Omicron COVID variant - Important Points

Updated May 2024

WHAT IS THE OMICRON VARIANT AND WHY IS IT ONE OF THE VARIANTS OF CONCERN (VOC)?

Omicron (scientific name B.1.1.529 or BA.1) is the COVID variant, first detected and reported in Botswana and South Africa in November 2021, when a sudden exponential (5-fold) rise in daily cases was seen over a short period of a week. It is a highly mutated variant with around 50 mutations in total out of which some 30 mutations are in the spike (S) proteins which are the important surface proteins helping the coronavirus to enter human body cells. This makes the Omicron variant highly transmissible and very fast spreading. Therefore, WHO classified it as a variant of concern (VOC) on 26^th November 2021.

For a comparison with the other previously circulating VOC, the Delta variant, largely responsible for the second COVID wave in various parts of the world including India, had around 17 mutations with 9 on the spike protein. The Omicron strain is now present in almost all countries globally. Due to the fast spread of this strain, Omicron has become the dominant COVID variant across the world in a short time.

Omicron subvariants were seen circulating in many parts of the world. BA.2 was subsequently identified in India, USA, UK, and some countries in Europe. It was called ‘stealth Omicron’ by some. BA.2 spreads faster and replaced the original Omicron variant (BA.1) as the dominant strain in USA, EU, UK, India, and several other parts of the world, including Asia and Africa. Since then, BA.2 has continued mutating and many of its sub-lineages emerged like BA.2.3.20, BA.2.75, and BJ.1. The sub-lineage BA.2.75 spread in many countries including India. All these sub-lineages are being further studied for their infectivity and immune escape.

Omicron strain showed further variants (sub-variants) in 2022. These sub-variants that subsequently emerged were BA.3, BA.4, and BA.5. In Jan 2022, BA.3 variant was also found in South Africa but that showed fewer mutations than BA.1 and is likely less infective or transmissible. BA.4 and BA.5 variants were detected in South Africa in April 2022, and then in other parts of the world including USA, EU, UK, and India. Sub-lineages of BA.4 (BA.4.6), and BA.5 (BF.7 and BQ.1), are under monitoring by WHO. BQ.1 is now dominant in USA and was also detected in India.

BF.7, (BA.5.2.1.7 – a sub-lineage of the Omicron sub-lineage BA.5) was detected in October 2022 in China and thereafter drove the wave there. BF.7 has also been detected in India, and in EU and USA. The symptoms are similar to the original Omicron strain, however, the infectivity and transmission are very high for BF.7, and current vaccines are unlikely to confer adequate protection against it.

BA.2.86, also known as the Pirola variant, is the latest Omicron subvariant detected in July 2023. It is a descendant of BA.2 and is notable for having more than thirty mutations on its spike protein, having made an evolutionary jump on par with the first appearance of the more contagious but generally less virulent Omicron lineage. BA.2.86 was designated as a variant of interest by the WHO on November 2023.

In December 2023, variant JN.1, a descendant of BA.2.86 was detected rising in many parts of the world including USA and India, and has been declared as a variant of interest by WHO. Its variants JN.1.7 and JN.1.18 are under monitoring. In 2024, the new coronavirus sub-lineage of JN.1.11.1 variant called KP.2, is behind many new Covid cases as it is more immune evasive and highly transmissible. It is nicknamed FLiRT variant after the technical names for the mutations. It has become the dominant strain of SARS-CoV-2 in circulation in many parts of the world including USA and India, and is fast replacing JN.1. KP.2 and its variant KP.3 are under WHO Variants under Monitoring currently.

Recombinant variants

These have been seen since Jan 2022. A recombinant variant occurs when an individual becomes infected with two or more variants at the same time, leading to a mixing of genetic material in the human body. Prominent among these is XE, a combination of BA.1 and BA.2 strains of Omicron detected in UK. Recombinants of Delta and BA.1 (XF and XD) have also been seen in a few cases but not showing community transmission yet. It is still to be ascertained if XE is more virulent, however, it has been estimated to be 10% more transmissible than the BA.2 strain.

A recombinant of BA.2.75 and BJ.1 called XBB is present in many countries. Its subvariant XBB 1.5 is being considered the most transmissible variant till now and as of 2023 was seen spreading across almost 30 countries globally, including the USA, UK, and India. Another sub-variant XBB.1.16 (Arcturus strain) is being seen causing a spike in COVID cases in some parts of India starting March 2023. The latest circulating strain is called Eris EG.5 which is a family of Omicron variants descended from XBB.1.9.2. The World Health Organisation (WHO) has classified XBB, with these 3 variants under VOI (variants of interest) after a surge in Covid infections in the latter half of 2023.

