Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ~6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.

Context-specific emergence and growth of the SARS-CoV-2 Delta variant

“…The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases [1][2][3] . The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions 4,5 .…”

Covariant Fitness Clusters Reveal Structural Evolution of SARS-CoV-2 Polymerase Across the Human Population

“…5L). These analyses demonstrate for the first time that the unique basal mutation G671S in the Delta VOC imposes a currently underappreciated level of evolutionary pressure driving the structural remodeling of its local environment, likely contributing to an elevated replication rate and to the increased viral load characteristic of Delta VOC (71)(72)(73)(74).…”

“…The copyright holder for this preprint this version posted January 7, 2022. ; https://doi.org/10.1101/2022.01.07.475295 doi: bioRxiv preprint possibility that the structural remodeling of the region around G671S contributes to the unique predatory behavior of the Delta VOC in driving the pandemic, likely through increased viral load (71)(72)(73)(74).…”

Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant

“…Different studies tried to assess the increased infectiousness of the Delta variant. The authors of [8] found a 55 % increased reproduction number of Delta compared to Alpha, while [9] agreed on a range of 40-60 % and [7] even observed 58-120 % increased effective reproduction numbers. In our simulations, we will therefore consider Delta to be 40 − 60 % more infectious than the previously dominant Alpha variant, while 60 % is potentially closer to the true value.…”

“…Additionally, we implement the effect of the B.1.617.2 (Delta) Coronavirus variant, which is considered to be 40% − 60% more infectious then the previously dominant B.1.1.7 (Alpha) variant; cf. [7][8][9]. In this paper, we focus on the comparison of different strategies based on our mathematical model that was already validated in [6].…”