Analysis of SARS-CoV-2 Delta variant transmissibility across New England, USA

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern became globally dominant shortly following its emergence in India in early 2021, owing to greater transmissibility compared to other variants.

Numerous reports have demonstrated the enhanced transmissibility of the Delta variant from the aspect of both epidemiological studies, with genomic surveillance revealing the spread of Delta through communities, as well as by in vitro analytical methods, where the spike protein of this variant bears enhanced affinity towards the human angiotensin-converting enzyme 2 (ACE2) receptor.

Study: Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Image Credit: RUKSUTAKARN studio / Shutterstock.com

However, transmissibility varies between populations based on innate demographics and vaccine adoption rates. To this end, a recent study published on the preprint server medRxiv* compares the transmissibility of the SARS-CoV-2 Alpha and Delta variants in six states across New England in the United States, finding variation in epidemiological dynamics based on community behavior.

About the study

In the current study, the researchers partnered with community genomics surveillance programs in Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island, and Vermont. These programs provided reverse-transcriptase qualitative polymerase chain reaction (RT-qPCR) data collected over the course of the pandemic, along with the rate of new cases discovered of each variant in each location.

Each state was noted to experience a similar change in variant frequency over time, with the Alpha variant becoming dominant in April 2021 and rapidly replaced by the Delta variant in June 2021. While a number of other minor SARS-CoV-2 variants constituted a large portion of total SARS-CoV-2 infections during the time that the Alpha variant was dominant, the Delta variant represented between 94-100% of all cases by the final week of 2021 and had become more widely dominant geographically.

Delta variant transmissibility

To compare the transmissibility of the Alpha and Delta variants, the group narrowed the time under examination to within 90 days following the first emergence of each variant. Interestingly, the Alpha variant at first appears to outpace the Delta variant during the early stages of outbreak, though the authors suggest that lacking surveillance data at this time caused an overestimation in transmissibility.

In total, the Delta variant was estimated to be 163% more transmissible than the Alpha variant in Vermont, 151% in Connecticut, 98% in Rhode Island, 95% in Maine, 75% in New Hampshire, and 37% in Massachusetts. The U.K. has reported an estimated 40-80% enhanced transmissibility for the Delta variant based on epidemiological data, and differences in population density, vaccine uptake, non-pharmaceutical interventions, and the presence of competing variants drive the variation observed.   

On average, the Delta variant became dominant in each location within 71 days, representing a range of 54-92 days across New England. No association between relative emergence speed and infections per capita was noted.

Given the genetic similarity of the Delta variant across New England, the difference observed in transmissibility is likely due to population-based differences. An association between vaccination rates and Delta variant emergence speed was found, with the variant taking longer to become dominant where vaccine adoption was high.

The timing of the Alpha and Delta variant outbreaks may have influenced the observed rate of Delta variant dominance. This is because, at the time of the Alpha variant outbreak, none of the population was yet vaccinated, while between 18-37% of the population was vaccinated by April.

As vaccination rates increased across New England, non-pharmaceutical measures such as lockdowns and travel restrictions were relaxed prior to the arrival of the Delta variant. Thus, these factors may have potentially caused the appearance of higher transmissibility.

Enhanced viral loads

RT-qPCR data with known SARS-CoV-2 variant origin were compared. As previously reported previously, the Delta variant was associated with a higher viral load than the Alpha or other variants.

This held true, even when accounting for the possibility of declining viral load in samples collected from individuals without recent infections and across different testing methods. Thus, the large viral load of the Delta variant may be the primary reason for its enhanced transmissibility.

Conclusion

While the complete mechanism behind the observed difference in Delta variant transmissibility between locations has yet to be elucidated, this study has demonstrated that factors such as the implementation and adherence to non-pharmaceutical measures and vaccine uptake strongly influence the dynamics of SARS-CoV-2 infections and outbreaks.

The authors suggest that, given the global dominance of the Delta variant, the next globally dominant strain to replace it is likely to emerge from the B.1.617.2 clade, to which the delta variant it belongs. However, it cannot be predicted when or where this variant will emerge, thus highlighting the importance of continued genomic surveillance.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Michael Greenwood

Michael graduated from Manchester Metropolitan University with a B.Sc. in Chemistry in 2014, where he majored in organic, inorganic, physical and analytical chemistry. He is currently completing a Ph.D. on the design and production of gold nanoparticles able to act as multimodal anticancer agents, being both drug delivery platforms and radiation dose enhancers.