While all these variants may be more transmissible than the original Omicron strain, these have not been confirmed to cause more severe disease or complications. WHO had included Omicron BA.1, BA.2, BA.3, BA.4, BA.5 and BA.1/BA.2 circulating recombinant forms such as XE as variants of concern (VOC), and newer variants BF.7, BQ.1, BA.2.75, BA.4.6 and XBB as variants under close monitoring.

However, as on February 2024, none of these variant strains are being considered as VOC.

DOES OMICRON HAVE DIFFERENT SYMPTOMS THAN EARLIER COVID VARIANTS?

The symptoms of the Omicron variant can vary from person to person. Typical symptoms of loss of smell or taste that are seen with other COVID variants are usually absent. Often people infected with the Omicron variant may be completely asymptomatic and diagnosed incidentally due to travel requirements and contact tracing.

The symptoms of the Omicron variant can include:

• fatigue and weakness
• irritation or scratchy feeling in the throat, with or without dry cough
• common cold symptoms like runny nose, sneezing, and congestion
• headache
• body ache, low backache
• mild fever, sometimes with chills/night sweats
• nausea, vomiting, loss of appetite

DOES OMICRON CAUSE MORE SEVERE COVID, AND INCREASE COMPLICATIONS OR DEATH RISK COMPARED TO EARLIER COVID VARIANTS?

Even though this variant spreads fast and therefore most countries are likely to witness a rapid rise in cases, the evidence so far suggests that the Omicron variant does not cause more severe disease, complications, hospitalization, or death as compared to previous COVID variants. This variant impacts the upper respiratory tract and has not been commonly observed to affect the lower airway, lung, or blood vessels. Most cases are mild and managed with home isolation and basic health care.

People with comorbidities should take care that they take their medicines regularly. Improving general health and well-being, and completing COVID vaccination are recommended. More evidence and research are awaited regarding the expected severity, long-term effects, and impact on the healthcare resources of the Omicron variant.

DO THE CURRENT AVAILABLE VACCINES PROTECT FROM COVID CAUSED BY OMICRON?

A decrease in the effectiveness of vaccines or evasion of immunity acquired through vaccination or previous COVID infection is a point of concern with the Omicron variant. Infections in fully vaccinated people (called ‘vaccine breakthrough’) and in previously infected people (re-infections) have been seen. This was also seen with the other VOC.

Vaccination and natural infection lead to the formation of neutralizing antibodies (humoral immunity) in the body. Most vaccines target the S protein therefore mutations in the variants can reduce the ability of the antibodies acquired earlier to target and kill the virus. However, immunity also comprises the cell-mediated component, called the T-cell response (white blood cells directly targeting and killing the virus). This continues to give longer protection even when neutralizing antibodies are rendered ineffective or reduced over time.

Therefore, as of now vaccination against COVID with any of the existing COVID vaccines remains the best way of protection against severe COVID, its complications, hospitalization, and death. It is important for everyone eligible to take both doses of the COVID vaccine available in their country. There is still more research needed on whether booster doses add value in protection against COVID variants, though most countries are administering boosters.

In August 2022, bivalent updated mRNA COVID vaccines that target both the original COVID strain and the Omicron strains (BA.1 or BA.4/BA.5) have been developed and approved. There is also evidence that the hybrid immunity of natural infection and vaccine-induced immunity continue to provide protection from the Omicron variant as well.

HOW IS THE OMICRON VARIANT DETECTED?

Omicron is detected by the RT-PCR test followed by genome sequencing to confirm the variant. The RT-PCR should test multiple genes including N (nucleocapsid), RdRp (RNA dependent RNA polymerase), and E (envelope), in addition to S (spike protein), as S protein ‘drop out’ is suggestive of a variant. Specific RT-PCR tests for Omicron have also been approved and launched in some countries. (like OmiSure and Krivida in India).

People with symptoms of Omicron infection should be tested for implementing timely isolation. Household contacts of a positive case who are symptomatic, or have comorbidities and are at high risk, should also be tested.

Travel regulations

In early 2022, when Omicron was spreading fast, travel regulations had been imposed. International travelers had to carry a pre-departure RT-PCR report to be checked at the travel destination. RT-PCR was also being done by many countries on arrival. If negative, home quarantine of 7 days (may vary depending on the destination country/state guidelines) was advised with monitoring for symptoms. Repeat testing to confirm negative status was usually done on day 8, followed by another week of self-monitoring for symptoms.

