NCM 2021: The first 100 days of establishing nanopore-based sequencing with major contributions to national genomic surveillance

COVID-19 was first detected in Indonesia, which has a population of approximately 270 million people, on 2nd March 2020. The GSI Lab responded by providing a SARS-CoV-2 detection service, delivering up to 5,000 COVID-19 tests per day. In May 2021, they submitted 1,759 genomic sequences to the GISAID database; however, this was only 0.098% of the total cases in Indonesia. There was also a large turnaround time (160 days) between sample collection and variant reporting. To bridge the gap in accurate, high-throughput sequencing, the Oxford Nanopore GridION was used to help with the COVID-19 detection program and Ariel's group shared their experience in this presentation. Initially, sample numbers were low, even though case numbers were high. Non-detected segments (NNN%) of RNA were close to 8% in June but improvements reduced this number to around 2% by September. Many health service providers were asking 'what is genome sequencing really for?', so the GSI lab began weekly reports to district governments and the Ministry of Health and started an open forum on facts, efficacy, viral spread, and effective case tracing. With effective communication of timely genomics, healthcare providers were six times more likely to send samples. Submission speeds to GISAID increased due to training in new bulk upload methods and implementing a submission portal, requiring submission form training to healthcare providers. A customised sample health record was created. To date, they have submitted over 16.5% of the total SARS-CoV-2 whole-genome sequences for Indonesia and have improved the availability of this technology to other islands in the archipelago; however, although the number of genome sequences has increased, so too has the infection rate, meaning that the percentage of cases sequenced still remains low. Together with Oxford Nanopore, Ariel's group propose to support a national genomic surveillance consortium using real-time and high-throughput genomic sequencing.