The fast spreading variant of coronavirus, the one first detected in the United Kingdom, is responsible for the recent spike in new cases in Nepal, the Ministry of Health said on Wednesday.

According to Dr Samir Kumar Adhikari, joint spokesperson for the Health Ministry, the UK variant, known as B.1.1.7, is seen in swab samples of a significant number of new cases.

“We would like to request everyone to be serious and follow safety measures, as the UK variant of virus is found spreading significantly in communities,” said Adhikari. “A number of schoolchildren, teachers and others are getting infected in significant numbers in recent days.”

The UK variant was first confirmed in Nepal in January.

The World Health Organisation’s collaborating centre in Hong Kong, where swab samples of three people who had returned from the UK in December last week, had been sent for whole-genome sequencing, confirmed that all three people were infected with the UK variant.

However, as the country saw a dramatic decline in the number of new infections and the government too had launched its vaccination drive, authorities as well as people started taking a carefree approach.

For the past few days, Nepal has been reporting a steady rise in the number of new coronavirus cases, just as the daily count started to surge in neighbouring India with which Nepal shares a long open border.

Scientists in the United Kingdom have said that the UK coronavirus is 40 to 70 percent more transmissible than the one that caused the first wave of coronavirus infection.

They have also said that the virus is 64 percent deadlier than the previous strains.

“Yes, the UK variant of virus might be responsible for the recent spike in new cases,” Dr Runa Jha, director at the National Public Health Laboratory, told the Post. “We have been finding S-gene target failure in polymerase chain reaction tests of late.”

Doctors say spike protein or S-gene targets failure in swab samples during the PCR tests, which are giving positive results, means they are infected with a new virus variant.

S-gene target or spike protein is one of the key biological characteristics of SARS-CoV-2, which enables the virus to penetrate host cells and cause infections.

Without spike protein, the coronavirus cannot infect people but doctors say that if the polymerase chain reaction tests are failing to detect the spike proteins in the swab samples of the infected people or if there is S-gene target failure, there is a possibility that the virus may have undergone mutations or the virus could be of a different variant than the one common in the country.

“We have found S-gene target failure regularly since February in swab samples of the infected people,” said an official at the Epidemiology and Disease Control Division on condition of anonymity. “We cannot say with confirmation if there is the presence of a new virus variant without performing whole-genome sequencing tests.”

Whole-genome sequencing needs to be performed to identify the new variant of the virus. However, state-run laboratories lack equipment for the examination. Some private laboratories in Kathmandu, however, can perform whole-genome sequencing, officials say.

“Yes, we have been finding S-gene targets missing in swab samples of the infected people,” Dr Krishna Prasad Paudel, director at the Epidemiology and Disease Control Division, told the Post. “We have preserved those swab samples in laboratories.”

According to the World Health Organisation, the UK variant of virus has been detected in more than 86 countries.

Jha, however, said that the coronavirus variant, the one which was responsible to infect a huge number of people last year, is also being detected in infected patients in recent days—stressing the need for more caution.

Experts said that taking the issue of spike protein missing lightly and not performing whole-genome sequencing is a sheer negligence of the authorities.

“I don’t understand why the authorities are taking such a serious issue so lightly,” Dr Baburam Marasini, former director at the Epidemiology and Disease Control Division, told the Post. “Concealing the problems won’t help us find a solution. Such tendency instead leads to a catastrophe.”

Doctors say that knowing the variant of the virus is important not only to contain its spread but also to know if the vaccine being used in the country works against the virus or not.

Nepal resumed its immunisation drive on Wednesday with a Chinese vaccine. The China-gifted 800,000 doses of Sinopharm vaccine arrived in Kathmandu on March 29. These vaccines are being administered to those who provide essential services defined by the government. These include postal and telephone service providers, public transportation workers, water supply and distribution staff, tourism sector—hotels and restaurants—employees, and workers engaged in production, sales and distribution of medicines, electricity supply, storage and transportation of consumer goods.

Nepal launched its vaccination drive with the Oxford-AstraZeneca type vaccine, which is manufactured by the Serum Institute of India under the brand name Covishield, on January 27.

The developers have said that the AstraZeneca vaccine has been found effective against the UK variant. Reports, however, suggest that the AstraZeneca vaccine is not effective against the South African variant, which had prompted the South African authorities to halt the use of the vaccine.

Reports suggest Sinopharm vaccines are effective against both UK and South African variants. But Sinopharm will need to assess results from overseas Phase III clinical trials to decide whether its two-shot vaccine should be followed by a booster shot, Reuters reported last month quoting a company executive.

Nepal so far has vaccinated a little over 1.8 million people. Nepal needs to inoculate 72 percent of its 30 million population against the coronavirus. The World Health Organisation-backed COVAX has committed to providing around 13 million doses of vaccine, enough to inoculate 20 percent of the total population (around 6 million).

However, India’s temporary ban on Covishield could come as an obstacle to the COVAX commitment.

The China-gifted shots will be sufficient to vaccinate around 400,000 people.

Nepal so far has reported 278,768 cases of coronavirus infections, with 3,038 deaths.

The Health Ministry said on Wednesday that 298 people were infected in the last 24 hours with two deaths. The number of active cases stands at 2,201 throughout the country.

Experts say Nepal does not yet know which variant is circulating in communities, and it has administered the AstraZeneca vaccine in the first two phases of vaccination and the Sinopharm vaccines now. While inoculating as many people as possible is a good idea, ascertaining the type of the virus variant is equally important.

“Knowing the virus variant is important to know if the vaccine works,” Dr Sher Bahadur Pun, chief of the Clinical Research Unit at Sukraraj Tropical and Infectious Disease Hospital, told the Post. “It also helps the authorities understand how infectious the virus is, how severely it affects the people after infections and make strategies accordingly.”

Meanwhile, the Health Ministry has urged agencies to take utmost caution, as the infection rate has been found high among schoolchildren in big cities like Kathmandu and Pokhara.

In a statement on Wednesday, the ministry called for enforcing safety measures strictly in public transportation of big cities and in other public places—shopping malls, bars, cinema halls, party palaces, health clubs, swimming pools and temples, among others.

The ministry has urged the local level and local administrations to encourage people to stay in home quarantine following their return from abroad and monitor if they are following safety measures properly.

“Increase contact tracing, antigen tests, and polymerase chain reaction tests as per the need,'' the statement reads.