Omicron variant: Role of genome sequencing and is India ready? CORE Diagnostics’ Dr Shivani Sharma explains

As WHO states, Omicron variant of Sars-CoV2 virus is likely to spread and possess a “very high” risk of infection surges.

Omicron variant: Role of genome sequencing and is India ready? CORE Diagnostics’ Dr Shivani Sharma explains
Omicron has revived the fear of another virus outbreak making people ponder whether the new virus could bring about similar or an even worse wave in India.

Just when the world started to snap back to pre-pandemic normalcy, the new ‘variant of concern’ – Omicron has left everyone jittery as more information is dropping. As WHO states, Omicron variant of Sars-CoV2 virus is likely to spread and possess a “very high” risk of infection surges. It’s a highly divergent variant with a high number of mutations, some of which are concerning and may be associated with higher transmissibility. Omicron has revived the fear of another virus outbreak making people ponder whether the new virus could bring about similar or an even worse wave in India. However, there are still considerable uncertainties including how transmissible the variant is & how well vaccines protect against the infection, transmission, clinical disease of different degrees of severity and death. Preliminary evidence suggests there may be an increased risk of reinfection with this variant, as compared to other variants of concern (VOCs). Financial Express Online caught up with Dr Shivani Sharma, Lab Director, CORE Diagnostics to understand more about the new variant, readiness of India’s diagnostic sector and more. Excerpts:

What do we know about the variant of concern?

Given mutations that may confer immune escape potential and possibly transmissibility advantage, the likelihood of a further potential spread of Omicron at the global level is high. Depending on these characteristics, there could be future surges of COVID-19, which could have severe consequences, depending on several factors including where these surges are taking place. The overall global risk related to the new VOC Omicron is assessed as very high.

Dr. Shivani Sharma, Lab Director, CORE Diagnostics
Dr. Shivani Sharma, Lab Director, CORE Diagnostics

Increasing cases, regardless of a change in severity, may pose overwhelming demands on health care systems and may lead to increased morbidity and mortality. The impact on vulnerable populations would be substantial, particularly in countries with low vaccination coverage. Till date, no deaths linked to Omicron variant have been reported.

Besides, many are curious about knowing if this new variant is likely to displace the highly contagious Delta variant. However, there is no firm evidence that Omicron is more dangerous than the Delta variant.

WHO has declared Omicron as a Variant of Concern (VoC): Should we be worried?

Omicron’s discovery has prompted considerable panic across the globe, resulting in countries banning international movements – barring entry of foreign travelers. As of now, much remains unknown, including whether it is transmissible and capable of causing more serious illness. There are reports that suggests efficacy of our current Covishieled and Covaxin vaccines against the virus and thus, our focus should be on bringing masses into vaccination coverage. At this point, a lot of people are not vaccinated, hence, based on what we know about Omicron, it only seems to be causing mild symptoms. Thus, we might get away with this fear.
There could be reduction in efficacy of the vaccine but it’s unlikely that the new virus will render the vaccine totally ineffective.

Our prime focus should be getting more and more people vaccinated, tested while taking other safety measures like social distancing, masking, etc.

‘Positive samples will be sent immediately for genomic sequencing. What role will genomic sequencing play?

For countries with access to diagnostic tests in which at least one gene target contains the S gene target: Prioritize specimens with SGTF (no detection for S gene and detection for other gene targets) for sequencing confirmation of the Omicron. While a sudden increase in SGFT may be indicative of circulation of the Omicron since the prevalence of Alpha variant (which also causes SGTF) is very low in most countries, confirmation of Omicron by sequencing is recommended. Enhanced surveillance and sequencing are recommended to characterize the circulating SARS-CoV-2 variants for a representative subset of confirmed cases. Timely reporting of genomic data to the public domain and the timely collection of metadata including clinical and epidemiologic data for careful interpretation of results.

How should we prepare ourselves for this new virus? How is India prepared?

To ensure that we manage the situation effectively there are three areas to focus on comprehensively.

Retrospective sampling

Conduct a retrospective review of available genomic sequences and S gene dropout data if available at country level, with sample collection dates dating from October 2021 through present.
If not already done, sequence specimens with S Gene target failure in the recent past, preferably from October 2021 through present.

Ensure timely reporting of genomic sequences to public domain (e.g., GISAID) to facilitate automated retrospective analysis.

For countries with such capacity, wastewater sampling may be an additional tool for the retrospective and prospective investigation of Omicron in the community.

Prospective sampling

Due to the risk of importation by incoming travelers from locations experiencing Omicron transmission, countries may increase sampling from inbound travelers. Positive rRT-PCR samples should be sequenced to confirm presence of the Omicron. National testing strategies should be updated to include available diagnostic tools for rapid testing and reporting and effective decentralization of testing.

WHO recommends that national testing capacity and genomic sequencing capabilities and appropriate planning be undertaken for possible surges in testing demand.

Despite uncertainties, it is reasonable to assume that currently available vaccines offer some protection against severe disease and death.

Efforts should be intensified by public health authorities to accelerate COVID-19 vaccination coverage in all eligible populations, but with priority for populations at high risk for serious disease who remain unvaccinated or not yet fully vaccinated. These include older adults, health care workers and those with underlying conditions putting them at risk of severe disease and death.

Public health and social measures (PHSMs)

The use of masks, physical distancing, ventilation of indoor space, crowd avoidance, and hand hygiene remain key to reducing transmission of SARS CoV-2, even in the context of emerging variants. However, PHSMs may need to be enhanced, to further limit interpersonal contact, to control transmission with a more transmissible variant.

The use of established PHSMs in response to individual cases or clusters of cases, including contact tracing, quarantine, and isolation, must continue to be adapted to the epidemiological and social context and enforced.

Guided by risk assessment, considering the epidemiological situation, response capacities, vaccination coverage and public perception, as well as uncertainties related to the rapidly evolving situation of Omicron, countries should be ready to escalate PHSMs in a timely manner to avoid overwhelming demands on health care services.

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First published on: 04-12-2021 at 12:00 IST