Strong need for continued Covid-19 genomic surveillance

The spread across India isn't uniform; therefore, different regions must adopt different strategies to contain the pandemic.

ByDebananda S Ningthoujam

Updated 12 Mar 2022, 6:48 pm


A recombinant virus containing genes from both Delta and Omicron has been reportedly detected in some parts of the world. This new variant has been dubbed Deltacron. According to Prof Lawrence Young, University of Warwick, "Deltacron is a product of both the Delta and Omicron variants circulating in the same population" (The Guardian, Mar. 11, 2022).

The definitive evidence for this new variant has been shared by the famed Pasteur Institute in France. This variant has now been identified in several regions of France. Genomes with a similar profile have also been detected in Denmark and the Netherlands. There are also some reports of Deltacron cases in the US and the UK. Dr Etienne Simon-Loriere, Pasteur Institute, warned that there could be several different recombinant viruses formed from recombination of Delta and Omicron variants.

As the number of Deltacron cases is still very low, there is not enough data yet about the severity of the variant or how effectively current vaccines will work against it. There is a strong need for continued genomic surveillance as the virus continues to circulate among under-vaccinated populations and in people whose vaccine-elicited immunity is dwindling. We have to remain watchful about how the variant spreads across the globe and how severe or contagious it turns out to be.

The technical name of the variant is Delta 21J/AY.4-Omicron 21K/BA.1, though it's better known as Deltacron. According to a MedRxiv preprint, the variant was first sequenced in January 2022. It has nearly the full-length spike protein of Omicron and a Delta backbone or "body." It's still too early to say if Deltacron will be highly transmissible, like Omicron, or cause severe disease. like Delta. Recombinants like Deltacron happen only when two different variants simultaneously enter the same human cell in an individual's body (The Wire, Mar. 11, 2022).

Earlier, Chinese scientists reported a recombinant of the Beta and Delta variants on January 20, 2022 and another such recombinant was also reported in Equatorial Guinea in the same month. It's not necessary that such recombinant variants will be more transmissible or more lethal but such possibilities cannot be ruled out. Therefore, continued genomic testing and surveillance are highly essential. Dr Maria von Kerkhove of the WHO also emphasizes the imperative need for robust COVID testing and sequencing around the world.

Persistent post-COVID symptoms

A study by scientists at the University of Oxford claims that even a mild infection of COVID-19 can lead to cognitive decline due to 'brain shrinkage' (The Print, Mar. 9, 2022). It was found that among COVID-infected people, there was a higher reduction in grey matter thickness, greater tissue damage in regions of the brain related to smell perception, and an overall decrease in the size of the brain. These findings have been published in the leading science journal, Nature.

If symptoms persist in individuals for two months or longer after recovery from COVID, it will be treated as LONG COVID. Many debilitating symptoms persist in such cases, of which three most common ones have been listed as - Fatigue, Difficulties in breathing, and Cognitive decline

Among these, cognitive decline is the most serious complication. Those who contracted COVID had difficulty performing cognitive tasks that they used to perform easily before, e.g. memory of events, matching pairs, and other tasks. This decline may be due to atrophy of parts of the cerebellum, which is involved in cognition. Such decline may result from inflammation of the spinal cord, or sensory deprivation due to not using the olfactory (smell) complex.


Some other long-COVID symptoms include brain fog, loss of concentration, sleep disturbances, heightened anxiety, and intense back pain etc.

New COVID hotspots

China has just ordered a full lockdown of Changchun, a city of about 9 million residents, amidst a fresh surge of COVID cases. A surge in cases was also reported in the nearby city of Jilin (News18, Mar. 11, 2022). Though the number of cases is not very high, it must be noted that China has a zero-tolerance policy of COVID control.

Scenarios of COVID ending

There may be three scenarios for a possible COVID ending: medical, political, and social (Business Standard, Mar. 10, 2022). Nobody knows for sure how COVID-19 will end. But past epidemics can provide some clues. According to Dr. Erica Charters, University of Oxford, there could be different types of endings that may not all occur at the same time.

A medical end may happen when the disease retreats. A political end will take place when the government stops preventive protocols. A social end will occur when the people (society) move on despite the pandemic. There is ample reason to believe that the end is near in the US-65 per cent Americans are fully vaccinated, and about 29 per cent are both vaccinated as well as administered booster doses.

We may look at the trajectories of some past pandemics. The 1918 Spanish flu killed about 500 million people globally and came in three waves. Another flu pandemic of 1957 killed about 116,000 Americans and another pandemic in 1968 killed 100,000 more. Another flu pandemic in 2009 didn't turn out to be as serious as it was anticipated; it fizzled out quite soon and quite unexpectedly.

