Nepal on high alert for Omicron

A student being administered the Pfizer BioNtech vaccine last week in Kathmandu. There are questions about the efficacy of current vaccines against the Omicron variant. Photo: AMIT MACHAMASI

The new Omicron coronavirus strain that is spreading concern about a new surge of the pandemic has not been detected yet in samples tested this week in Nepal, but virologists urge caution and stricter enforcement of precautions.  

The variant B.1.1.529, also known by the Greek alphabet Omicron, is said to have evolved in southern Africa, and has already been detected in Hong Kong, Belgium, the UK, Czech Republic, Italy, Germany and the Netherlands.

Israel, in fact, now requires all foreign travelers to quarantine for two weeks. Nepal on Saturday announced restrictions on travelers from six southern African countries as a precaution.  

A private lab which had been conducting genetic sequencing tests on about 50 samples every week from Kosi, Bheri and Teku hospitals, so far has found only the Delta variant and not the Omicron strain. Nepali health experts say it is too early to speculate about the new variant, and making a judgment on response. But they advise even stricter adherence to precautions.

“Let’s not panic but prepare, Omicron has spread faster in South Africa but it is also the relatively less vaccinated region,” says virologist Sher Bahadur Pun at Teku Hospital. Only 24% of South Africans have fully inoculated against Covid-19, 28.7% are partially vaccinated. Nepal's figures are only slightly better at 27.4% and 31.6% respectively. 

It is only because of advances in genetic sequencing technology that a new coronavirus strain is identified in South Africa on 24 November and within four days was designated as a variant of concern by the WHO. Already, Omicron has become a household word, synonymous with a new, possibly deadly, phase in the Covid-19 pandemic.

South Africa, where daily cases spiked from 200 to three times that number, have called the travel bans unnecessary and hasty, and that the new variant was not making people seriously sick. But preliminary evidence suggests an increased risk of re-infection, immune escape, and lower vaccine efficacy because of multiple mutations in its spike protein.

“The new strain seems to be spreading fast but what we need to look at is what is happening in countries where Delta has established itself as the dominant strain and that data will determine if it is stronger or more lethal in Nepal,” says Sameer Dixit of Centre for Molecular Dynamics Nepal. “We need to wait a couple of weeks to see if Omicron will replace Delta, overspread, co-exist, or do nothing.”

Dixit’s Centre has partnered with the Birat Nepal Medical Trust in the EPIINTEL Initiative under the supervision of Nepal Health Research Council to monitor the genetic composition of new variants in the country.

The fact that the new variant has over 30 mutations in its spike protein is a cause for concern. Most current Covid vaccines might be rendered ineffective, except for the Chinese VeroCell and Indian Covaxin which are made from the inactivated virus, and do not only target spike proteins. Experts recommend keeping a close eye on countries that primarily administered VeroCell to monitor their response to Omicron.

Similarly, it is yet to be seen how the new variant will affect people with natural immunity. While initial reports point to an increased risk of re-infection, those who have previously recovered from Covid-19 will have antibodies against all proteins, not just spike protein, unlike vaccinated individuals.

Given that most vaccines against Covid-19 including Pfizer, Moderna, J&J and AstraZeneca primarily target the spike protein, chances are that these jabs will be significantly less effective against variant B.1.1.529. 

Even if the re-infection rate is high, it doesn’t mean severe symptoms. The WHO previously designated Gamma and Beta strains as the variants of concern, but these did not spread much and caused only mild symptoms – before the arrival of the deadlier Delta strain.

Nepal has 30 million new doses of different vaccines in the pipeline, and the government is inoculating everyone from 12 years and above with the Pfizer jabs. The new challenge is to increase intake among those who have so far refused to be inoculated such as pregnant women, new mothers and those with co-morbidities – and after that to start administering booster shots nationwide

Pun adds: “Now that the Omicron strain is here, our priority should be to vaccinate as many remaining people as possible, especially because people have started becoming complacent due to the declining number of Covid cases. We must be on high alert and follow safety precautions and genetic sequencing of the variants.”

Adds Sameer Dixit: “We are at a very early stage, but a travel ban is not the way to prepare for what might be ahead. The restrictions can only do so much, at best it prevents early transmission but once the virus is in, it won’t take long to overwhelm the health system as we saw during the second wave. So we must up our vaccinations, keep distance and mask up. That is the only way.”

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