New Delhi: It’s been a fortnight since India started seeing a spurt in COVID-19 cases, for which the emergence of the Omicron variant’s new sub-lineage XBB.1.16 has been blamed. While most scientists say that this is a ‘minor wave’, not much is known about this newer strain still. Omicron, since its emergence in January 2022, has now branched out to more than 600 sub-lineages. Experts also unanimously believe that India has reached a stage of endemicity – when a certain infectious disease becomes stable to the extent that it doesn’t overwhelm the health infrastructure every time it appears again.
What has India learnt from this surge? The Wire explains in five points.
1. Caseload, hospitalisation, deaths and test positivity rate
India’s COVID-19 caseload has steadily risen, with the country now reporting close to 10,000 cases on a daily basis. The deaths per day, on a country-wide basis, have hovered between 15-20. But a key piece of information missing in these statistics is the profile of the patients who are dying. The three years of the pandemic have, so far, shown that the elderly with comorbidities and immunocompromised persons are at the highest risk of mortality.
While there is no official information about the recent trends, co-chairman of the Indian Medical Association (IMA)’s task force on COVID-19, Rajeev Jayadevan, who has been interacting with various clinicians, says, it remains the same. “Otherwise healthy people are not dying,” he said.
Empirically, there has been a slight increase in hospitalisation numbers but no evidence suggests that healthcare facilities are overwhelmed. The daily bulletins issued by the Union Ministry of Health and Family Welfare do not give any information on this critical indicator. However, some state bulletins do give this information. Take, for example, Delhi. As the numbers below indicate, the number of patients currently being treated at hospitals has gone up – so is the number being admitted to ICUs – but a majority of infected people are recovering at home.
However, what has made headlines is the rising test positivity rate (TPR), i.e, the number of people who are testing positive for every 100 tests. In the very early phase of the pandemic in 2020, the World Health Organisation (WHO) said that a TPR of more than 5% should be cause for concern.
The country’s positivity rate has been hovering between 7-8% on a daily basis for a few days now.
According to a recent analysis done by the Union health ministry, as many as 129 districts scattered across 26 states have more than 10% TPR and another 100 districts have more than 5% TPR. Delhi itself is recording a TPR of more than 25% now. But all the experts The Wire reached out to said that in the current scenario, TPR is a misleading indicator because the denominator has changed.
“Positivity rate is going up only because those who are showing symptoms, already, are getting tested unlike a scenario before where random people [those who might not be infected] would also get tested,” Vinod Scaria, a scientist at Institute of Genomics and Integrative Biology, said.
Since only those who have symptom (and therefore the disease) are getting tested, invariably the test positivity rate would be high. Now, those without symptoms (and perhaps not infected) are not getting tested – unlike in the past, when people got tested even if they had the smallest of doubt.
While people who are showing symptoms are getting tested, the actual number of people who are infected may be higher. Recent analyses have found that nearly two-thirds of people who have COVID-19 are asymptomatic.
2. XBB.1.16 – the culprit at present
The Omicron variant of SARS-CoV-2 has evolved much more rapidly than other variants. After the variant evolved into various sub-variants, these sub-variants, or parts of them, have also been recombining to emerge as what are called recombinant forms of Omicron. XBB.1.16 is a recombinant of two sub-lineages of BA.2 – a sub-subvariant of Omicron. Not much is known about it yet. Maria Van Kerkhove, WHO’s technical lead on COVID-19, had said at a press conference on March 29 that XBB.1.16 is something to watch out for.
She also said that lab studies, until then, had not indicated any increase in the severity of the disease caused by XBB.1.16. But it has shown increased ‘pathogenicity’ as compared to XBB.1.5 – which is spreading across Europe and the US. In other words, XBB.1.16 has a tendency to make more people sick than the other recombinants but the disease may not necessarily be severe.
XBB.1.16, which is currently dominant in India, and XBB.1.5, are quite similar – the former has one additional mutation as compared to the latter. “A preliminary analysis from the US reports that there is no difference in number of deaths per hospital admissions of patients with XBB.1.5 compared to other Omicron lineages,” said a WHO analysis of XBB.1.5. If this is an indicator, then XBB.1.16 may not behave very differently.
A recently published pre-print paper by a group of Japanese scientists, said, “Notably, XBB.1.16 had an effective reproductive number (Re) that was 1.27- and 1.17-fold higher than the parental XBB.1 and XBB.1.5, respectively, suggesting that XBB.1.16 will spread worldwide in the near future.” The reproductive number indicates how many people can get infected by one infected person.
The team led by Rajesh Karyakarte, dean of the microbiology department at Pune’s BJ Government Medical College, was the first to isolate XBB.1.16 in India. “Our study also confirmed that it might spread faster but may not cause serious illness in the general population,” he told The Wire.
Genome sequencing is key to knowing what is currently the dominant strain of the virus. In India, INSACOG – a consortium of labs – is responsible for genome sequencing. According to INSACOG’s latest information, of the total positive samples which were sequenced, 60% belong to XBB.1.16 – which clearly indicates that it has become the predominant strain. The dashboard has data available till April 14, 2023. For the week ending April 7, XBB.1.16 accounted for more than 77% of the sequenced samples.
