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

Earnest, Rebecca; Uddin, Rockib; Matluk, Nicholas; Renzette, Nicholas; Turbett, Sarah E; Siddle, Katherine J.; Adams, Gordon; Tomkins-Tinch, Christopher H.; Me, Petrone; Rothman, Jessica E.; Breban, Mallery I.; Koch, Robert Tobias; Billig, Kendall; Fauver, Joseph R.; Vogels, Chantal B.F.; Bilgüvar, Kaya; Kumar, Bony De; Landry, Marie L.; Peaper, David R.; Kelly, Kevin; Omerza, Greg; Grieser, Heather; Meak, Sim; Martha, John; Dewey, Hannah B.; Kales, Susan; Berenzy, Daniel; Carpenter-Azevedo, Kristin; King, Ewa; Huard, Richard C.; Novitsky, Vlad; Howison, Mark; Darpolor, J. Kebbeh; Manne, Akarsh; Kantor, Rami; Smole, Sandra; Brown, Catherine; Fink, Timelia; Lang, Andrew S.; Gallagher, Glen R.; Pitzer, Virginia E.; Sabeti, Pardis C.; Gabriel, Stacey; MacInnis, Bronwyn; Tewhey, Ryan; Adams, Mark D.; Park, Daniel J.; Lemieux, Jacob E.; Grubaugh, Nathan D.; Altajar, Ahmad; DeJesus, Alexandra; Brito, Anderson; Watkins, Anne E.; Muyombwe, Anthony; Blumenstiel, Brendan; Neal, Caleb; Kalinich, Chaney C.; Liu, Chen; Loreth, Christine; Castaldi, Christopher; Pearson, Claire; Bernard, C.; Nolet, Corey M.; Ferguson, David; Buzby, Erika; Laszlo, Eva; Reagan, Faye L.; Vicente, Gina; Rooke, Heather M.; Munger, Heidi; Johnson, Hillary; Tikhonova, Irina; Ott, Isabel M.; Razeq, Jafar; Meldrim, James C.; Brown, Jessica; Wang, Jianhui; Vostok, Johanna; Beauchamp, John; Grimsby, Jonna; Hall, Joshua C.; Messer, Katelyn S.; Larkin, Katie; Vernest, Kyle; Madoff, Lawrence C.; Green, Lisa M.; Webber, Lori; Gagne, Luc; Ulcena, Maesha A.; Ray, Marianne C.; Fisher, Marissa; Barter, Mary; Lee, Matthew D.; DeFelice, Matthew; Cipicchio, Michelle; Smith, Natasha L.; Lennon, Niall J.; FitzGerald, Nicholas; Kerantzas, Nicholas; Hui, Pei; Harrington, Rachel; Downing, Randy; Haye, Rashida; Lynch, Ryan P.; Anderson, Scott; Hennigan, Scott; English, Sean E.; Cofsky, Seana; Clancy, Selina; Mane, Shrikant; Ash, Stephanie; Baez, Stephanie; Fleming, Stephen M.; Murphy, Steven; Chaluvadi, Sushma; Alpert, Tara; Rivard, Trevor; Schulz, Wade; Mandese, Zoe M.

doi:10.1016/j.xcrm.2022.100583

Cited by 127 publications

(98 citation statements)

References 30 publications

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“…The model-inference system estimates a 49.82% (95% CI: 25.22 -90.79%) attack rate by Delta, despite the large number of infections during the previous two waves. This large attack rate was possible, due to the high transmissibility of Delta, as reported in multiple studies (12)(13)(14)(15)(16), the more conducive winter transmission conditions (Fig 3A ), and the immune erosion from Delta relative to both the ancestral and Beta variants (17)(18)(19). .…”

Section: Pandemic Dynamics and Key Model-inference Using Gauteng Prov...mentioning

confidence: 76%

COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

Yang¹,

Shaman

2021

Preprint

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Within days of first detection, Omicron SARS-CoV-2 variant case numbers grew exponentially and spread globally. To better understand variant epidemiological characteristics, we utilize a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa and decompose novel variant transmissibility and immune erosion. Accounting for under-detection of infection, infection seasonality, nonpharmaceutical interventions, and vaccination, we estimate that the majority of South Africans had been infected by SARS-CoV-2 before the Omicron wave. Based on findings for Gauteng province, Omicron is estimated 100.3% (95% CI: 74.8 - 140.4%) more transmissible than the ancestral SARS-CoV-2 and 36.5% (95% CI: 20.9 - 60.1%) more transmissible than Delta; in addition, Omicron erodes 63.7% (95% CI: 52.9 - 73.9%) of the population immunity, accumulated from prior infections and vaccination, in Gauteng.

