Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia.

Ariel Pradipta,Harryyanto Ishaq Agasi,Meutia Ayuputeri Kumaheri,Anuraj H Shankar,Anindya Pradipta Susanto,Lilik Duwi Wahyudi,Pratiwi Sudarmono

doi:10.3389/fgene.2022.801332

Abstract

Early detection of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) variants and use of data for public health action requires a coordinated, rapid, and high throughput approach to whole genome sequencing (WGS). Currently, WGS output from many low- and middle-income countries (LMIC) has lagged. By fostering diverse partnerships and multiple sequencing technologies, Indonesia accelerated SARS-CoV-2 WGS uploads to GISAID from 1,210 in April 2021 to 5,791 in August 2021, an increase from 11 submissions per day between January to May, to 43 per day between June to August. Turn-around-time from specimen collection to submission decreased from 77 to 5 days, allowing for timely public health decisions. These changes were enabled by establishment of the National Genomic Surveillance Consortium, coordination between public and private sector laboratories with WGS capability, and diversification of sequencing platform technologies. Here we present how diversification on multiple levels enabled a rapid and significant increase of national WGS performance, with potentially valuable lessons for other LMICs.

Highlights

The Corona Virus Disease-2019 (COVID-19) pandemic has continued (Wang et al, 2021; World Health Organization, 2021) driven by low vaccination rates, premature reduction in physical distancing, and the emergence of variants
From March 2020 to April 2021, the Consortium had recorded 1,210 SARS-CoV-2 sequences; this was 0.073% of 1,668,360 recorded infections in Indonesia, with a monthly average of 140 days from specimen collection to sequence uploading to GISAID
In the middle of 2020, SARS-CoV-2 variants presented a significant challenge to pandemic management

Summary

INTRODUCTION

The Corona Virus Disease-2019 (COVID-19) pandemic has continued (Wang et al, 2021; World Health Organization, 2021) driven by low vaccination rates, premature reduction in physical distancing, and the emergence of variants. By bringing together a mix of technologies and public health experts from both the public and private sectors, high throughput workflows and technologies were established in a low-resource setting This catalyzed an acceleration to nearly 4 times more SARS-CoV-2 WGS per day, and a 93% reduction in the delay from specimen collection to sequence availability in the GISAID database. To meet the need for rapid WGS, the MoH and NGSC diversified the approach by broadening the network to include a private sector social enterprise doing high-throughput PCR diagnostics, and repurposing its workflows for real-time sequencing This catalyzed more diversity within the network in five core areas: 1) introduction of the latest Oxford-Nanopore Technology (ONT); 2) increased use of high throughput workflows; 3) more streamlined information management and bioinformatics; 4) transition to sequencing primarily as a public health tool for pandemic mitigation; and 5) increased inter-laboratory cooperation coupled with friendly competitive challenges. Efforts are ongoing to gather more accurate reports on vaccination status, comorbidity, clinical outcome, and other relevant information to uncover the possible impacts of variantrelated COVID-19 surges (Ramasamy et al, 2020; Challen et al, 2021; Davies et al, 2021; Ozono et al, 2021)

CONCLUSION

Findings

ETHICS STATEMENT