WHO declared COVID-19 as a pandemic on March 11, 2020 and it has raged across the globe for two years now. The global health agency will monitor the global decline in cases, hospitalizations and deaths before deciding if the international health emergency is over. Covid cases are waning in US and dropped globally by five per cent in the past week. However, cases are seen rising in some other places such as the UK, Hong Kong, and New Zealand.

Poor people in many countries still are in dire need of vaccines and medications. In Latin America and the Caribbean alone, over 248 million people have not had their first vaccine dose. Countries with low vaccination rates will still see surges in illnesses, hospitalizations and deaths. Dr Ciro Ugarte, Director of health emergencies, PAHO says that we're still not out of the pandemic and we still need to tackle this raging pandemic with a great lot of caution!

Possible End of COVID


"The thing about the pandemics is that they don't have an official endpoint", says William Hanage, Harvard University (El Pais, Feb. 9, 2022). The only way to reach a clean end to the pandemic is when you completely eradicate the virus. According to the leading scientist, the best-case scenario is that the immunity elicited by Omicron and the rate of vaccination administered so far means that we may no longer see serious waves of infection. The worst-case scenario is that a new variant arises and it is capable of causing either severe infections or capable of triggering a severe strain in the healthcare system due to the massive number of people it infects. This healthcare load may not just be due to the number of people that the variant infects but also due to the doctors and nurses it infects, compromising the healthcare capacity needed for hospitalized patients.

Omicron most probably may not be the last variant of SARS-CoV-2 that we will see. This view has also been publicly shared by Dr Leana Wen, George Washington University, USA (Deseret News, Feb. 4, 2022). She further adds that the BA.2 subvariant of Omicron will not be the last COVID-19 variant.

Mutating and evolving new variants is the nature (dharma/karma) of a virus. Whether a new variant is concerning depends on if it's more contagious, more virulent, or if it can escape prior immunity from infections or vaccinations. That's why increasing the level of vaccination globally is of utmost importance. The more population immunity we have, the less number of viruses will spread and mutate, and less will be the chance of new variants emerging. That's how the world can rapidly emerge from the clutches of the pandemic. According to Paul Duprex, University of Pittsburgh, USA the pandemic may end via various scenarios (Boston Herald, Jan. 16, 2022):

1. A vaccine or treatment is developed and ends the pandemic just as polio was eradicated by the polio vaccine (the mRNA vaccine seems to be working in that manner but it could not be jabbed worldwide) (pharmaceutical ending).

2. The wildfire burns itself out: (that's how the Spanish flu of 1918 ended) all those infected either die or develop immunity (medical ending).

3. People ultimately get tired of the virus and learn to live with the disease (social ending).

Dr Anthony Fauci, Director, NIAID, USA has just released a pandemic preparedness plan for America. The crux of the plan is what is called "Prototype Pathogen Approach." The plan is to take about 20 families of potential pathogens (5 of them are of highest priority) and establish certain commonalities within each family and work out diagnostic tests, vaccine platforms, multiplex diagnostics and therapies. You need not immediately develop vaccines against all seven families, but you may take a few initial steps such as developing a prototype vaccine, and putting it through phase 1 clinical trials. When you get an outbreak within that particular family, you don't have to start from scratch. The potential pathogen families that can trigger global outbreaks include rhinovirus, flavivirus, alpha virus, and coronavirus etc.

The other arm of the plan includes development of small molecule antiviral drugs that can be used across all lines of certain viruses such as flavivirus, arenavirus or alpha virus etc.

According to Dr Anurag Agrawal, Director, IGIB, Delhi, the Covid situation is stabilising in metro cities such as Delhi and Mumbai (News18, Feb.1, 2022). However, it is still a problem in Tier 2 cities such as Lucknow, Kanpur, Patna, Vadodara, Surat and others. The spread across India isn't uniform; therefore, different regions must adopt different strategies to contain the pandemic. We must all remain vigilant, take care of standard protocols, and beware of letting our guards down.

(The views expressed are personal)


First published:12 Mar 2022, 6:48 pm


COVID-19 pandemicdelta variantomicrondeltacron

Debananda S Ningthoujam

Debananda S Ningthoujam

The author teaches and studies microbial biochemistry and biotechnology at Manipur University


Top Stories

Loading data...

IFP Exclusive

Loading data...


Have a complaint, a suggestion or just some feedback about our content? Please write to and we’ll do our best to address it.