Thread by @NavroopSingh_

Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
medrxiv.org/content/10.110…

The origin of SARS-CoV-2 outbreaks in North India in 2021

The April 2021 outbreak in Delhi was preceded by outbreaks in the states of Kerala, Maharashtra and Punjab. While no VOC was identified in Kerala in Jan 2021, the outbreak in Maharashtra has been related to B.1.617.1.

and in Punjab to the introduction of B.1.1.7. These were found to be phylogenetically related, with a strong phylogenetic connection between Delhi and Punjab for B.1.1.7, and between Delhi and Maharashtra for B.1.617 lineages, as shown in Figure 4A and B.

The B.1.1.7 outbreak in Punjab was notable for multiple polytomies in the phylogenetic tree and clusters spanning multiple districts, suggesting a mass super- spreader event (Fig 4C).

This is relatable to mass public gatherings and rallies held in different parts of North India since January 2021 and highlights the important role of social factors in SARS-CoV-2 outbreaks.

Expansion of B.1.1.7 and B.1.617 lineages in North India
To determine whether the outbreak in Punjab and Delhi may have led to seeding of B.1.1.7 across North India, for which these are the main travel hubs, we analyzed the temporal trend of the SARS-CoV-2 lineages.

Despite limitations of lower sequencing than for Delhi, we see the same recurring pattern with initial seeding by B.1.1.7 in February to March and replacement by B.1.617.2 in April 2021.

Our data indicates B.1.617.2 shows high transmissibility and surges without any increase in CFR. We estimate the transmissibility to be as much as 50% greater than B.1.1.7. Viral load of B.1.617.2 appears to be higher than B.1.1.7 and based on data from India and UK.

so does vaccination break-through rate. While immune escape seems less for B.1.617.2 compared to B.1.351 or P.1 (Li et al., 2021), overall, we note that B.1.617.2 is capable of creating very fast- rising outbreaks with vaccination breakthroughs.

We would re-emphasize that prior infections, high seropositivity and partial vaccination are insufficient impediments to its spread, as seen in Delhi, and strong public health response will be needed globally for its containment.