The allergy, Immunology and Cell Biology Unit of Sri Jayewardenepura University Director Dr. Chandima Jeewandara assures that the deadly Indian variant of the Covid-19 virus was not detected in Sri Lanka so far while cautioning the public to stay indoors and strictly follow health guidelines to contain the current outbreak of the UK strain which could equally be deadly, if mishandled.
The Unit is exclusively performing genetic sequencing for the Covid-19 virus since March 2020, since the deadly global pandemic marked its entry here.
In an exclusive interview with the Sunday Observer, Dr. Jeewandara answers some of the pressing questions about the current outbreak and efficacy of available vaccines against the new variants of the Covid-19.
Excerpts of the interview:
Q: How many strains of the Covid-19 virus are circulating in Sri Lanka currently?
A. Our unit (Allergy Immunology and Cell Biology Unit) is the only institution in Sri Lanka which is carrying out genetic sequencing for the Covid-19 virus since March 2020. We have clearly identified three main clusters of infection. The very first one we experienced in March and April last year.
Most of them were returnees from Middle East and European countries. The initial strains that circulated in Sri Lanka belonged to different lineages as majority of the infections were due to returnees from overseas.
They were from different countries. Then we had a calm period which was followed up with a massive outbreak in a rehabilitation centre. After that, there was another massive outbreak in the community from Minuwangoda at a clothing factory and the Peliyagoda fish market which we call the second wave.
The second outbreak was due to a Sri Lankan lineage called B.1.411. It had specific mutations which were found only among SARS coV-2 genome. But luckily the infections due to this particular lineage had very mild symptoms. More than 90 percent of the patients were asymptomatic. This lineage continued to be the predominant strain to cause Covid-19 infections in Sri Lanka until the beginning of April.
During this wave, we have sequenced viruses belonging to B.1.1.7 (UK lineage) and B.1.351 (South African lineage) and several other European variants. However, none were leaked into the community as they were detected from returnees.
At the beginning of the second week of April, we observed a specific phenomenon in the routine RT-PCR in our laboratory. Interestingly, one of the PCR tests used (TaqPath) which looks for three genes in the viral RNA leads to one of the three signals being negative.
This is called Spike Gene Target Failure (SGTF) which can serve as a proxy for carriage of a specific mutation in the S gene.
This was similarly observed in the UK also in December 2020 where labs started reporting this finding of SGTF. Later, when they did the whole genome sequencing, they found that the reason for this SGTF was due to a specific deletion called 69-70 deletion of the SARS coV-2 genome which was confirmed with whole genome sequencing (B.1.1.7 lineage originated from the UK).
Later, we were also able to confirm that this small cluster of infection with SGTF and suspected of the UK variant from the Boralesgamuwa area belonging to the B117 lineage which is also called a variant of concern.
Apart from the Boralesgamuwa area similar reports were seen in the Colombo Municipal Council area and samples received from the Kurunegala District which was also confirmed with the B1.1.7 variant.
Q: What is genome sequencing?
A. A genome sequence is a unique way in which an organism’s genetic material is organised. In the case of viruses, this unique RNA sequence is used to create proteins using the host cell’s machinery (in the case of SARS-CoV-2, human cells serve as host cells).
Changes in the sequence change viral proteins and these changes can then influence functions of the virus, such as infectivity and virulence (severity of infection caused).
Genome sequencing uses techniques to decipher this unique genetic code and this helps differentiate one viral strain from another and consequently the differences in protein created by these differences in viral strains.
Q: Why it is important?
A. By sequencing the entire viral genome, researchers can pinpoint the genetic changes that occur in the virus as it spreads through the population.
- Understand the transmission of the virus
- Design treatments and vaccines
- Monitor viral evolution
- Prepare for the future
Q: What is a Variant of Concern (VOC) and how many do we have in Sri Lanka
A. A variant for which there is evidence of an increase in transmissibility, more severe disease (e.g. increased hospitalisations or deaths), and significant reduction in neutralisation by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures is called a VOC.
There are few VOCs currently specified by the World Health Organisation (WHO), which are the UK variant (B.1.1.7), the South African variant (B.1.351) the Brazilian variant (P.1) and variants defined in USA.
These have specific mutations in the spike protein, which assigns them to these particular variants. Out of them, Sri Lanka is increasingly identifying the UK variant after the New Year and that’s the only VOC we have detected in Sri Lanka.
Q: What are the latest findings from your laboratory?
A. As an initial analysis, we carried out analysis of mutations in 43 samples obtained from CMC, Boralesgamuwa and Kurunegala. All these samples had the 69/70 deletion and the N501Y mutation, specific to the UK variant, B.1.1.7. Therefore, we confirmed that the B.1.1.7 is currently circulating in Sri Lanka and is responsible for the current massive outbreak.
