The Ministry of Health and Population said that it has been studying the virus variant responsible for Covid-19 infection in people returning from India.

For this, the ministry has directed all agencies concerned to send suspected swab samples to the National Public Health Laboratory for whole-genome sequencing.

“Results of the whole-genome sequencing may come within this week,” said Dr Chuman Lal Das, director at the Epidemiology and Disease Control Division. “We are concerned about the BA.2.12.1 sub-lineage of the Omicron variant of SARS-CoV-2.”

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

Recent surge in new cases of the coronavirus in India has been attributed to the BA.2 subvariant of Omicron and its sub-lineage BA.2.12.1. India recorded 3,451 new cases and 40 deaths on Monday. The number was 2,288 and 10 deaths on Tuesday.

Officials at the Health Ministry say they have already alerted all health desks set up along the land crossings with India to step up vigilance and send all swab samples from infected people for whole-genome sequencing.

“Many people returning from India have been tested positive for the coronavirus,” said Das. “We have collected swab samples of those infected and have been performing whole-genome sequencing.”

Thousands of people are believed to have returned home from India of late for local elections set to be held on Friday.

Along with the BA.2.12.1, there are also concerns about BA.4 and BA.5 variants, which are found to be effective at reinfecting people with previous infections from BA.1 or other lineages. The World Health Organisation said that it is tracking BA.4 and BA.5 as the sub-variants have been circulating in several countries of Africa and Europe.

Both sub-variants have additional mutations in the spike region, a part of the virus that is used to invade human cells, and unique mutations outside of that region, according to a WHO report. Such mutations are associated with “potential immune escape characteristics,” according to the report.

Officials said that gene sequencing, which is being carried out on a regular basis in the country, is the only way to know the virus variant responsible for the infection. Officials said that the number of new cases are increasing in the Bagmati province and in the districts of the Tarai region.

Despite the detection of infection in the people returning from India, authorities concerned have not started contact tracing.

“Infected people should follow the safety measures and isolate themselves,” said Dr Samir Kumar Adhikari, joint spokesperson at the Health Ministry. “Health agencies under the respective local levels are responsible for carrying out contact tracing.”

Public health experts say that apathy towards contact tracing of the infected people could spell disaster in the country.