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Six variants of Covid-19 in the country: Three ‘variants of concern’ in SL 

16 May 2021

  • Authorities urged to expedite vaccination programme  

  • Fast transmission results in virus mutations: Prof. Malavige  

  • Present PCR test kits not sufficient to identify new variant: Kumudesh  

  • Covid deaths could increase to hundreds: Dr. Colombage  

By Yumiko Perera    Sri Lanka is currently facing its third Covid-19 wave, and the upcoming weeks are nothing short of crucial, especially given the alarming number of new cases being reported daily and the increasing numbers of Covid-19 variants found in the country. Sri Lanka recently revealed that it had detected its first case of the Indian variant of Covid-19, also known as B.1.617, which was detected in a person who was in quarantine after recently returning from India.  While the Indian variant had been detected among several other samples obtained from across the country for testing, a report released by the Department of Immunology and Molecular Medicine of the University of Sri Jayawardenepura revealed that these six variants had been detected in the samples they had received for testing until 30 April.  As per the report, the variants detected thus far in Sri Lanka include the UK variant (B.1.1.7), the Sri Lankan variant (B.1.411), the Nigerian variant (B.1.525), the South African variant (B.1.351), Denmark/European/Middle East variant (B.1.428), along with the Indian variant (B.1.617).  Speaking with The Sunday Morning, Prof. Neelika Malavige from the University of Sri Jayewardenepura Department of Immunology and Molecular Medicine said: “Although the Indian variant has not been detected in the community so far, the UK variant (B.1.1.7), which is more prevalent in the community, is responsible for the ongoing spike in cases.” According to Prof. Malavige, a majority of these variants are more subtle and less fatal than others, but the stronger and more potent variants seem to have an increase in transmissibility and increased disease severity.  “The higher the rate of transmission, the faster the virus mutates. If we are to curb the spread of the virus, we need to speed up the vaccination process and make sure human activities would be minimal,” Prof. Malavige noted. She went on to say that the spread of the virus is closely being monitored by carrying out PCR and rapid antigen tests in those who are symptomatic. She further highlighted the need to conduct tests on close contacts of those confirmed to be Covid-positive, to identify as many infected individuals as possible and lessen the chances of further community spread.  While Sri Lanka has over 130,000 Covid-19 infections with over 105,000 recoveries since the onset of the pandemic, fatalities have neared the 900 mark, and travel restrictions have been imposed again. Against this backdrop, according to College of Medical Laboratory Science (CMLS) President Ravi Kumudesh, laboratory services are facing several issues.  He said the PCR test kits Sri Lanka has at hand may not suffice to identify cases of the new variants of the virus that may spread across the island. Kumudesh said that the PCR test kits have very low sensitivity, and are thus not able to detect certain variants of the virus.  Speaking with The Sunday Morning, he said: “Up until now, most laboratories that conduct PCR tests do not have the ability to detect most variants that can be found in the island at present. There is a shortage of reagents, and without them, laboratories are unable to make the most of the PCR machines we have at hand.” According to Kumudesh, the “S Gene Deletion” process can be used to detect the UK variant and the Denmark variant, but is futile when it comes to detecting other variants of the virus.  “The ‘S Gene Deletion’ uses a reagent that can’t be found in most government hospital laboratories, and these government laboratories have a reagent that has very low sensitivity. Since most laboratories in government hospitals lack the infrastructure and resources to detect the different variants of the virus that can be found on the island today, this needs to change,” he said.  Out of the four main variants of the virus that have been detected across the world, apart from the Indian variant, only the Brazil variant, the UK variant, the Denmark/European/Middle East variant and the South African variant can be detected through the PCR reagents, according to Kumudesh.  “If we are to study a variant, it has to be done through a process called gene sequencing, which is done through a gene sequence analyser. None of the laboratories under the Ministry of Health have one of these machines at present, and the only gene sequence analyser on the island can be found at the Sri Jayawardenapura University laboratory," said Kumudesh.   The World Health Organisation (WHO) has declared four variants of the coronavirus as “variants of concern” based on several factors. Out of the four variants that the WHO has dubbed as such, three have been detected in the island so far.  “The Indian variant, the UK variant, and the South African variant have been identified as ‘variants of concern’ by the WHO because they have proven to be stronger and more fatal than the rest of the variants that have been detected. They spread faster, the death rate is visibly higher, and they also do not react to the vaccinations as positively,” said Kumudesh. “While sequencing is not an easy job, or something that can be established overnight, we had it brought down before the pandemic,” Prof. Malavige said with regard to the concerns Kumudesh had raised.   Reiterating that they are ramping up their sequencing process to meet the current needs, Prof. Malavige concluded: “Sequencing should be done in a scientific manner, and the WHO has given us guidance on how to proceed.” Vietnam is ranked as No. 1 in the Asian region in terms of controlling the spread of Covid-19, while Sri Lanka is estimated to presently be at No. 10, as there has been a 28% increase compared with the previous week.  Before the Sinhala and Tamil New Year celebrations in April, the average cases reported had been around 150 a day. The numbers have now shot up to the thousands. While the first week of May alone saw 13,192 cases, exceeding 2,000 cases daily, the numbers only seem to be rising further.  Government Medical Officers’ Association (GMOA) Executive Committee member Dr Prasad Colambage highlighted that the number of fatalities has been oscillating between 20-30 a day.   Given the daily average of 25 Covid-19 fatalities that are being reported, Dr. Colmbage stated that he fears the fatalities may reach up to 250 in just 10 days. Against this backdrop, Dr. Colombage urged authorities to expedite the vaccination process.   

VARIANT 

 DISTRICTS IN WHICH VARIANT HAS BEEN DETECTED 

UK variant (B.1.1.7) 

 Colombo, Kurunegala, Kalutara, Kandy, Polonnaruwa, Mannar 

  Indian variant (B.1.617) 

Colombo 

  South African variant (B.1.351) 

Colombo 

Nigerian variant (B.1.525)   

Bandaragama (Kalutara), Colombo 

Sri Lankan variant (B.1.411) 

  Batticaloa, Colombo 

Denmark/European/Middle East variant (B.1.428) 

Jaffna 


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