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New method used to sequence COVID-19 genomes in Auckland outbreak


Dr Nikki Freed and Dr Olin Silander

Dr Nikki Freed and Dr Olin Silander


Scientists at Massey University sprang into action last week as the Government made the first announcements about a new COVID-19 outbreak in Auckland.

Dr Nikki Freed, Dr Olin Silander, and PhD student Markéta Vlková were quickly shoulder-tapped by colleagues at ESR (Institute of Environmental Science and Research) to help sequence and confirm the SARS-CoV-2 genomes (the virus that causes the COVID-19) from these new cases.

The School of Natural and Computational Sciences’ senior lecturers in genetics, Dr Freed and Dr Silander have recently developed faster, cheaper way to sequence the SARS-CoV-2 genome to track the evolution and transmission of the virus among people who have tested positive. Their results and method of sequencing are now being used internationally.

Dr. Freed received the first four index cases from the Auckland District Health Board on Wednesday midday. Less than eight hours later the Massey team were able to upload the fully sequenced genomes to the New Zealand SARS-CoV-2 database. This provided ESR with an initial advance look at the genome data and they were able to provide a preliminary report to health officials. ESR received the specimens late that same day for sequencing, which confirmed the results and was used informal reporting to the Ministry of Health.

The next day Dr. Freed and Ms. Vlková sequenced more genomes from managed isolation cases and ten samples from the community. Dr. Silander worked from home to assemble the genomes and upload the genomes in record time. This data indicated that the new cases were unlikely to be from separate outbreaks, and none appeared to be connected to cases in managed isolation.

In addition to providing the genome data in unprecedented time, the team’s results served as aninitial analysis of the genome sequences produced by New Zealand’s reference laboratory ESR, who also used the rapid method developed by the Massey team.

Dr Freed says rapid and cost-efficient whole-genome sequencing of the virus that causes COVID-19 is critical for understanding viral transmission dynamics: “Genome sequencing looks into the makeup of the virus and identifying subtle differences in the sequence of the ribonucleic acid can help them to identify the sources of outbreaks. With our method, the genome sequence can be determined in a single day.

“The outbreak in Auckland demonstrates the utility of the method we developed at Massey for rapid genome sequencing which cuts the typical time for preparing and sequencing the samples in half. Our method requires only around 30 minutes of hands on time, as compared to 2 hours with the other method. It can be performed on multiple samples at a time.”

The rapid genome sequence aided the Ministry of Health and ESR investigations to determine that the positive cases seen were all linked (both through contact tracing and sequence data).

The team’s method is currently being used worldwide by sequencing facilities in Australia, Canada, Germany, Spain including the Oregon SARS-CoV-2 Genome Sequencing Center at Oregon Health Sciences University in the US.

The rapid genome sequencing method the team developed was enabled via funding from the Health Research Council of New Zealand and Ministry of Health.

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