The key to ending the pandemic | Daily News
Herd Immunity:

The key to ending the pandemic

Genomic sequencing is very important in tackling COVID
Genomic sequencing is very important in tackling COVID

COVID-19, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an ongoing global health emergency that has been the hot potato across the globe for nearly two years. Sri Lanka, also a victim of the COVID-19 pandemic, is currently facing the third wave of the virus. During this third wave, Sri Lanka has been detecting various variants of Coronavirus, which is a critical situation.

Exacerbating the situation, Sri Lanka has also detected a considerable number of cases from the deadly Indian variant of COVID-19, known as the Delta variant.

However, many Sri Lankans do not yet have a sufficient understanding of these variants, and the Daily News, therefore, spoke to Dr. Chandima Jeewandara, Director of the Allergy, Immunology and Cell Biology unit (AICBU) of the University of Sri Jayewardenepura to provide clarity on this crucial issue.

Q. What is the prevalence of Coronavirus variants in Sri Lanka according to your studies? How many have been identified?

A. We have detected multiple variants belonging to different lineages. These are the main ones we have sequenced in our laboratory at AICBU. Most importantly, we have detected three variants of concern (Alpha, Beta and Delta). The only variants of concern (VOC) we haven’t observed in the country is Gamma.

The Sri Lankan situation can be defined in three waves: First Wave – multiple imported lineages; Second Wave – B.1.411 Sri Lankan lineage; and Third Wave: B.1.1.7. – Alpha.

Q. What is genome sequencing, and what is the importance of genome sequencing in combating a pandemic such as COVID 19?

A. At the centre of each Coronavirus is its genome, a twisted strand of nearly 30,000 ‘letters’ of RNA, placed like bricks next to each other. These genetic instructions force infected human cells to assemble up to 29 kinds of proteins that help the Coronavirus multiply and spread.

A genome sequence is a unique way of organizing an organism’s genetic material. In the case of viruses, the host cell’s machinery is employed to produce proteins from this unique RNA sequence (in SARS-CoV-2, human cells serve as host cells).

Changes in the sequence called mutations can alter viral proteins, which can impact the virus’s activities, such as infectivity and virulence (severity of infection caused). (An alteration in any of these bases causes a mutation, effectively changing the shape and behaviour of the virus). Viruses mutate all the time and most changes are not important. Some even harm the virus. But others can make the disease more infectious or threatening – and these mutations tend to dominate.

Genome sequencing employs tools to decode this unique genetic code, which aids in distinguishing one viral strain from another and, as a result, the variations in the protein produced by these viral strain differences.

Q. What is significant about the Delta and Delta Plus variants? Why should the public be extra careful with regard to these variants?

A. As we all know, multiple SARS-CoV-2 variants are circulating globally. One of these variants is the B.1.617 lineage, detected in India earlier this year. Early evidence suggests that its sub-lineage B.1.617.2, known as the Delta variant, is more transmissible than contemporary lineages.

It is the fourth VOC described by WHO because it is twice more transmissible than the previous variant.  

The Delta variant contains multiple mutations in the spike protein. At least four mutations are important.

One of these is called L452R, first reported in Denmark in March last year. This mutation has been found to be more transmissible than wild-type strains and has also been associated with reduced antibody efficacy and reduced neutralisation by vaccine sera.

The mutation P681R has been associated with chemical processes that may enhance transmissibility.

The D614G mutation was first documented in the US early in the pandemic, having initially circulated in Europe. There is evidence that variants with this mutation spread more quickly.

Another mutation in Delta is T478K. This was present in around 65 percent of occurrences in variant B.1.1.222, first detected in Mexico last year and associated with higher infectivity.

The Delta Plus variant contains an additional mutation called K417N on the Coronavirus spike, which has been found in the Beta and Gamma variants, first found in South Africa and Brazil respectively (Beta was linked to increased hospitalisation and deaths during South Africa’s first wave of infections, while Gamma was estimated to be highly transmissible).

By July 3, 2021, (1) B.1.1.7 had been reported from at least 160 countries; (2) B.1.351 from 113 countries; (3) P.1 from 64 countries; and (4) B.1.617.2 from 96 countries.

Q. Currently, how do you identify the spread of the Delta variant in Sri Lanka?

A. As of today, a total of 19 cases have been identified from our laboratory. B.1.617.2 (Delta) virus has been identified within the Colombo Municipal Council area (Colombo 2, 5, 9, 10 and 14), National Institute of Mental Health and Teaching Hospital Karapitiya, Galle.

Q: Are the symptoms for cases of the Indian variant different?

A. Yes, there are slight differences. We have observed that it is different to the ‘classic’ Coronavirus symptoms according to the National Health Services (NHS). Accordingly, symptoms such as fever, cough and loss of smell and taste might be prevalent.

