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Consortium for Surveillance of SARS-CoV-2 Sequence and Structure in LMICs: Leveraging the capabilities and networks of the Wellcome-funded International Units

Funder: Wellcome Trust

Principal Investigators: Philip Bejon, Le Van Tan, Anuraj Shankar

Locations: Viet Nam and Indonesia

Timeline: April 2021 – April 2022

Objectives:

The goal of this Consortium is to deliver large-scale real-time SARS-CoV-2 whole genome sequencing capacity (WCS) to hospitals and local governments across Wellcome Africa-Asia programme countries. This effort, when combined with epidemiological and clinical information, will inform interventions and policy decisions during the current pandemic.

Virus genome data are combined with clinical and epidemiological datasets in order to help to guide public health interventions and policies. Subsequent analyses will enable the evaluation of novel treatments and non-pharmacological interventions on SARS-CoV-2 virus populations and spread and provide information on introductions versus community transmission and outbreaks.

These data will also allow researchers to identify and evaluate emerging genetic changes and understand how they affect the ability of the virus to transmit from person to person and to cause severe forms of the disease.

Impact:

Shared technologies, bio-informatics, experience, and funds across the Wellcome Africa-Asia Sequencing Consortium has led to better and faster SARS-CoV-2 WGS. This includes contribution of nearly 6,000 SARS-CoV-2 WGS to GISAID, comprising 20-30% of all WGS from Vietnam or Indonesia, and nearly 4x acceleration of WGS throughput, thereby enabling the first detections of the Alpha, Delta, and Omicron variants in Vietnam or Indonesia. This was possible by strengthening the WGS capacity for the national Centers for Disease Control, and the Ministries of Health in Vietnam and Indonesia, and with specific institutions in Vietnam including the Hospital for Tropical Diseases, and National Institute of Hygiene and Epidemiology; and in Indonesia it led to establishment of the public private partnership social enterprise known as the Genomik Solidaritas Indonesia Laboratory (GSI Lab) as the highest throughput molecular diagnostics and WGS facility in the country. Key lessons include the need for global and local partnerships across the Africa Asia Program, and to foster use of multiple technologies and skillsets, and interdisciplinary teams of scientists focused on genomics.

Outputs:

Pradipta A, Kumaheri MA, Wahyudi LD, Susanto AP, Agasi HI, Shankar AH, Sudarmono P. (2022). Accelerating detection of variants during COVID-19 surges by diverse technological and public health partnerships: a case study from Indonesia. Front Genet 2022 13:801332. Available from: https://doi.org/10.3389/fgene.2022.801332

 

COVID-19 outbreak response in Viet Nam

Principal Investigator: Le Van Tan

Locations: Viet Nam

 

SARS-CoV-2 Sequencing

 OUCRU Viet Nam has dedicated our whole molecular diagnostic facilities and sample processing systems for COVID-19 diagnostics. A team of 15 senior research staff at OUCRU has teamed up with the diagnostic group at the Hospital For Tropical Diseases in Ho Chi Minh City to perform COVID-19 diagnostics.

As of July 2021, the lab can process some 1500 tests per day. By July 5, 2021, the OUCRU/HTD diagnostics team had conducted PCR testing for 140,000 individuals in Ho Chi Minh City, Viet Nam.

We have been leading real-time whole-genome sequencing to inform Viet Nam’s outbreak response, especially in Ho Chi Minh City. The turnaround time is 24 hours. Ho Chi Minh City is one of the few places in Southeast Asia where whole-genome sequencing of SARS-CoV-2 has been successfully applied for outbreak response.

 

Key milestones are:

  • The Tan Son Nhat international airport outbreak in February 2021. Rapid whole-genome sequencing found that the SARS-CoV-2 variant A.23.1 was responsible for this outbreak. Therefore, the outbreak in Ho Chi Minh City at the time was epidemiologically unrelated to the ongoing outbreak in Hai Duong and Quang Ninh, which was caused by the Alpha variant (B.1.1.7).
  • The ongoing citywide outbreak: Since the second week of May 2021, several clusters of symptomatic SARS-CoV-2 infection of unknown origin have been detected in Ho Chi Minh City. Using whole-genome sequencing, our team showed that while both the Alpha and Delta variants were responsible for these clusters, the Delta variant with higher transmissibility has become the dominant variant responsible for the current outbreak in the city.
  • Collectively, these whole-genome sequencing data have been critical to informing COVID-19 response in Ho Chi Minh City and Viet Nam as a whole, contributing to the overall success of SARS-CoV-2 control in Viet Nam. We were recently recognised by the People’s Committee of Ho Chi Minh City for our contribution to the COVID-19 outbreak response in the city.

 

Capacity building:

We have trained our colleagues at the Institute of Pasteur in Nha Trang on the whole-genome sequencing of SARS-CoV-2. They can now operate the sequencing platform independently with remote support from our team in Ho Chi Minh City. Similarly, the team at OUCRU Hanoi has transferred sequencing protocols for direct sequencing to the National Insititute of Hygiene and Epidemiology (NIHE) in Hanoi, who are applying this independently. The OUCRU Hanoi team works with the National Hospital for Tropical Diseases and aims to sequence all epidemiologically relevant viruses weekly.

 

Papers published in international journals:

  • Le Van Tan. COVID-19 control in Viet Nam. Nature Immunology [Internet] 2021;22(3):261-261. Available from: https://doi.org/10.1038/s41590-021-00882-9
  • Nguyen Thi Tam, Pham Ngoc Thach, Trang Dinh Van et al. Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Viet Nam. PLOS ONE [Internet] 2020;15(11):e0242537. Available from: https://doi.org/10.1371/journal.pone.0242537
  • Nguyen Van Vinh Chau, Le Nguyen Thanh Nhan, Lam Anh Nguyet et al. Absence of SARS-CoV-2 antibodies in pre-pandemic plasma from children and adults in Viet Nam. [Internet] 2021;Available from: https://doi.org/10.1101/2021.07.12.21260379
  • Nguyen Van Vinh Chau, Nguyen Thi Thu Hong, Nghiem My Ngoc et al. Rapid whole-genome sequencing to inform COVID-19 outbreak response in Viet Nam. Journal of Infection [Internet] 2021;82(6):276-316. Available from: https://doi.org/10.1016/j.jinf.2021.03.017
  • Nguyen Van Vinh Chau, Nguyen Thi Thu Hong, Nghiem My Ngoc et al. Superspreading Event of SARS-CoV-2 Infection at a Bar, Ho Chi Minh City, Viet Nam. Emerging Infectious Diseases [Internet] 2021;;27(1):310-314. Available from: https://doi.org/10.3201/eid2701.203480
  • Ton That Thanh, Nguyen Thi Thanh Nhan, Huynh Kim Mai et al. The Application of Sample Pooling for Mass Screening of SARS-CoV-2 in an Outbreak of COVID-19 in Viet Nam. The American Journal of Tropical Medicine and Hygiene [Internet] 2021;104(4):1531-1534. Available from: https://doi.org/10.4269/ajtmh.20-1583