The AICBU was the first laboratory in Sri Lanka to introduce Oxford Nanopore Sequencing, the second to own a benchtop next-generation genome sequencing machine and the first to purchase an Illumina NextSeq 550 and iSeq 100. The team conducted Sri Lanka’s first COVID-19 Whole Genome Sequencing run on 18th April 2020 using this technology. Since then, it has carried out over 75 sequencing runs to produce over 3032 high-quality genomic datasets. 76.8% of this data was generated using Oxford Nanopore sequencing and the remainder using Illumina.
During the four major outbreaks in Sri Lanka since March 2020, the team was able to identify and report every lineage that drove the outbreak within a very short time. This is reflected in GISAID Data Deposition statistics which indicate that Sri Lanka was one of the countries with the lowest average number of days to deposit sequences, surpassing developed countries such as the USA and Norway.
The unit is 1 of just 4 laboratories in the government sector that have the capacity to conduct genome sequencing of SARS-CoV-2 in Sri Lanka and more than 94% of genomes uploaded to GISAID in the country are from the AICBU thanks to its 5 genome sequencers and GPU-powered bioinformatics setup specially dedicated to Oxford Nanopore Sequencing. Additionally, during the Delta-wave in Sri Lanka, we were able to train 183 medical laboratory technologists from the Ministry of Health.
Illumina’s “sequencing by synthesis” (SBS) chemistry is a widely adopted sequencing technique in the modern scientific world which has generated ~90% of the publicly available genome sequencing data. SBS chemistry uses fluorescently labelled nucleic acid bases that bind to the complementary bases of the original DNA strand from the sample at each sequencing cycle generating a sequence with an accuracy of 99.9% (Q30). NextSeq550 is one of the mid-high range bench top sequencers of Illumina that supports massively parallel (120 Gigabase output) sequencing and DNA microarray experiments.
External uses
NextSeq550 platform can be used to perform targeted sequencing, metagenomics, whole genome sequencing of viruses and bacteria, and even human transcriptome and exome sequencing for research purposes.
The iSeq100 is a small bench top sequencer that uses semiconductor chip sequencing technology combined with a single channel of Illumina’s proprietary sequencing by synthesis (SBS) chemistry. Even though the iSeq100 cannot generate a high throughput like other Illumina sequencers, its output of 1.2 Gigabases is sufficient for small-scale sequencing experiments without the loss of accuracy.
External uses
The iSeq 100 System is capable of handling small whole-genome experiments such as bacteria, viruses, and plasmid sequencing as well as targeted sequencing of a set of genes or gene regions, gene expression analysis, or 16S metagenomics.
MinION is a powerful portable sequencing device that delivers immediate access to gigabases of long-read data. The pocket-sized, USB-powered MinION allows us to sequence anything, anywhere-from the bench to the field, with real time analysis providing immediate access to actionable results.
External uses
The MinION is capable of sequencing whole genomes/exomes, whole transcriptome(cDNA), smaller transcriptomes (direct RNA) and can be used in targeted sequencing, metagenomics and multiplexing for smaller samples.
