Objectives

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.

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.

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.