550 out of about 62,000 Covid-19 cases in Singapore infected with Delta variant

SINGAPORE – Of the roughly 62,000 Covid-19 cases recorded in Singapore as at end-May, 550 had been infected with the Delta variant of the coronavirus first detected in India.

This figure includes 428 local and 122 imported cases, the Ministry of Health (MOH) told The Straits Times on Tuesday (June 8).

“Variants are detected through viral genomic sequencing, and in Singapore, the National Public Health Laboratory performs sequencing for all confirmed Covid-19 cases,” said an MOH spokesman.

“This is unlike some countries who typically sequence a smaller proportion of their confirmed cases.”

The ministry was responding to queries from ST on the proportion of Covid-19 cases in Singapore infected with the Delta variant.

According to data on global database GISAID that ST accessed on Wednesday, 20 people in Singapore were infected with the Delta variant in the past four weeks.

GISAID is an online platform where research groups from all over the world can upload genetic sequences of the virus that causes Covid-19.

The 20 cases account for about 87 per cent of the Covid-19 cases from Singapore reported on that platform over the same period.

Given that variants of concern are thought to be more transmissible, this number may seem alarmingly high. But experts caution that data on GISAID is not reflective of the national situation.

Associate Professor Raymond Lin, director of the National Public Health Laboratory at the National Centre for Infectious Diseases (NCID), said submission to GISAID is voluntary – it is up to laboratories which cases to select and how many sequences to upload.

“If there is no submission from a country, the entry will state ‘the lowest in the world’. So comparison of numbers submitted and reported on GISAID may not be as meaningful,” Prof Lin said.

For instance, the platform on Wednesday reflected zero delta variant cases in Canada, Argentina and Sri Lanka over the past four weeks.

Prof Lin added that GISAID data may instead be more indicative of a country’s overall capacity and resources for sequencing.

“In Singapore, we perform sequencing for all confirmed cases, however, not all cases have successful sequencing due to inadequacy of specimen material. All those with high-quality sequence, we submit to GISAID,” he said.

Genomic sequencing refers to the technique used by public health authorities and researchers to “read” the genetic sequence of a pathogen.

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While the genetic code of the pathogen that causes Covid-19 is largely the same, variants will show slight differences in their genetic code.

Since this sequence is unique to each variant, this technique allows the authorities and scientists to identify them.

Dr Sebastian Maurer-Stroh, executive director of the Agency for Science, Technology and Research’s (A*Star) Bioinformatics Institute, agreed with Prof Lin, saying countries with more intense sequencing efforts will rank high on GISAID.

But he added: “Higher number of genomes is not a sign of having more of a specific variant than other countries unless both compared countries have the same surveillance intensity. For example, it is not true that Britain has more Delta variant cases than India.”

GISAID data showed that there were 16,779 Delta variant Covid-19 cases in Britain over the past four weeks, compared with India’s 330.

Imported cases had also been isolated upon arrival in Singapore. ST PHOTO: KUA CHEE SIONG

Dr Maurer-Stroh said that to get a better picture of how prevalent a variant is, it is more useful to look at the frequency of variants in countries with high genomic surveillance effort.

He cited how the proportion of cases infected with the Delta variant in Britain rose from 25 per cent a few weeks ago to the current figure of 67.5 per cent reflected on the site on Wednesday.

As for Singapore, GISAID data last week showed the proportion of Covid-19 Delta variant cases at 91 per cent, compared with the 87 per cent reflected on Wednesday.

The MOH spokesman said all necessary action to protect public health has been taken promptly, including isolating and ring-fencing Covid-19 cases in the community. Imported cases have also been isolated upon arrival in Singapore.

“We have also stepped up our testing, contact tracing and vaccination programme to keep Covid-19 under control,” she said.

While the Delta variant appears to be more transmissible, Singapore has adapted its measures accordingly and the number of locally transmitted cases has decreased over the last two weeks.

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Said the MOH spokesman: “Studies are ongoing to get a more complete understanding of these variants and we will adjust our strategies as more information is made available.”

MOH figures also show that the number of local Delta variant cases in Singapore is the highest caused by a variant of concern, among four such variants that have been detected here.

Variants of concern are more easily transmitted from person to person.

As at May 31, a total of 449 local cases of infection involve a variant of concern. They include:

– 428 people infected with the Delta variant

– Seven people infected with the Alpha variant, first detected in Britain

– Nine people infected with the Beta variant, first detected in South Africa

– Five people infected with the Gamma variant, first detected in Brazil

NCID’s Prof Lin said that the properties of variants of concern are still under study.

“Singapore’s sequencing efforts have been focused on helping to determine the chain of transmission leading to clusters of cases. By understanding that, we try to interrupt or reduce such transmission,” he added.

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