With the Omicron variant of the coronavirus spreading fast across the globe, scientists have been trying to understand its ability to break past the current protection afforded by vaccines and cause severe disease.

Data on the Omicron variant, first reported to the World Health Organisation on November 24, remains preliminary but most studies suggest it is more transmissible than even the Delta variant that caused India’s deadly second wave of Covid-19 this summer.

The World Health Organisation has observed that Omicron is spreading at a rate not seen with previous variants. Scroll.in looked at the evidence available to understand the efficacy of vaccines against Omicron and the severity of disease that it causes.

A highly transmissible variant with global spread

Many European countries, the United Kingdom, Australia, and the United States, have been recording their highest daily cases in several weeks. The World Health Organisation on Saturday said Omicron has been detected in 89 countries and continues to spread. The Netherlands on Saturday announced a strict lockdown extending till January 14, the BBC reported.

A month since South Africa detected the first Omicron case, the country’s daily cases have touched 26,000-28,000, up from 300 in early November. In South Africa, the Omicron variant makes up 98% of genome sequenced samples.

In the United Kingdom, where the daily caseload has risen beyond 88,000, genome sequencing suggests 2.4% cases are of Omicron. The United Kingdom’s official dashboard updated on Saturday said 90,418 positive cases were reported. In the United States, 3% of samples analysed are of Omicron and the country is recording 1.18 lakh cases daily on an average.

Conflicting evidence over severity of infection

These are still early days and conflicting research is emerging. Omicron has 26-32 mutations in its spike proteins, making entry into a host cell much easier than previous variants.

A University of Hong Kong study found that Omicron multiplies 70 times faster in the respiratory tract than the Delta variant or the original Sars-CoV-2 virus. The study also found that the replication of Omicron slows down substantially in the lung tissues.

“The Omicron variant replicated less efficiently (more than 10 times lower) in the human lung tissue than the original SARS-CoV-2 virus, which may suggest lower severity of disease,” stated the study, which is under peer-review for publication.

However, Dr Michael Chan Chi-wai, principal investigator and associate professor at School of Public Health in Hong Kong, cautioned that “a very infectious virus may cause more severe disease and death even though the virus itself may be less pathogenic.”

Dr Anurag Agrawal, director of CSIR-Institute of Genomics and Integrative Biology, made a similar observation. “A more transmissible virus that is less virulent is more fatal than a less transmissible virus that is more virulent,” he said. Essentially, a highly infectious variant that leads to a rapid rise in cases could leave health systems overwhelmed, depriving many of access to oxygen and medicines, thereby pushing up the fatality rate.

A study by the Imperial College London, however, said there was no evidence to suggest Omicron is less severe than Delta. The conclusion was derived after comparing Delta and Omicron infected cases and the proportion of those who reported symptoms and those who sought hospitalisation with both variants. The study analysed RT-PCR confirmed Covid-19 samples in England. There were 1.22 lakh Delta cases, 1,846 cases of Omicron confirmed through genome sequencing, 11,329 cases likely to be Omicron and another 1.96 lakh cases detected through the S-gene target failure test.

A pathological lab equipped to screen Covid-19 patients through the Taqpath RT-PCR, or the S gene target failure test, at a government hospital in Chennai. Photo: Arun Sankar/AFP

What do we know about breakthrough cases and reinfections?

Reinfection means a person infected with Covid-19 in the past contracts the infection again, while a breakthrough infection is when a fully-vaccinated person tests positive. There is growing evidence to support the theory that Omicron is able to break past the immunity of host cells, generated by either past infection or vaccines and cause reinfections as well as breakthrough infections.

A study in Hong Kong, published in the Clinical Infectious Disease of Oxford Academic on December 16, isolated two Omicron strains called HKU691 and HKU344-R346K in Hong Kong. The HKU344-R346K has a mutation R346K in its spike protein. Spike proteins are present on the surface of the virus and help in accessing entry into a host cell. HKU344-R346K accounts for 8.5% of Omicron strains recorded by the Global Initiative on Sharing Avian Influenza Data, or GSAID.

