50 India 'double mutant', 137 S Africa variant cases in Singapore so far: COVID database

Wong Casandra
·Senior Reporter
·6-min read
SINGAPORE - DECEMBER 15: Travellers wearing protective mask walk along the transit area of Changi International Airport terminal on December 15, 2020 in Singapore. From mid-January, Singapore will allow a limited number of business travellers from any country to visit up to 14 days under a new segregated travel lane arrangement where they will be housed within dedicated facilities undergoing regular testing and observe all safety measurement management measures. As of 14 December, the Ministry of Health confirmed 5 new imported COVID-19 cases with no cases in the wider community bringing the country's total to 58,325. (Photo by Suhaimi Abdullah/Getty Images)
Travellers wearing protective masks walk along the transit area of Changi International Airport terminal on 15 December, 2020 in Singapore. (Getty Images file photo)

SINGAPORE — At least 50 cases of a new "double mutant" Indian COVID-19 variant and 137 of the South African strain have been detected in Singapore, according to the Global Initiative on Sharing All Influenza Data (GISAID), the world's largest database of novel coronavirus genome sequences.

The first case of the Indian variant – or B.1.617 – in Singapore was detected on 26 February, while the first case of the South African variant – or B.1.351 – was detected on 7 February, according to the database.

Forty-seven cases of the Indian variant were submitted to the database over the "last four weeks", though the exact time period was not specified. One hundred and six cases of the South African variant were also recorded in the GISAID during the same period.

Figures of Indian
Figures of Indian "double mutant" variant (left) and South African variant cases in Singapore as submitted to the database, screencapped on 21 April, 2021. (SCREENCAP: GISAID)

According to the database, Singapore's latest occurrence of the Indian variant was logged last Wednesday (14 April) by a team of medical researchers at the National Public Health Laboratory (NPHL), one of whom was named as NPHL director Raymond Lin Tzer Pin. 

The laboratory is one of the National Centre for Infectious Diseases' public health units.

Singapore's latest occurrence of the South African variant – or B.1.351 – was logged on the same day by the same team.

Submission by a team at the NCID's National Public Health Laboratory, screencapped on 21 April, 2021. (SCREENCAP: GISAID)
Submission by a team at the NCID's National Public Health Laboratory, screencapped on 21 April, 2021. (SCREENCAP: GISAID)

There were a total of 144 submitted cases of the UK variant – or B.1.1.7 – in Singapore, with 60 detected over an unspecified time period of four weeks, according to the GISAID.

The Ministry of Health (MOH) last confirmed in end-January that 25 cases of the UK variant were detected in Singapore between 23 December last year and 26 January. No other variants were detected in Singapore then, according to the local authorities.

Three cases of the Brazilian variant – or P.1 – were logged in the database in the past four weeks. The latest cases of the UK and Brazilian variants were submitted on 14 and 8 April, respectively.

Figures of UK variant (left) and Brazil variant cases in Singapore as submitted to the database, screencapped on 21 April, 2021. (SCREENCAP: GISAID)
Figures of UK variant (left) and Brazil variant cases in Singapore as submitted to the database, screencapped on 21 April, 2021. (SCREENCAP: GISAID)

The GISAID is the world’s biggest database of SARS-CoV-2 sequences, storing more than 700,000 genomes from more than 160 countries, according to peer-reviewed academic journal Science Magazine. Researchers around the world have used the GISAID to assess mutations and prevalence of COVID-19 variants.

Cases with two other variants of interest – labelled as such by the World Health Organization (WHO) – that were detected in Singapore were also submitted to the GISAID database. They are four cases of the Californian variant – or B.1.427/B.1.429 – and four cases of the B.1.525 mutation. Instances of both variants were last recorded into the database in late March.

It is unclear how many of the different variant cases logged in the GISAID are imported or local infections.

Yahoo News Singapore has reached out to the MOH, NCID, and NPHL for comment.

Figures of Californian variant (left) and B.1.525 variant cases in Singapore as submitted to the database, screencapped on 21 April, 2021. (SCREENCAP: GISAID)
Figures of Californian variant (left) and B.1.525 variant cases in Singapore as submitted to the database, screencapped on 21 April, 2021. (SCREENCAP: GISAID)

Contagious and concerning variants 

Out of many thousands, three variants of concern – the UK, South African, and Brazilian strains – have attracted international attention due to their increased transmissibility and virulence.

The trio share a particular mutation – named N501Y – that is thought to make them more contagious. This mutation occurs on the virus' spike protein, which attaches to human cells.

The South African and Brazilian variants, as well as variant of interest B.1.525, share another key mutation – named E484K – that is suspected to reduce the immunity acquired either by a past infection or a vaccine.

The UK variant first emerged in September last year and is said to be up to 70 per cent more transmissible than previously dominant variants. According to WHO data, the strain has spread to over 130 countries, including Singapore.

The South African variant, which was detected in August, is thought to be 1.5 times more transmissible and can potentially increase the risk of in-hospital mortality by 20 per cent, according to the WHO. It has spread to over 80 countries, and is listed as not officially verified in Singapore in WHO weekly epidemiological reports.

Studies have shown the Brazilian variant to be as much as 2.5 times more contagious than the original virus and more resistant to antibodies.

The particular variant, which emerged in December last year in or around the northern Brazilian city of Manaus, has spread to over 50 countries. It was first identified in Japan, where it was detected in travellers returning from Brazil.

Global concerns have also been sparked by the emergence of the "double mutant" Indian strain with the E484Q and L452R mutations, which appears to be the main driving force behind a surge in new cases in the country. It has been detected in at least 17 countries.

A Singapore Mutation Report generated by outbreak.info using information from the GISAID, as screencapped on 21 April, 2021. (SCREENCAP: outbreak.info)
A Singapore Mutation Report generated by outbreak.info using information from the GISAID, as screencapped on 21 April, 2021. (SCREENCAP: outbreak.info)

On Tuesday, the MOH announced a slew of revised border measures to take effect from 11.59pm on Thursday, including stricter ones for travellers arriving from India as well as lifting bans for those with recent travel history to the UK and South Africa.

Preliminary studies show that the vaccines from AstraZeneca and China's Sinovac are partly effective against the Brazilian variant. The Pfizer-BioNTech vaccine, one of two approved for use here, has also been proven effective against the strain, but studies have shown that it is less effective against the South African variant.

Two new Moderna vaccines designed to protect against the South African and Brazilian variants have yielded promising results when tested in mice, according to recent data. The original Moderna vaccine is approved for use in Singapore.

As of last Sunday, some 1.36 million individuals in Singapore have received at least one dose of either the Pfizer-BioNTech or Moderna vaccine, with more than 849,700 of them having received their second dose of the same vaccine and completed the full vaccination regimen.

A breakdown of how many of each vaccine type is administered here is not publicly available.

To date, Singapore has recorded 60,880 coronavirus cases, of which over 4,000 are imported.

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