results and presentations held place which allowed the participants to present their understandings. Beside the training, this event provided a great opportunity for the researchers to expand their professional network.

The three episodes of ” Covid Kurakani Panel Discussion Series: TV Talk show” were recorded in Nepalgunj, Biratnagar, and Kathmandu on 18^th July, 29^th July and 8^th August 2022 respectively. The panel discussion series were organized by BNMT Nepal, under ‘Covid Kurakani’ project which is a public engagement supplement to the Wellcome Trust funded COVID genomic surveillance project, Epidemic Intelligence (www.epiintelnepal.org ).

The COVID Kurakani panel discussion series is a series of three television talk programs, each of which was recorded live in the form of moderated panel discussions in the three districts. The panel discussion series comprised of dialogue among stakeholders of the Epidemic Intelligence project on the pathogen genomic sequencing and its application in the pandemics. Each recording lasted for approximately 2 hours. They are currently being edited to generate a clear, engaging 30 minutes programme to be broadcasted on Galaxy 4K TV’s ‘This Morning Live’.

This programs aimed to improve understanding of the need for and importance of, pathogen genomic sequencing in the response to emerging diseases and also help researchers, public health professionals and policy makers to understand the perspectives, concerns and perceived benefits of sequencing among public stakeholders to improve the design of future sequencing activities.

The three episodes were targeted to three distinct cohorts of participants, i.e. research participants of EI project, researchers and academics, and health workers. First episode of Covid Kurakani discussed on topics such as: basic concepts of COVID-19, the importance and use of pathogen sequencing in tracking diseases, sequencing procedures in the lab, and findings of the EI project. The distinguished panelists for the first episode were: Dr. Abhilasha Karkey, Dr. Bishnu Marasini, Ms. Kritika Dixit, Dr. Prakash Bahadur Thapa, Mr. Naresh Babu Shrestha and Mr. Rajindra Napit. The panel discussion was moderated by Dr. Sameer Mani Dixit.

In the second episode; application of Pathogen sequencing, use of genomic data in public health response, role of regulating bodies in promoting pathogen sequencing researches etc. were discussed. The eminent panelists for the second episode were: Dr. Den Acharya, Dr. Gehanath Baral, Dr. Sulochana Manandhar, Dr. Suresh Mehta, and Mr. Rajindra Napit. The panel discussion was moderated by Dr. Sameer Mani Dixit.

Finally, in the third episode, the discussion was moderated based on themes: prospects and challenges of pathogen sequencing, country’s strategies to strengthen pathogen sequencing, and plan for the use of pathogen sequencing in the country, etc. Dr. Buddha Basnet, Ms. Lilee Shreshta, Dr. Pradip Gyanwali, Dr. Sameer Mani Dixit, and Dr. Sangeeta Kaushal Mishra were the prominent personalities as panelists for the episode. The panel discussion was moderated by Dr. Abhilasha Karkey, Vice director, OUCRU Nepal. The total number of targeted participants in the three episodes was 99. The panel discussion was also attended by representatives of our partner organizations, Centre for Molecular Dynamics Nepal and Oxford University Clinical Research Unit, and BNMT Nepal staff.

The Review Meeting of the Epidemic Intelligence (EI) project was conducted on 19^th July 2022 and 30^th July 2022 in EI project districts: Banke and Morang respectively. The objectives of the meetings were:

• to share the current status and preliminary findings of the EI projects.
• to share an overview of all BNMT’s projects.

The programs were attended by different government and non-government stakeholders, representatives of our partner organizations, and other NGOs and the project team. In Banke district, the review was conducted in the presence of distinguished guests such as: Dr. Binod Kumar Giri, Director, Provincial Health Directorate (PHD), Lumbini Province; Dr. Badri Chapagain, Medical Superintendent, Bheri Hospital; Mr. Roshan Lal Chaudhary, Director, Province Public Health Laboratory (PPHL), Lumbini Province; Mrs. Sunita Paudel, Acting Health Officer, Health Office (HO), Banke; Dr. Bishnu Marasini, Senior Research Officer, Nepal Health Research Council (NHRC); Dr. Abhilasha Karkey, Director, Oxford University Clinical Research Unit (OUCRU); Dr. Sameer Mani Dixit, Biomedical Research Scientist, Center for Molecular Dynamics – Nepal (CMDN), etc. The total number of participants in Banke was 52. In Morang district, honourable guests such as Mr. Gyan Bahadur Basnet, Director, PHD, Province 1; Mr. Sagar Prasai, Senior Public Health Administrator (Sr. PHA); HO Sunsari, Dr. Suresh Mehta, Sr. PHA, HO Morang; Mr. Jaybendra Yadav, Director, PPHL; Mr. Shambhu Sah Senior Pharmacy Officer, Province Health Logistic Management Center (PHLMC); Dr. Suman Pant, Research Officer, NHRC; Dr. Sameer Mani Dixit, Biomedical Research Scientist, CMDN; Dr. Sulochana Manandhar, Molecular Microbiologist, OUCRU, etc were present in the meeting. The total number of participants in Morang was 42.