A. Also, headaches, sore throat and a runny nose are more common symptoms with the new variant.

Q: How fast is it spreading? Transmissibility? Why is it more contagious?

A: The Delta variant is 60 percent more transmissible than the Alpha variant, B.1.17. Delta has a key mutation on the spike protein – which the Coronavirus uses to latch on to human cells – called L452R. 

And also, this virus appears ‘fitter’ than previous variants.

From data collected in the lab, it looks like Delta’s mutations make it spread more quickly in the cells in a person’s airways, which means an individual is likely to emit more viruses when infected. Adding to that, the Delta variant is the most contagious variant found to date, with transmissibility that is approximately two times faster than the older strain: B117 – Alpha – 29 percent faster; B1351 – Beta 25 percent; P1 – Gamma – 38 percent; and B16172 – Delta – 97 percent.

R0 values can further give an understanding regarding the spread of the virus. It is a mathematical term that indicates how contagious an infectious disease can be. It can also be referred to as the reproduction number; as an infection is transmitted to new people, it reproduces itself. Therefore, it will give out the average number of people who will contract the disease from one infected person.

Q. Are the currently available vaccines effective against the Delta variants?

Delta seems to be around 60 percent more transmissible than the already highly infectious Alpha variant (also called B.1.1.7) identified in the United Kingdom in late 2020.

WHO emergency listed vaccines offer protection against developing severe cases, hospitalization and death due to the Delta variant.

People who’ve been vaccinated are much less likely to end up in hospital. And you need the entire course of vaccination in order to give you that complete immunity to protect you against the Delta variant.

Delta is moderately resistant to vaccines, particularly in people who have received just a single dose.

A Public Health England study published on May 22 found that a single dose of either AstraZeneca’s or Pfizer’s vaccine reduced a person’s risk of developing COVID-19 symptoms caused by the Delta variant by 33 percent, compared to 50 percent for the Alpha variant.

A second dose of the AstraZeneca vaccine boosted protection against Delta to 60 percent (compared to 66 percent against Alpha), while two doses of Pfizer’s jab were 88 percent effective (compared to 93 percent against Alpha).

The main goal of these vaccines is to prevent severe disease because what we want is for people, even if they get the infection, to recover from it and not become seriously ill.

Q. Could the variant cause a new wave?

Modelling has already shown that if the new variant is as transmissible as feared, it could lead to another significant spike in infections because it will outpace jab coverage.

Q. How can we contain the virus at this stage where you find many sub-clusters and patients from all over the country?

A. Patchy surveillance means the picture there is less clear.

Eventually, it becomes dominant in Sri Lanka, but we need to aim at achieving to get the effect to be somewhat blunted by vaccination.

These are populations at risk of a localized outbreak from Delta, so I think it’s crucial to keep still tracking and watch this as much as possible.

For example, vaccine coverage in Colombo is about 50 percent versus other districts.

It is a race between the rate of the spread of the variant and the rate of vaccination in Sri Lanka.

Both jabs offer greater protection against the Indian variant after two doses: Pfizer at 88 percent and AstraZeneca at 60 percent. The AstraZeneca figure is also expected to increase over time as immunity builds. These two vaccines are only around 33 percent effective against the new variant after one dose.

Could there be further mutations as the virus spreads? How effective will the present vaccines be in that case? Will scientists have to create modified vaccines to take on the new variants?

There are a number of factors that are contributing to increased transmission around the world. WHO experts also have clearly voiced several concerns to which I also agree.

The first are these variants of concern, including the Delta variant.

The second factor is that we have increased social mixing and increased social mobility, which increases the number of contacts that individuals have.

The third factor is the relaxation or the inappropriate use of public health and social measures. Proven public health and social measures that we know prevent infections, reduce the spread by somebody who is infected with the virus to others and save lives.

And the fourth factor is the uneven and inequitable distribution of vaccines.

Preliminary evidence from England and Scotland suggests that people infected with Delta are about twice as likely to end up in hospital than those infected with Alpha. People who have had one vaccine dose are 75 percent less likely to be hospitalized than unvaccinated individuals, and those who are fully protected are 94 percent less likely to be hospitalized.

The main goal of these vaccines is to prevent severe disease because what we want is for people, even if they get the infection, to recover from it and not become seriously ill.

Q. Finally, according to your research studies, how long will the pandemic run and can we have hope of getting back to normal soon?

A: Most probably with the development of herd immunity. We seem to be achieving this by acquiring protective immunity against COVID 19 by increased immunity levels, after more people have been infected with the current wave and the increased rolling out of vaccines. However, going back to normality will require a vaccine that both stops people falling ill and prevents them spreading the virus. That, will take about five years.

However, I am hopeful that by the end of the year, there’s sufficient immunity to make transmission rates low, so there is no ‘crisis’, but we would still need to keep wearing face masks and be extra careful with hand hygiene and social distancing.

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