Till April 14, 2,598 XBB.1.16 samples have been found, with Gujarat accounting for the maximum number (947), followed by Maharashtra (433).
However, these numbers come with a significant caveat — the dashboard does not say of all the positive samples, how many were sequenced. That is, there is no figure in the public domain to say what proportion of positive samples are being sequenced. Another issues is that half of the XBB.1.16 samples have come from just two states – Gujarat and Maharashtra – which reveals that either disproportionately fewer samples are being sent from the other states or there is a time lag in reporting data. Both these scenarios could prevent a complete picture from emerging in real-time. Nonetheless, all available data suggests XBB.1.16 is the dominant form of Omicron circulating in India.
3. Beyond ‘not-so-severe’
There is near unanimity among experts that like all other forms of Omicron, this one too shall run its course without causing any serious alarm. Only the immunocompromised and those who have other comorbidities should take special care. However, there is another concern which does not get adequate attention in the ‘not-so-severe’ discourse, which is, long-COVID.
Anurag Agrawal, dean of Ashoka University’s Biosciences and Health Research department, says there is no definitive evidence to suggest that one variant of COVID-19, which caused severe disease, has more potential to cause long-COVID than variants which causes mild illness. One study published in 2022 said. “Long-COVID is a multisystem disease that develops regardless of the initial disease severity”. However, another one published in 2023, which took into account several published studies, said:
“Although no definitive conclusions can be made on this matter, it seems reasonable to hypothesize that the infection in the period characterised by the predominance of early sublineages belonging to the Omicron family may be associated with a lower risk of developing long‑COVID.”
Agrawal says immunity kept changing with different waves of COVID-19. “And long-Covid may not be separated from immunity.” And therefore, he suggested that making a comparison between long-COVID caused by different variants of novel coronavirus may be difficult.
India has not conducted any long-term study to understand the prevalence of long-COVID in its population. A JAMA paper quoted a study to say that the British population data suggests 22-38% of people with the infection will have at least one COVID-19 symptom 12 weeks after initial symptom onset, and 12-17% will have 3 or more symptoms. Given the huge caseload of India, any prevalence closer to these estimates would account for a significant number of people suffering from Long COVID which may further get exacerbated due to reinfections.
“Clearly there is an elevated risk of thrombotic diseases, heart attack and strokes, after SARS-CoV-2 infection and if you keep getting infected again and again, one doesn’t know [the impact],” Agarwal said.
4. Reinfections and emergence of new sub-variants
Practically everyone who has contracted COVID-19 recently is likely to be a case of reinfection. Even towards the end of the massive second wave in mid-2021, India had shown seropositivity of more than 90% – that is, more than 90% population of the country had been infected at least once by then.
And reinfections are to be expected because the antibody protection acquired after infection goes down after 90 daysl. This decreases the immune system’s ability to completely prevent reinfection, though the ability to protect against severe disease may still exist.
Asked if there was any evidence to suggest that the possibility of reinfection after one sub-lineage of Omicron was more than the other, Jayadevan replied, ‘none’. “The shortest interval I have seen of people getting reinfected is one month. On average, it is possible to get reinfected after 6 months,” he added.
But why does one subvariant of Omicron spread faster than several others? After all, we have had more than 600 forms by now. There is no clear answer to this but experts say a lot depends on the host environment.
“If two forms or sub-variants – A and B – infect an immunocompromised person, there they will find a very good host environment to survive [since the immunity offered would be less] and the recombination might take place. It is neither the original A nor the original B but some of A and some of B [that emerges],” Vineeta Bal, an immunologist who is with the Indian Institute of Science Education and Research, said.
Karyakarte added it is also about the mutations or the combinations of mutations acquired in this process. “[It is the particular type of] the mutations, or their combinations, which give the advantage to evade the immune response and spread faster,” he added, and said, it is impossible to project which one can be better than the others.
5. Ebb and Flow: What to expect
With the virus becoming endemic in India and most parts of the world, one can expect ebbs and flows in cases as new sub-variants emerge. Unless there is a major mutation, cases are unlikely to overwhelm the healthcare system. But amidst these ebbs and flows, experts advise taking precautions, especially for a vulnerable sections of the population.
More than 90% of the Indian population has taken two doses of the COVID-19 vaccine, according to the Union health ministry. While there is no official data about the the third dose, the coverage has been low. Experts urge that the elderly, people with comorbidities and immunocompromised persons should take the third jab – if not the entire population.
Wearing masks in crowded spaces and adequately ventilating indoor spaces remain effective and less resource-intensive preventive measures. As far as healthcare is concerned, Bal suggests, hospitals will have to remain prepared to bring some of the infrastructure that was created in earlier waves back, should the hospitalisation numbers rise amidst these unpredictable and not-so-frequent ebbs and flows.