Bihar struggles to speed up genome sequencing

The Indian SARS CoV-2 genomics consortium’s (INSACOG) direction to its empanelled laboratories to prioritise and expedite genome sequencing of Covid-19 samples of February has put a break to Bihar’s efforts to fast-track testing with leftover samples of two previous months, said state health officials.

The INSACOG, a forum set up under the union ministry of health and family welfare to study and monitor genome sequencing and virus variation of circulating strains of Covid-19, had asked its 38 empanelled laboratories across India on February 9 to conduct genome sequencing with fresh samples.

The Indira Gandhi Institute of Medical Sciences (IGIMS), which is Bihar’s lone institute empanelled with the INSACOG, had earlier prepared 40 samples of two previous months as it waited for reagents for over a fortnight after the last round of tests on January 18.

The IGIMS had to delay by a week till Sunday to initiate the third round of sequencing before it could get the right mix of fresh samples having high viral load [below 25 cycle threshold (CT) value], said sources familiar with the development.

The result is expected within a week’s time.

“Conducting next generation sequencing with fresh samples will help understand the current variant situation in the strains of Covid-19,” said Dr Namrata Kumari, professor and head, department of microbiology, IGIMS.

Bihar has been slow in genome sequencing. It has so far tested only 72 samples since the launch of the testing facility at the IGIMS on January 3. Of them, 67 had Omicron, four Delta while result was inconclusive in one sample.

Officials blamed the slow pace of genome sequencing in Bihar to shortage of reagents and complete absence of standard scientific institutes like those for genomics, biotechnology, immunology, bioinformatics, proteinomics, fermentation technology, etc. Even the AIIMS and the ICMR’s Rajendra Memorial Research Institute of Medical Sciences in Patna were not part of the INSACOG due to lack of genome sequencing facility.

Bihar, given its small sample size of sequencing, has not been able to contribute much to the INSACOG study to assess the severity of Covid-19 variants and their sub-lineage.

It had asked its empanelled institutes to begin sampling and genome sequencing of patients admitted in hospitals due to Covid-19. It sought information on Covid patients suffering from co-morbidities, including chronic obstructive pulmonary disorder, asthma, diabetes, hypertension, renal, heart disease; whether patient required ICU, oxygen/ventilator support; if patient was fully or partially vaccinated, name of vaccine, suspected re-infection, etc.

The IGIMS was yet to respond.

In fact, barring scientific institutions in New Delhi, Maharashtra, Karnataka and Andhra Pradesh, which have done higher number of genome sequencing, hardly any other state had contributed much to the study, said INSACOG officials.

Dr Dhiren Gupta, a senior clinician of the Sir Ganga Ram Hospital, New Delhi, said: “The vaccine effectiveness of a third shot is about 70% against BA.2 (sub-lineage of Omicron) as against 63% in case of BA.1, two weeks after the booster shot. This level is likely to fall over time. However, protection against an infection 25 weeks after the second shot was 9%, a UK-based study on mRNA vaccination found.”

He said the key question was whether a BA.1 infection provides protection against BA.2 and vice-versa.

He said the possibility of reinfections was rare and even if they happened, the cases were mild.

Dr Saumitra Das, director of the National Institute of Biomedical Genomics, a key member of the INSACOG, did not respond to this reporter’s queries on how effective was the antibody of BA.1 versus BA.2 and vice-versa; possibility of Covid reinfections and severity of cases; vaccine efficacy against BA.1 and BA.2 and severity of different variants of Covid-19.

Dr Sujeet Kumar, director, National Centre for Disease Control, New Delhi, another active member of the consortium, also did not respond.

Abhay Kumar, scientist II, department of microbiology, IGIMS, advocated continuing genome sequencing, despite the decrease in the number of new Covid-19 cases pan India. He said the purpose was not just to detect the presence of Omicron/Delta variants in the population, but to continuously monitor the genomic variations over time.

“RT-PCR based detection kits are designed to detect only one kind of variant, whereas genome sequencing can identify all kinds of existing and novel variants. Besides, earlier waves contained a mixed spread of more than one variant,” said Kumar. Hindustan Times