People who test positive are to be immediately isolated, and the sample sent for gene sequencing to confirm Omicron. Thereafter such people are treated by institutional or home isolation in accordance with the regional administrative policies, till they test negative. It is advisable to check the COVID travel and testing guidelines of the individual country to which one is planning to travel.

With the drop in cases and easing of curbs, from Apr-May 2022, most countries have already done away or are in the process of doing away with mandatory testing for fully vaccinated people. Many countries have removed all COVID regulations including vaccination requirement. However, some regulations have been re-introduced in some countries for flyers from specific countries where Omicron strains especially the latest BF.7 and recombinant variants are spreading, so it is wise to check entry requirements of the particular country being travelled to.

WHAT IS THE TREATMENT FOR COVID CAUSED BY THE OMICRON VARIANT?

COVID treatment protocols are to be followed for the disease caused by the Omicron variant. If a person has symptoms, they are mostly mild and are treated with home isolation, rest, and a nutritious diet. Medicines like paracetamol for the symptoms of fever, body ache, and headache can be taken. Warm fluids and antiseptic gargles for throat irritation, steam and saline drops for nasal congestion, and multivitamins for general health may also be taken.

The need and effectiveness of existing or new approved antivirals (like molnupiravir), as well as the antibody cocktail, are not yet established for the Omicron variant. These may only be considered by medical practitioners in high-risk cases, with significant comorbidities or in those not vaccinated. For the majority of cases, these medicines are not required and should not be indiscriminately used. Antibiotics (like azithromycin etc.) are also not required in most cases and should not be used without a medical prescription or established need.

Oxygen monitoring and watching out for red flag (alarm) signs continue to be recommended throughout the symptomatic phase. Hospitalization should only be considered after discussion with the treating physician if the following alarm signs develop:

• oxygen saturation being <94% over 3 readings in a single day or falling below 90% anytime
• development of breathlessness or chest pain/pressure
• >3 days of high fever not responding to medication
• severe weakness and fatigue preventing self-monitoring or care
• inability to eat or take medicines orally
• mental confusion or altered consciousness
• comorbidities are uncontrolled or worsening.

Self-isolation is recommended for 7 days after symptom-onset or following a positive test, and till there is no fever for 3 consecutive days. This is to be followed by a week of self-monitoring of symptoms and mask wear when near others or when in public spaces. No re-testing is needed after the isolation period is over. The 7-day isolation is based on that being the period of the person shedding the virus and being infective. However, symptoms like weakness, fatigue, throat irritation, dry cough, nasal congestion, headache, and indigestion may sometimes continue longer, and subside more gradually.

IS THERE REASON TO PANIC? HOW CAN WE PROTECT OURSELVES DURING CURRENT AND SUBSEQUENT WAVES?

It is natural for viruses to keep mutating. There is no need to panic, spread fear, or overreact in terms of restrictions or disrupting life. In fact as of May 2023, WHO does not consider COVID as a public health emergency of international concern, anymore.

It is likely that the Omicron variant will infect the majority of the population in many countries. It is important to know that the Omicron variant seems to cause mild disease, and its fast and vast spread may actually help by replacing the more severe Delta variant. However, research on its long-term effects is still ongoing.

The Omicron variant is spreading across several countries including India constituting the ‘3rd wave’ of COVID. Many countries have already crossed the peak and are showing a decline in cases, while some are still in the rising phase of the next wave. Hospitalization rates have been seen to be far less than previous variants of concern, and are not showing a concerning rise or trend. Mortality has been extremely low and mostly due to other associated uncontrolled comorbidities. However, the load on healthcare systems can be significant when the spread becomes huge impacting different people with comorbidities, unknown health status, and limited healthcare access, especially in highly populated countries with unevenly distributed health resources. The relative protection of different vaccines is also still not ascertained and is being studied.

Therefore, the health administration in most countries is playing on the side of caution. Though gradually curbs and mask mandates have been relaxed and most public places and activities have opened up, it is still advisable to keep the following in mind in case there is still a significant or increasing number of COVID cases in your area:

• COVID vaccination course should be completed (2 doses + precautionary booster dose) of the vaccine available in one’s country.
• Mask is advised to be worn if suffering from symptoms like cough, cold, etc., or while taking care of a symptomatic or high-risk person. Avoid mingling in public if having a fever or other symptoms like sneezing, or coughing.
• Test in case suggestive symptoms of COVID are present and in accordance with the travel norms notified.

Also read:

Coronavirus Types and SARS-CoV-2 Variants

COVID Vaccines – Important Points

COVID Home Care, Isolation and Treatment – Important Points

Cough – Mechanism, Types and Management

Reference

WHO Omicron Update