Fifth Wave of COVID-19 Devastates Hong Kong – How Next-Generation Sequencing Can Help with Latest Outbreak

Hong Kong’s government had the COVID-19 pandemic under control with its strict COVID zero strategy. However, after the highly infectious Omicron variant caused another COVID-19 outbreak this January, the Hong Kong healthcare system has found it increasingly difficult to maintain this approach.

With a record 55,000 daily new infections reported on March 3 and climbing death rates driven by unvaccinated elderly, the COVID-19 outbreak is pushing the region’s healthcare system to the brink. 

Hong Kong’s government has imposed the toughest restrictions, while the region’s 7.4 million residents have been ordered to take PCR tests three times later this month. As more details emerge, local media have reported about the length and strictness of the lockdown to occur when the COVID-19 testing is conducted.

Comparing Three Major COVID-19 Tests

COVID-19 tests can be categorized into three groups: the rapid antigen test, PCR test, and NGS (Next-Generation Sequencing).

• Rapid antigen test

The goal of the rapid test is to screen for positive cases as soon as possible. Tests can be done within 10-30 minutes, while the efficiency and low-price allow testing to be conducted on a large scale. However, rapid antigen tests come with the downsides of higher false-positive and false-negative rates compared to other COVID-19 tests. Therefore, a PCR test is often conducted following the rapid test to confirm test results.

• PCR test

 The principle of the PCR test is to screen a gene fragment from a sample for the SARS-CoV-2 nucleotide sequence. In order to conduct the PCR test, professional laboratory staff and instruments are required. It typically takes around 4 hours to get the test results.

However, since PCR’s accuracy and sensitivity are higher than those of rapid antigen tests, a positive result from a PCR test is still the general way to confirm a COVID-19 infection in most countries around the world.

• NGS(Next-Generation Sequencing)

With its ability to detect the presence of the SARS-CoV-2 by sequencing specific regions of the viral genome, NGS provides the most accurate result of all the COVID-19 tests. Additionally, the characteristic of identifying the virus variants precisely makes the work of pandemic prevention easier.

NGS Plays a Crucial Role in COVID-19 Surveillance by Monitoring The Variants 

Each RNA strand of the SARS-CoV-2 contains around 30,000 nucleotides. Every nucleotide contains key information regarding how the virus works, spread, and replicate. Whenever there is a slight change in the sequence of the virus, the virus tests, contagious, and even the symptoms to the vaccine could be changed accordingly.

PCR testing provides higher accuracy and can be conducted on a large scale. But as new COVID-19 variants emerge, gene sequencing plays an even more crucial role in COVID-19 surveillance, as it is more efficient and accurate, greatly improving efforts to trace the origins of the virus and find intermediate hosts. 

NGS technology is able to identify the SARS-CoV-2 gene expression on a large scale, revealing the mutation and progression of the virus. 

There are many biotechnology companies investing in the research and development of NGS technology in monitoring the coronavirus variants, including Illumina, Thermo Fisher Scientific and Qiagen. Illumina has provided the system used to sequence the first SARS-CoV-2 genome in China, which allowed for accelerated development of PCR tests and vaccines.

The Illumina COVIDSeq™ Test allows over 3,000 clinical samples to be run in one day through its exclusive system NovaSeq™ 6000, with relatively high sensitivity and specificity compared to the traditional sequencing. 

It has received the Emergency Use Authorization (EUA) from the FDA and the Pandemic Special Access Route (PSAR) from the Health Sciences Authority(HAS) of Singapore. Outside the U.S, Illumina provides the RUO(Research Use Only) version, considering more health administrations in the world are now issuing the health policy according to the genomic information from the virus. 

Fight Against the COVID-19 Pandemic Together With The Power from the Government and the Resource from the Biotechnology Companies

The battle against the COVID-19 pandemic is still ongoing. With the novel genomic sequencing technology provided by the biotech companies, the world can monitor the pandemic and identify the new variants before it causes another outbreak in the near future.

Author

Aurora Mau