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Section: Pandemic Dynamics and Key Model-inference Using Gauteng Prov...mentioning

confidence: 76%

COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

Yang¹,

Shaman

2021

Preprint

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“…The circulation of the Delta variant coincided with high transmissibility and with a large number of severe disease cases. In fact, infection with the Delta variant is characterized by the generation of an average of 6 times more viral RNA copies per milliliter than Alpha infections [ 12 ]. In Tunisia, the detection of the Delta variant decreased from August to December 2021 (data not shown).…”

Section: Discussionmentioning

confidence: 99%

“…The Alpha variant, B.1.1.7 lineage (20I/501Y.V1, VOC-202012/01), also known as the UK variant, has an unusually high number of mutations and is more transmissible than the wild-type virus [ 10 ]. The Beta variant, B.1.351 lineage (501.V2, 20H/501Y.V2, VOC-202012/02), first detected and reported in South Africa in early October 2020, shares several mutations with B.1.1.7 and reduces vaccine effectiveness to some extent [ 11 , 12 ]. The Gamma variant, P.1 lineage (20J/501Y.V3, VOC-202101/02), emerged in December 2020 in Brazil [ 13 ]; it has 10 mutations in the spike protein that may affect its ability to be recognized by antibodies [ 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…The Gamma variant, P.1 lineage (20J/501Y.V3, VOC-202101/02), emerged in December 2020 in Brazil [ 13 ]; it has 10 mutations in the spike protein that may affect its ability to be recognized by antibodies [ 14 , 15 ]. The Delta variant (B.1.617.2, AY.1 and AY.2 VOC-21APR-02) was first described in India and then widely spread all over the world [ 11 , 12 ]. This variant has eight mutations in the spike protein and is characterized by increased transmissibility in comparison with the Alpha variant [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…The Delta variant (B.1.617.2, AY.1 and AY.2 VOC-21APR-02) was first described in India and then widely spread all over the world [ 11 , 12 ]. This variant has eight mutations in the spike protein and is characterized by increased transmissibility in comparison with the Alpha variant [ 11 , 12 ]. In November 2021, a new VOC designated the Omicron variant (B.1.1.529) was first described in Botswana and in South Africa.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19

Chouikha

Laamari

Haddad-Boubaker

et al. 2022

Viruses

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Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.

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Impact of Risk Factors on COVID‐19 Outcomes in Unvaccinated People With Rheumatic Diseases: A Comparative Analysis of Pandemic Epochs Using the COVID‐19 Global Rheumatology Alliance Registry

Yazdany,

Ware,

Wallace

et al. 2023

Arthritis Care & Research

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ObjectiveApproximately one third of individuals worldwide have not received a COVID‐19 vaccine. Although studies have investigated risk factors linked to severe COVID‐19 among unvaccinated people with rheumatic diseases (RDs), we know less about whether these factors changed as the pandemic progressed. We aimed to identify risk factors associated with severe COVID‐19 in unvaccinated individuals in different pandemic epochs corresponding to major variants of concern.MethodsPatients with RDs and COVID‐19 were entered into the COVID‐19 Global Rheumatology Alliance Registry between March 2020 and June 2022. An ordinal logistic regression model (not hospitalized, hospitalized, and death) was used with date of COVID‐19 diagnosis, age, sex, race and/or ethnicity, comorbidities, RD activity, medications, and the human development index (HDI) as covariates. The main analysis included all unvaccinated patients across COVID‐19 pandemic epochs; subanalyses stratified patients according to RD types.ResultsAmong 19,256 unvaccinated people with RDs and COVID‐19, those who were older, male, had more comorbidities, used glucocorticoids, had higher disease activity, or lived in lower HDI regions had worse outcomes across epochs. For those with rheumatoid arthritis, sulfasalazine and B‐cell–depleting therapy were associated with worse outcomes, and tumor necrosis factor inhibitors were associated with improved outcomes. In those with connective tissue disease or vasculitis, B‐cell–depleting therapy was associated with worse outcomes.ConclusionRisk factors for severe COVID‐19 outcomes were similar throughout pandemic epochs in unvaccinated people with RDs. Ongoing efforts, including vaccination, are needed to reduce COVID‐19 severity in this population, particularly in those with medical and social vulnerabilities identified in this study.

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

Cited by 127 publications

References 30 publications

COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19

Impact of Risk Factors on COVID‐19 Outcomes in Unvaccinated People With Rheumatic Diseases: A Comparative Analysis of Pandemic Epochs Using the COVID‐19 Global Rheumatology Alliance Registry

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