The study found that only 24% of samples collected from people vaccinated with Pfizer-BioNTech were able to neutralise the HKU344-R346K and 20% were able to produce an immune response to neutralise the HKU691 variant. None of those vaccinated by Sinovac could produce antibodies to neutralise either strain. “Our data suggest that the Omicron variant may be associated with lower Covid-19 vaccine effectiveness,” the study concluded.

Another study by the Imperial College London had similar findings. The study found that the immune response against the Omicron variant is reduced by 4.5 times compared to the Delta variant. “This means that there will be a drop in vaccine efficacy. This is predicted to result in a drop in vaccine efficacy against severe disease (hospitalisation) from 96.5% against Delta to 80.1% against Omicron for the Pfizer-BioNTech booster,” the study noted. This also means that a booster dose may provide temporary protection from infection by the Omicron variant.

Hospitalisation rates and deaths low, but experts warn of lag

Data from South Africa suggests Omicron might be causing fewer deaths than Delta, but it may be too early to tell. During its third wave in June-July, South Africa reached a peak of over 26,000 daily cases and recorded over more than 500 deaths daily. In the latest fourth wave that began in November, daily cases crossed the previous peak with 26,976 cases, but deaths have remained lower, hovering below 100. Experts, however, warn that the number of fatalities may rise in the coming days since there is a lag between a rise in infections and deaths.

South African health minister MJ Phaahla said past infections and vaccination may have helped keep Omicron infections mild. “We believe that it might not necessarily just be that Omicron is less virulent, but we believe that this coverage of vaccination, also in addition to natural immunity of people who have already had contact with the virus, is also adding to the protection,” Phaahla was quoted as saying by the Washington Post.

Vaccine efficacy lower, but T-cell immunity remains

Although Omicron can cause both breakthrough cases and reinfections, there are indications that the body is able to protect itself better from severe disease due to T-cell mediated immunity. T-cells are part of the immune system that fight off a foreign infection. They kill infected cells on a spree to ensure the healthy ones are protected.

On December 15, the World Health Organisation held a meeting to discuss ongoing studies. Several researchers said T-cells in vaccinated people are able to prevent severe disease due to Omicron. Vaccination may then help in preventing deaths, even if there is a spike in breakthrough infections and booster doses may help further.

Dr Anthony Fauci, director of National Institute of Allergy and Infectious Diseases in the United States, said preliminary data shows that two doses of the Moderna vaccine are not effective against Omicron, but a third dose does provide protection. Similar studies show that vaccine efficacy declines against Omicron, but is not nullified largely due to T-cells.

What is happening in India

In India, most cases of Omicron have so far been limited to people with an international travel history and are mild infections, said the health ministry’s joint secretary Lav Agarwal on Friday.

Maharashtra, with 40 Omicron cases – the highest among all Indian states – has not seen a single intensive care unit hospitalisation due to the new variant. None of the patients had any lung involvement, although this pool is too small to extrapolate to the entire population. At least 29 of those tested positive for Omicron were fully-vaccinated. Data showed that of the 40 cases, 27 were completely asymptomatic and the rest had mild symptoms.

The government is urging caution in view of the variant’s global spread. In its latest press briefing on December 17, the ministry of health and family welfare urged people to mask-up, socially distance and avoid crowded gatherings.

Niti Aayog member Dr VK Paul said several European countries, with high Delta prevalence in the population and 60-80% vaccination coverage are now seeing a surge in cases of Covid-19. “The steep rise in several countries shows that a new phase of pandemic is being experienced there,” said Paul during the briefing.

Paul said available evidence suggests that Omicron and Delta are combined factors behind the present surge in other countries. Till December 17, India had recorded 109 Omicron cases across 11 states after the first case of the new variant in the country was reported on December 1. So far, India has not recorded a rise in cases, as seen in many other countries.

Daily new cases remain below 7,500, a constant decline since May when India saw the peak of the second wave. The positivity rate, too, has been hovering at 0.65% since the last one week. States have been told to monitor districts where the positivity rate and total number of positive cases against tests carried out is above 5%.

Currently, five districts – Champhal, Khawzawl, Mamit and Serchhip in Mizoram and Namsal in Arunachal Pradesh – are recording a positivity rate of more than 10%, and 19 districts between 5-10%. Although the speed of transmission seems slower in India for now, Indian Council of Medical Research director Dr Balram Bhargava has warned that Omicron could lead to a change.