We need better testing, genome sequencing and mortality data

The second wave of the covid pandemic has overburdened our health system. There have been reports of a decline in testing in several Indian states and cities. Some states have allegedly given thresholds for positivity rates to private laboratories, which they are not allowed to breach. It is extremely difficult to get home collection of samples. In Delhi, on 3 May, only 61,045 tests were administered. Of these, 16% were rapid antigen tests (RATs). At some of the free testing sites, both RAT and reverse transcription-polymerase chain reaction (RT-PCR) tests are administered to each patient. Thus, there may be some double-counting too. On the other hand, Delhi conducted more than 100,000 tests in the middle of April. With the new wave, testing numbers declined, and positivity rates are a function of testing.

Today, it takes 3-4 days for test results to be reported. Timely tests and release of reports are essential for several reasons. 1) Pending test results, most people do not take pre-emptive medicines. If they get their reports in four days, this window when people are most infectious is lost. 2) This increases chances of hospitalization. 3) Infected patients risk spreading the infection to others. 4) Robust and reliable health statistics and epidemiological data help in efficient allocation of financial and technical resources and targeted health interventions.

The evolution of new variants of covid warrants not only an increase in testing, but subsequent genome sequencing. According to a report by Johns Hopkins University, India has genetically sequenced less than one-tenth of reported cases, and it ranks India at No. 102 in coronavirus genetic sequencing. While India has the capacity to carry out a large number of sequences every day, our problem is the unavailability of metadata. In layman’s terms, metadata describes the sample from which the DNA/RNA sequence was obtained. Note that a new variant can increase the possibility of a false negative outcome from a RT-PCR test.

India set up Sars-CoV-2 Genomics Consortium last December to study the evolution of the virus. The viral genome sequencing data is generated and analysed by eight regional sequencing laboratories and then sent to National Centre for Disease Control (NCDC), Delhi, for collation and integration. The NCDC also collects data regularly from states. Unfortunately, if genomic sequences lack proper metadata, one can’t identify fatal variants. This data has to be collected by overburdened frontline healthcare workers, who do not have any incentive to do so. There is an immediate need for further investment in genome sequencing infrastructure and incentivizing states and healthcare workers to collect metadata appropriately.

Another perennial issue is the quality of our mortality statistics. There have been reports of under-reported deaths. The registration of births and deaths is governed by the Registration of Births and Deaths (RBD) Act, 1969. However, the implementation of this statute is vested with state governments. Even before the pandemic, deaths were under-reported, but the pandemic has accentuated this problem. In a global assessment of civil registration systems (CRSs) across countries, India’s CRS was rated the lowest on a vital statistics performance index (<0.25). Owing to the covid pandemic, the collection of accurate data on deaths and fatality causes is all the more important right now. This can aid us in carrying out targeted vaccination in clusters where the fatality rate is high. In any case, covid or not, India requires robust and reliable mortality statistics.

The latest CRS data suggest that in Chhattisgarh, Meghalaya, Tripura, Jammu & Kashmir, Assam, Telangana, West Bengal, Rajasthan, Karnataka and Kerala, only 50-80% of deaths are registered within 21 days (a statutory requirement). Whereas, in Manipur, Arunachal Pradesh and Nagaland, less than half of all deaths are registered within the stipulated timeframe.

If at all a death gets reported, the cause of death does not. Among deaths registered under the CRS, only 21.2% nationally have the cause of death medically certified. In states like Jharkhand (4.6%), Uttar Pradesh (5.1%), Uttarakhand (11.1%), Odisha (11.1%), Kerala (11.9%), Assam (12%), Rajasthan (13.1%), Bihar (13.6%), Himachal Pradesh (15%), Haryana (20.4) and Gujarat (23.4), the proportion of medically-certified deaths is very low.

According to CRS data, in 2018, around 86% of total deaths were registered, of which just 21.2% were medically certified. Only 18.5% of total deaths in the country were medically certified for cause of death. Moreover, 13.1% of total medically-certified deaths with a ‘medical certificate of cause of death’ were classified under the category ‘Symptoms, signs & abnormal clinical and laboratory findings not elsewhere classified’ (ICD R-99). By the numbers, this is India’s eighth leading cause of death. A high number of cases classified as ICD R-99 can be attributed to: 1) Non-awareness among health professionals of relevant ICD codes; or 2) Lack of expertise and equipment to determine the cause of death. If a death is classified as R-99, technically, this should raise a red flag, as it could be on account of a new potentially-fatal contagion.

A robust healthcare system that can respond to a health crisis has to rely on reliable mortality statistics, along with information on the cause of death. Under-reporting doesn’t serve any purpose; it just makes the situation worse. Correct mortality statistics don’t bring back the dead, but save lives.

These are the authors’ personal views

Bibek Debroy & Aditya Sinha are, respectively, chairman and assistant consultant at the Economic Advisory Council to the Prime Minister.

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