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India’s COVID crisis flags need to forecast variants

The rise of more-transmissible viral mutants demands new ways to prevent, detect, track and treat SARS-CoV-2 infections.

As head of one of India’s main genomics laboratories, I am part of the consortium that first reported the B.1.617 strain of SARS-CoV-2 as a potential variant of concern. I keep asking myself how we might have predicted its danger sooner, tracked it rapidly and stalled its spread.

This year, I saw what felt like a year of deaths in a couple of weeks, among my friends, colleagues and family. There were ill people all around, calling for help, oxygen and beds. The health-care challenges were beyond imaginable. I can state with sad confidence that such catastrophic events are unavoidable without preventive measures. With just 5% of the world fully vaccinated, simple public-health interventions — masks, ventilation, quarantines — remain the cornerstone of containment. Limiting transmission gives the virus less chance to mutate.

Yet variants of concern continue to emerge. My colleagues and I are tracking the spread of the sublineage B.1.617.2, determining how effective vaccines are against it and advising on optimal approaches to vaccination. It will not be enough to stop the pandemic.

Strategies for tackling COVID-19 must include new, faster ways to spot and stop the spread of alarming new mutants. This requires: more sharing of data and methods; funding to develop better predictions and simpler tests; and integration of genomics, informatics and public health.

Faster identification means both more sequencing and more-targeted sequencing. The technologies are established. Last July, my institute ran the first assessment of Illumina’s high-throughput COVIDSeq assay, now the default global platform for sequencing SARS-CoV-2 genomes. The assay was used to develop a structured genomic-surveillance service for the Indian state of Kerala. I believe that this contributed to a timely and appropriate public-health response in the state, where there have been fewer deaths than in the rest of India, despite a similar prevalence of B.1.617.2.

The Indian SARS-CoV-2 sequencing consortium (INSACOG) began operations in January, when there were about 15,000 new infections each day in this nation of 1.4 billion people. The original plan was to randomly sequence samples from 5% of all cases. But, like many, we had not anticipated an extreme spike in infections. A 30-fold increase in daily cases, plus the difficulty of shipping samples around a country more than 13 times the size of the United Kingdom, with fewer resources, made this impossible.

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