On 10^th May 2022, a seminar on application of genomics to understanding infectious diseases was organized at the Institute of Medicine, Tribhuvan University Teaching Hospital, Maharajgunj, Kathmandu. The seminar was attended by 55 participants including the students from public health faculty and relevant BNMT Nepal team. In the seminar, professors, Dr Stephen Baker from University of Cambridge and Dr Sarah Dunstan from University of Melbourne presented about the subject focusing on genetics, human genetic variation and genetic methods, Genome Wide Association Studies, Antimicrobial resistance, how do antimicrobials work, impact of AMR in Shigellabacteria etc. This was followed by lively Q&A session and discussions with the audiences.

On 16^th December 2021, Mid-term review of the Epidemic Intelligence project was held in Kathmandu.

Epidemic Intelligence is a consortium project to collect and sequence SARS CoV-2 samples to improve our understanding of the emergence and ongoing transmission of the virus in Nepal. The project has recruited over 1,000 participants since July 2021 and over five hundred patient samples have been successfully sequenced by 16 November 2021. All samples sequenced to date are Delta variant and sub-lineages, with no community transmission of Omicron identified in Nepal by 16 November 2021. However, continued surveillance to monitor for emerging variants is essential. The cohort is being followed up at 3 and 6 months for clinical and mental health outcomes, LONG COVID symptoms and the association of variants with vaccine types.

The objective of the mid-term review was to share the project progress and the preliminary findings with the Nepalese government and non-government stakeholders and the project collaborators. The program was conducted with the enthusiastic presence of the distinguished guests i.e. Bhawani Prasad Khapung, Honorable State Minister, Dr Dipendra Raman Singh, Director General, Department of Health Services, Dr Taranath Pokharel, Policy, Planning and Monitoring Chief, Ministry of Health and Population, Dr Pradip Gyanwali, Executive Chief, Nepal Health Research Council (NHRC), Dr Allison Gocotano, WHO along with representatives from the consortium partners, Center for Molecular Dynamics (CMDN), NHRC, Oxford University Clinical Research Unit-Nepal, Liverpool School of Tropical Medicine, the medical superintendents from three project hospitals and BNMT team. In the program, the presentations focused on the brief introduction of the project followed by work being done by the partner organizations, and preliminary findings of the SARS-COV-2 gene sequencing. This was followed by open Q and A session on research methodology, omicron variants and community transmissions, challenges and learnings and future scale up of the surveillance.

There was an encouraging reception and trust towards the project by the key stakeholders. The government officials highly appreciated the project as an important step to respond to emerging pandemic threats and also regarded it as a good quality research with the greater possibility of impacting in national health policies in future. They thanked all participants and their families, collaborating hospital and field staff for extraordinary efforts and support. They extended best wishes for the successful completion of the project, committing to extend support as and when required.

A one-day Research Ethics and Informed consent training was organized by BNMT Nepal in Nepalgunj, Banke. The main objective of the training was to improve the skills and knowledge of BNMT team members regarding the ethical principles governing research in human participants and the procedures and principles to be followed during the informed consent process for research studies. The training was facilitated by Principle Investigator of the project, Dr. Maxine Caws, Acting Executive Director Raghu Dhital, Research Manager Kritika Dixit, Research Officer Swastika Shrestha, Research Associate Rajan Paudel and Consultant Anne Goldie. The Epidemic Intelligence Project Manager, Target TB Project Manager, Regional Manager Monitoring and Evaluation Officer, research staff, District Program Coordinators and Community Health Supervisors participated in the training.

Training focused on the ethical principles to be considered in the development and conduct of research involving human participants with an emphasis on the three core principles – respect for persons, beneficence and justice.

The training comprised of presentations, experience sharing, brainstorming, group work and role play to engage the participants in active discussion and learning. The training also emphasized the importance of a complete and appropriate Informed Consent process when inviting participants to take part in research studies. Participants reviewed and discussed existing consent forms and participant information sheets to highlight any issues that may arise.  

The training was conducted with appropriate precautionary measures to protect against COVID transmission.

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On 4^th August 2021, District level Planning and Sharing Meeting for the Epidemic Intelligence project was organized in Nepalgunj, Banke district. The objectives of the meeting were

• to share and plan the Standard Operating Procedures/study protocol with concerned district level stakeholders
• to develop common understanding on detail implementation plan

The meeting was conducted with the active presence of distinguished government guests, Dr. Prakash Thapa, Medical Superintendent, Bheri Hospital; Ms. Kalpana Ghimire, Lab Technician, Provincial Public Health Laboratory and Mr. Dhir Jung Shah, Chief of Health Office, Banke; along with Dr. Maxine Caws, Principle Investigator, BNMT Nepal, Mr. Raghu Dhital, Acting Executive Director, BNMT Nepal as well as the project managers, district program coordinators and community health supervisors of BNMT Nepal.

Amid the COVID19 restrictions and risks, utmost precautionary measures were strictly followed in the meeting.

The meeting was successful in communicating and engaging all the distinguished government officials on detailed implementation plan and study protocols. The meeting also discussed about the forms and formats to be used in the project. We thank all the participants for their time, expertise, enthusiastic contributions and valuable ideas contributed during this meeting. We look forward to working together for the successful delivery of the Epidemic Intelligence project.

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