Covid-19 virus genomic tracking used in Guangdong Province, China

Researchers at Oxford and Guangdong Centre for Disease Control and Prevention have conducted a new study to ‘describe the epidemiology and genetic make-up’ of the Covid-19 outbreak in Guangdong province.

Guangdong province is China’s most populous region and was the second largest epidemic centre next to Hubei where Wuhan is located.

The study shows that how ‘early and intensive testing and tracing’ assisted the interruption of virus transmission.

The combination of genome sequencing and epidemiology reveals three phases of the outbreak in the province from January and February.

The introduction of new cases into the province, the rise and fall of local transmission as well as the import of new cases from international travellers.

There is over 100 million people in the province and testing was quickly introduced: by the 19th March, 1.6 million tests had identified 1,388 positive cases.

Enhanced surveillance techniques from the end of January monitored all travellers returning from Hubei province as well as other provinces to Guangdong province.

Close contacts were also monitored as well as all hospitalised patients.

From analysing genomes ‘generated from infected individuals’, the researchers concluded that the outbreak in the province was ‘not caused by one large chain of transmission.’

Instead, there were ‘hundreds’ of independent introductions from outside the province.

‘Locally-transmitted chains of infection are shown by their genetic information to be limited in size and duration.’

This shows that screening and intervention methods implemented in the province were effective in ‘interrupting local transmission’, according to the researchers.

The study also shows that the genome of SARS-CoV-2 (the virus that causes COVID-19) could be rapidly sequenced and analysed in near-real time.

‘Due to the speed and nature of this outbreak, different experimental approaches were attempted;

‘Good results were obtained using the handheld MinION sequencing device (developed by Oxford Nanopore Technologies) and a sequencing protocol developed by the ARTIC Network.’

Senior author, Professor Oliver Pybus, of the Department of Zoology and the Oxford Martin School said:

“We know already that changes to the COVID-19 genome accumulate more slowly than for other viruses such as influenza.

“This means the COVID-19 virus is moving and transmitting faster than it mutates.

“So, it’s crucial to analyse the virus genomes in combination with detailed epidemiological information, which is what we achieved in this study.”

Dr. Jing Lu, from Guangdong Provincial Institution of Public Health, Guangdong Centre for Disease Control, said:

“To get the best and most powerful insights we need to combine virus genome information with epidemiology and other data.

“Our work in Guangdong Province shows that high levels of very early testing, together with active case tracing and strict isolation, can bring an outbreak under control.”