When in the third week of January last year, a man who had returned from Wuhan, China, was suspected to have been infected with the coronavirus, Nepali authorities sent swab samples collected from him to Hong Kong.

Since Nepal did not have the facility to conduct tests, the swab samples had to be sent to the World Health Organization’s collaborating centre in Hong Kong.

A year later, amid reports of new variants of the coronavirus being detected in various countries, Nepal finds itself in a tight spot.

The National Public Health Laboratory is planning to send swab samples collected from three people who returned from the United Kingdom some two weeks ago to Hong Kong to ascertain if they are infected with the new variant of the coronavirus.

Swab samples from six of eight people returning from the UK had been collected.

According to officials, they have tested positive for Covid-19 but there is no way to determine whether they have contracted the new variant of SARS-CoV-2, which causes Covid-19.

“The UN Health agency’s Nepal office could send the samples [to Hong Kong] by Saturday,” Dr Bikash Devkota, chief of Quality Standard and Regulation Division at the Ministry of Health and Population, told the Post. “We have also directed the National Public Health Laboratory to send the other three samples to the WHO’s collaborating centre for tests.”

Officials could not provide an answer as to how long it will take to get the results back.

“Due to a lack of capacity at the National Public Health Laboratory, we have to send these samples abroad,” Dr Basudev Pandey, director at the Epidemiology and Disease Control Division, told the Post. “Yes, we should be able to do this test on a regular basis within the country, as the virus keeps changing its form, and we do not know if the new variant has already entered our country.”

Public health experts, however, have cautioned about the possible rapid spread of the new variant of the virus, as cases have been reported in various countries since it was first detected in the UK.

Officials say since there is no facility to perform whole-genome sequencing in Nepal, there is no way to ascertain if the new variant is already here.

Whole-genome sequencing is a comprehensive analysis of the entire DNA sequences of an organism’s genes. Researchers believe that the whole-genome sequencing of the coronavirus could be instrumental in tracking the severity and properties of the virus.

Sameer Mani Dixit, director of research at the Centre for Molecular Dynamics- Nepal, however, says whole-genome sequencing is possible at his laboratory and that they could have provided results by now, had the authorities sought their assistance.

“Had the authorities trusted us, we would have provided the results by now,” Dixit told the Post. “Performing the tests on time not only gives us knowledge about the gene of the viruses circulating in our country but also helps us take measures to contain the spread.”

According to Dixit, his laboratory has the capacity and trained human resource and had already performed whole-genome sequencing tests for the government and the reports were matched with the report of the UN health agency’s collaborating centre.

Public health experts say that sending three samples of people returning from the UK for whole-genome sequencing after several days does not help in containing the infection, as the new variant of the virus has already reached dozens of countries, including India, and people are entering regularly from those countries.

The Nepal government has spectacularly bungled its response to Covid-19 ever since the country reported its first case last year.

As of Wednesday, 263,193 people have tested positive for the coronavirus throughout the country including 1,899 deaths. In the last 24 hours, 409 people tested positive with six deaths.

With almost all sectors now open, including schools, the contagion could turn more severe, and the new variant of the virus could make the situation worse.

According to the Business Standard, the new variant first confirmed in the UK has been detected in at least 41 countries and territories as of Wednesday.

“What are we going to do once we confirm that those people who returned from the UK have the new variant of the virus?” said Professor Jeevan Bahadur Serchand, an infectious and tropical disease research specialist at the Institute of Medicine. “Actually, we do not know yet which strain of the virus is circulating in the country.”

According to Serchand, the authorities’ focus has been on those returning from the UK while anyone arriving from abroad can carry the new virus variant into the country.

“The lackadaisical approach of the authorities since the start of the pandemic is one of the reasons for the massive spread of the virus,” said Serchand.

The existence of a new and highly transmissible coronavirus variant was announced by the UK’s health secretary on 14 December, after Covid-testing laboratories reported that a growing number of their positive samples were missing a signal from one of the three genes their PCR tests used to confirm.

On December 22, authorities in Nepal directed all international airlines not to bring passengers from the United Kingdom or those transiting through the country from December 24 onwards.

Experts say the government failed to pay attention to the fact that there should be facilities for gene sequencing. There is a tendency among the authorities in Nepal to wait for the disaster to happen, according to them.

Now with the new variant causing havoc across the globe, authorities are clueless as to what their response should be.

Dixit said in the times of a crisis or a pandemic, the government must pull out all the stops and should not hesitate to seek support from the private sector.

“We had provided training and some reagents including personal protective equipment to the National Public Health Laboratory to perform polymerase chain reaction tests [last year],” Dixit told the Post. “I do not understand why there is a problem in seeking help from private laboratories which can perform gene sequencing.”

Experts say that the coronavirus, which continues to spread throughout the country, might have mutated several times by now.

Most of the people infected in the initial few months were asymptomatic and symptomatic cases started to increase later.

Health Ministry officials admit that no one knows which variant of the virus is circulating in the country.

The officials, however, did not have a justification as to why the authorities did not focus on setting up facilities to perform gene sequencing when new variants were expected by scientists the world over.

Experts say even as the government has not been successful in containing the virus, it has spent billions of rupees so far—some of which it should have invested in setting up the facilities for performing gene sequencing. Basically there was a lack of willingness, according to them.

Dr Pradip Gyawali, executive chief of the Nepal Health Research Council, admitted that the country should have set up the facilities for genome sequencing long ago.

“We hope to start performing genome sequencing tests within the country very soon,” said Gyawali. “These tests will be carried out at government as well as private laboratories.”

But at a time when government authorities have given up all measures—testing, tracing and treating, the chances of containing the spread of the virus—and its new variant—are slim even if the facilities are set up for genome sequencing.

“The new variants of the virus have been identified in about 40 countries, possibly even more, and we have just started discussions on setting up the facilities for gene sequencing,” said Dr Sher Bahadur, Pun, chief of the Clinical Research Unit at the Sukraraj Tropical and Infectious Disease Hospital. “And then our focus has only been on those returning from the UK.”

According to Pun, without facilities for gene sequencing when the new variants have emerged as a headache for many developed countries, Nepal looks set to invite yet another catastrophe, as it has yet to have a proper plan on inoculating the population.

“Virus mutation is quite natural and a very contagious and deadly variant could develop within a country,” said Pun. “A pandemic requires continuous study and stepping up of facilities.”