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

• Published in: Cell reports. Medicine Vol. 3; no. 4; p. 100583
• Main Authors: Earnest, Rebecca, Uddin, Rockib, Matluk, Nicholas, Renzette, Nicholas, Turbett, Sarah E., Siddle, Katherine J., Loreth, Christine, Adams, Gordon, Tomkins-Tinch, Christopher H., Petrone, Mary E., Rothman, Jessica E., Breban, Mallery I., Koch, Robert Tobias, Billig, Kendall, Fauver, Joseph R., Vogels, Chantal B.F., Bilguvar, Kaya, De Kumar, Bony, Landry, Marie L., Peaper, David R., Omerza, Greg, Grieser, Heather, Meak, Sim, Martha, John, Dewey, Hannah B., King, Ewa, Huard, Richard C., Novitsky, Vlad, Darpolor, Josephine, Manne, Akarsh, Kantor, Rami, Smole, Sandra C., Brown, Catherine M., Fink, Timelia, Lang, Andrew S., Gallagher, Glen R., Pitzer, Virginia E., Sabeti, Pardis C., Gabriel, Stacey, MacInnis, Bronwyn L., Altajar, Ahmad, DeJesus, Alexandra, Brito, Anderson, Watkins, Anne E., Muyombwe, Anthony, Blumenstiel, Brendan S., Neal, Caleb, Kalinich, Chaney C., Liu, Chen, Castaldi, Christopher, Pearson, Claire, Bernard, Clare, Nolet, Corey M., Buzby, Erika, Laszlo, Eva, Reagan, Faye L., Vicente, Gina, Rooke, Heather M., Munger, Heidi, Johnson, Hillary, Tikhonova, Irina R., Ott, Isabel M., Razeq, Jafar, Meldrim, James C., Brown, Jessica, Wang, Jianhui, Vostok, Johanna, Beauchamp, John P., Grimsby, Jonna L., Messer, Katelyn S., Vernest, Kyle, Green, Lisa M., Webber, Lori, Gagne, Luc, Ray, Marianne C., Fisher, Marissa E., Barter, Mary, Lee, Matthew D., DeFelice, Matthew T., Cipicchio, Michelle C., Smith, Natasha L., Fitzgerald, Nicholas A., Kerantzas, Nicholas, Hui, Pei, Harrington, Rachel, Haye, Rashida, Lynch, Ryan, Cofsky, Seana, Clancy, Selina, Mane, Shrikant, Ash, Stephanie, Baez, Stephanie, Fleming, Steve, Murphy, Steven, Alpert, Tara, Mandese, Zoe M., Adams, Mark D., Park, Daniel J., Lemieux, Jacob E., Grubaugh, Nathan D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.04.2022; Elsevier
• Subjects: COVID-19; COVID-19 - epidemiology; genomic epidemiology; Humans; New England - epidemiology; Public Health; SARS-CoV-2; SARS-CoV-2 - genetics; transmissibility; variant of concern; viral emergence; viral sequencing; VOC; New England; COVID-19; SARS-CoV-2; viral emergence; genomic epidemiology; transmissibility; viral sequencing; variant of concern; VOC
• ISSN: 2666-3791; 2666-3791
• DOI: 10.1016/j.xcrm.2022.100583

The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%–80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant’s respective emergence period, finding that Delta emerged 1.37–2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%–167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1–10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta’s enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability. [Display omitted] •SARS-CoV-2 Delta variant emerges 1.37–2.63 times faster than Alpha (state range)•Delta is on average 63%–167% more transmissible than Alpha (state range)•Delta infections average 6.2 times more viral RNA copies per milliliter than Alpha•Variant transmissibility estimates depend on innate, population, and data factors The SARS-CoV-2 Delta variant displaced the previously dominant Alpha variant by mid-2021, ostensibly because of 40%–80% increased transmissibility. To determine whether this difference is uniform across populations, Earnest et al. estimate variant-specific logistic growth rates and effective reproductive numbers for six states in New England finding substantial heterogeneity.