Samples to be sent to UK to widen whole-genome sequencing testing

Nepal is sending swab samples from people with Covid-19 every month to the UK for full genome sequencing tests. The National Public Health Laboratory said the move is aimed at monitoring whether the new variants have been circulating in the country.

“As we do not have the capacity to perform whole-genome sequencing on a large scale, we are planning to send swab samples to the UK,” said Dr Rhona Jha, director of the laboratory. “Our plan is to send in at least 150 swab samples each month.”

The Department of Health and Population has signed an agreement with Public Health England to perform full genome sequencing of SARS-CoV-2, which causes Covid-19.

According to Jha, as per the agreement, Nepal will send 150 swab samples every month for a year. Public Health England has agreed that the tests will be carried out free of charge.

Whole genome sequencing is a comprehensive method for analyzing the complete DNA sequences of an organism’s genes. Researchers believe that whole-genome sequencing of the coronavirus could be useful in tracing the severity and characteristics of the virus.

It is not that whole genome sequencing is not performed in Nepal. The national laboratory itself has the capacity to perform the tests. Besides the national laboratory, a private laboratory, Kathmandu University and Tribhuvan University also have the technology to perform whole genome sequencing tests.

“But we can’t do hundreds of tests in a month,” Jha said. “We were planning to test about 48 samples in our lab and send about forty samples to India every month for tests.”

The Department of Epidemiology and Disease Control said the delta variant of SARS-CoV-2 is responsible for the current spread of infection.

The variant has been prevalent since the start of the second wave of coronavirus infections in April and May and has killed more than 8,000 people in Nepal.

“The delta variant is responsible for the spread of infection over the past several months,” said Dr. Krishna Prasad Poudel, a spokesperson for the Ministry of Health. “We have been monitoring the virus variant regularly within the country and by sending swab samples from infected people to India and other countries.”

The study shows many mutations even in fast-spreading delta variants – the Ay.4.2 (Delta Plus) variant, AY.63 and others.

A new variant of Covid-19 – B.1.X or B.640 – was recently identified in France, and is said to have an unprecedented mutation.

The WHO Collaborating Center in Hong Kong discovered the first case of coronavirus in Nepal in January last year of a 31-year-old man who had returned from Wuhan, China.

Health authorities also sent swab samples for whole-genome sequencing to the WHO collaborating centre, Institute of Genomics and Integrative Biology in India, which confirmed the presence of alpha, delta and delta plus variants in Nepal.

Public health experts say that as the Covid-19 virus continues to mutate, regular whole-genome sequencing testing is a must for transmission rate and risk.

“Overall, whole genome sequencing tests should be done on five percent of all positive cases,” said Dr. Prabhat Adhikari, an infectious disease and critical care expert. “If we don’t have the capacity to do the tests with that many, we should do as many tests as possible. Instead of sending the swabs abroad, we should try to get the tests done inside the country.”

Experts say the risk of contracting Covid-19 is far from over.

Although cases in Nepal have decreased recently and the vaccination campaign has been expanded, there are concerns about sudden infections as well as an increase in infections due to new variables.

According to doctors treating Covid-19 patients, of the total hospitalizations in Nepal, 20 per cent are fully vaccinated people.

Studies show that vaccines are also not 100% effective in preventing infection. In such a context, experts say the authorities should continue their efforts to curb the spread of the virus.

Scientists say that sooner or later the coronavirus will become endemic, which means it will continue to circulate in the pockets of the world’s population for years to come.

“Eliminating this virus right now from the world is a lot like trying to plan a staging route to the moon. It’s unrealistic,” Michael Osterholm, an epidemiologist at the University of Minnesota in Minneapolis, was quoted by Nature as saying in an article published earlier this year. “.

In Nepal, 11,500 people have died from coronavirus infection since the pandemic began.

In the past 24 hours, 385 people have tested positive for the coronavirus (367 in 9,921 PCR tests and 18 in 2,776 antigen tests). Four deaths were recorded on Monday.

Over the past few weeks, the positivity rate has been hovering below 5 percent. The World Health Organization recommends that the positive percentage remain below 5 for at least two weeks before authorities consider lifting virus restrictions.

The number of active cases across the country is currently 7,269.

To date, 7,952,386 people (26.2 percent of the total population) have been fully vaccinated in the country. Nepal has received 23,163,930 doses of Covid-19 vaccines – Vero Cell, AstraZeneca, Janssen and Pfizer-BioNTech.

Experts say that since the virus can be transmitted rapidly around the world, there is still a high possibility of it entering Nepal as well due to the increased mobility of people globally.

“Authorities should at least sequence the whole genome of people who became infected after immunization,” Adhikari said. “Smear samples from pocket regions, if there is any sudden spike in new cases, should also be sent for whole genome sequencing.”

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