Q: Why is the B.1.1.7 lineage important?
A. The mortality rates associated with the B.1.1.7 infection is 55 percent higher than with the original SARS-CoV-2 virus. The transmissibility is also 50 percent higher. The countries which have been affected by B.1.1.7 have seen their cases rising exponentially, with more younger people also getting affected. The B.1.1.7 is responsible for 81 percent infection in Punjab.
The B.1.1.7 is also responsible for 50 percent of infections in Delhi. So, B 1.1.7 still is an important variant in many parts of India causing significant morbidity and mortality. Therefore, the B.1.1.7 plays a huge role in the current Covid-19 epidemic in India, in addition to the B.1.617, Indian variant.
Q: Did you find the Indian variant which is causing so much of death and suffering, in any of the samples referred to your laboratory up to now?
A. No.
Q: Can you explain in layman terms what is a mutation and how it happens?
A. There are three terms that you need to understand.
Mutation, variant and strain. Although the terms mutation, variant, and strain are often used interchangeably in describing the epidemiology of SARS-CoV-2, the distinctions are important.
Mutation refers to the actual change in sequence: Genomes that differ in sequence are often called variants.
This term is somewhat less precise because two variants can differ by one mutation or many. Strictly speaking, a variant is a strain when it has a demonstrably different phenotype. For example a difference in antigenicity, transmissibility, or virulence.
Q: What causes the virus to mutate?
A. Mutations arise as a natural by-product of viral replication.
RNA viruses typically have higher mutation rates than DNA viruses. Corona viruses, however, make fewer mutations than most RNA viruses because they encode an enzyme that corrects some of the errors made during replication.
In most cases, the fate of a newly arising mutation is determined by natural selection.
Those that confer a competitive advantage with respect to viral replication, transmission, or escape from immunity will increase in frequency, and those that reduce viral fitness tend to be culled from the population of circulating viruses.
Q: Will the new variant eventually be more widespread than the current virus?
A. As the B.1.1.7 variant is more transmissible than other SARS-CoV-2 lineages, it eventually could be the most commonly found lineage of SARS-CoV-2 in Sri Lanka very soon replacing the Sri Lankan lineage. However, while we still have so many people with no immunity to the virus, we should still see different lineages that are spreading in different parts of the world might leak into Sri Lanka.
Q: The consignment of this Oxford-AstraZeneca vaccine doses were ordered and received in January this year. Are these vaccines effective against the currently spreading UK variant?
A. Oxford-Astrazeneca, Pfizer, Moderna, Sputnik V are effective against this variant. There is no reduction of the efficacy of vaccine against this variant. That is very clear. All vaccines registered under WHO are effective against the UK variant.
As I mentioned earlier if the infections start spreading exponentially, it would acquire a couple of mutations a month. There will be very bad mutations accumulating which might lead to losing the vaccine’s efficacy against those strains. We have witnessed such situations in South Africa, Brazil and even in some parts of the UK.
We don’t want this to happen in Sri Lanka. Therefore, we are trying hard to contain the spread of the virus, so there will not be such mutations until the vaccination drive is complete.
Q: From an immunologist point of view, how can we contain the virus at this stage where you find many sub clusters and patients from all over the country?
A. Unlike in the past, we have a new variant which is creating a lot of problems –such as more symptoms, lung infections, and possibly more deaths in the future.
The possible action should be to contain the spread until vaccination is complete. Vaccination is the final and the only answer.
To stop the spread, people need to strictly adhere to health guidelines - wear masks, maintain social distancing, perform hand washing. And unless it is absolutely necessary, people should stay in the safety of their homes.
When stepping out, a safe two meters must be maintained between people and because the virus can transmit easily, it is safe to meet people outdoors.
The Health Ministry has already issued new Covid-19 guidelines in view of the rapid spread of the UK variant in the country.
The health authorities have increased testing and begun isolating areas where a spike in infections have been reported. In addition the Epidemiology Unit has expedited administering the second doses of the AstraZeneca as a matter of priority.
Israel has almost completed its vaccine drive and the UK is expected to open the country by summer after having a good coverage of vaccinations. We must try to replicate their success story.
Q: About 900,000 have received the first dose of the vaccine by now. Can they contract the virus and if yes how long should they wait to get the second dose?
A. Sri Lanka, until last Monday has not completed the vaccination schedule. Everyone as of today has partial immunity. The majority of the people vaccinated will not develop severe symptoms comparatively to the people who did not receive it.
If you have acute symptoms, the vaccine (second dose) must be delayed till you recover, but others must complete the schedule.
Q: If you contract the virus, how long should you wait to get your second dose?
A. When you have an infection you should delay it until you recover.