COVID-19: India should test, sequence in a smart, integrated manner to make a difference, say experts

A section of experts Down To Earth spoke to, have said India’s COVID-19 testing and genomic sequencing done in a smart and integrated manner and shared on time, can make all the difference as the numbers of tests decline globally.

The experts also underlined the importance of COVID-19 testing in genomic sequencing and said the more tests were conducted, the greater the chances that newer variants would be discovered.

The experts’ comments came even as the World Health Organization (WHO) last month warned of declining testing rates across the globe. Low income countries were conducting just five tests per day per 100,000 people, far below the goal of 100 per day, it said.

Currently, India’s daily testing figures hover around 200,000-300,000. It was around 400,000-600,000 in March-April and more than 10, 00,000 in February and January, when the omicron wave was peaking.

On June 14, 2022, 321,873 tests and 6,594 new cases were recorded in the last 24 hours, with a weekly positivity rate of 2.32 per cent. A week ago, 307,716 daily tests were conducted and a weekly positivity rate of 0.97 per cent was recorded June 7, according to the Union Ministry of Health and Family Welfare.

So, is India testing enough?

“It is not advisable to put an absolute number on how many tests should be done. The positivity rate is important — if it’s low, then we’re doing enough tests. But if it is going up, then we need to do more. The aim is to keep the positivity rate down,” Shahid Jameel, virologist and former head of the Indian SARS-CoV-2 Genomics Consortium (INSACOG), told DTE.

The positivity rate is increasing — driven mostly by an increase in the caseload of Maharashtra, Kerala, Karnataka and Himachal Pradesh. But it is still below five per cent, the standard set by the WHO to assess if the pandemic is under control.

Jameel cited the data from June 8, when 313,361 tests were conducted with a positivity rate of 1.8 per cent and said India was conducting enough COVID-19 tests.

But he empahsised that the type of tests being conducted was key. Reverse transcription–polymerase chain reaction (RT–PCR) tests take some time. But they have a higher sensitivity as compared to the rapid antigen test.

“But it’s a little more complicated than that. Through the course of the pandemic, we have learnt that repeat antigen testing is actually more sensitive,” Jameel said.

RT-PCR tests are recorded by the system. But exactly how many home tests are being conducted and what their results are is not known.

However, media reports have confirmed that their sale shot up during the third wave. Omicron was far more contagious than delta and has comparatively milder symptoms. Hence, experts believe it is likely that we missed a lot more cases during the third wave.

While cases are increasing, low hospitalisation rates are the reason experts are not really worried.

“Medically, the pandemic may not be over, but it’s over as far as India’s political and social machinery goes. I would only get worried if hospitalisation rises, not if a few thousand cases go up in a country of India’s size,” Jameel said.

Testing and sequencing

Anurag Agarwal — a biologist with Ashoka University and the former head of Council of Scientific And Industrial Research (CSIR)-Institute for Genomics and Integrative Biology, an INSACOG partner — noted that testing and tracing was not being considered the way out of the pandemic at this point.

“Low testing is not as much of a problem as it seems on the surface, but does have consequences for surveillance,” he said.

So, how have India’s surveillance efforts been faring?

INSACOG — a consortium of 38 laboratories to monitor the genomic variations in the SARS-CoV-2 — last published its weekly bulletin April 25, in which it noted a total of 243,957 samples have been sequenced till date. BA.2, a sub-lineage of omicron, remains the dominant variant in India.

“BA.2.10 and BA.2.12 are BA.2 sub-lineages that have been detected and many old BA.2 sequences have been reclassified into these new sub-lineages. So far, these sub-lineages are not reported to be associated with increased severity of disease,” the body noted.

On May 21, the body published a press release according to which BA.4 and BA.5 had been recorded in Tamil Nadu and Telangana respectively. No other information has been shared since then.

This is not the first instance of infrequency. On the evening of April 27, INSACOG released its bulletin after a gap of three months.

India’s genome sequencing efforts have not been up to mark. More than two years into the pandemic, the country is still sequencing only 0.4 per cent of total cases, a marginal increase from 0.2 per cent in September 2021, according to the Global Initiative on Sharing Avian Influenza Data (GISAID) — the world’s largest database of novel coronavirus genome sequences.

“It is very disappointing that our sequencing data is not publicly available in real time. There’s a big time lag. Unless that information is available, it is very hard to understand how the virus is behaving,” Jameel said.

According to India’s protocol of genome surveillance, only a subset of the positive cases are sent for sequencing. Every state is supposed to send samples that are collected from 10 different locations — five hospitals and five community areas.

“But with low testing, it is difficult to identify new clusters and thus new variants can be missed. Heterogeneity with almost no testing in some places, compounds the problem,” Agarwal said.

India’s sequencing efforts are not the only issue. Even if it is sequencing at high density and discovers a low prevalent variant, the surveillance will not have any impact if it is not acted upon.

“That’s precisely what happened when the delta variant emerged. Sequencing is just a tool to aid public policy. You must have an effective policy of how you will use these tools,” Jameel said.

South Africa’s robust system offers some lessons. The country has shown that it is not really about the amount of sequencing but rather how it is done in an integrated and smart way.

“They have used a small but effective sequencing programme to repeatedly inform the world about the emergence of new variants in a timely manner,” Agarwal said. 

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