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      Clinical severity of, and effectiveness of mRNA vaccines against, covid-19 from omicron, delta, and alpha SARS-CoV-2 variants in the United States: prospective observational study

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      1 , 2 , 3 , 4 , 5 , 4 , 4 , 6 , 7 , 8 , 8 , 9 , 9 , 10 , 11 , 11 , 12 , 12 , 13 , 14 , 14 , 15 , 16 , 16 , 17 , 18 , 18 , 19 , 20 , 20 , 21 , 21 , 22 , 22 , 23 , 24 , 25 , 26 , 26 , 27 , 27 , 28 , 28 , 29 , 29 , 3 , 7 , 8 , 30 , 30 , 31 , 31 , 32 , 32 , 32 , 2 , 2 , 2 , 2 , 2 , 2 , 30 , 31 ,
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          Abstract

          Objectives

          To characterize the clinical severity of covid-19 associated with the alpha, delta, and omicron SARS-CoV-2 variants among adults admitted to hospital and to compare the effectiveness of mRNA vaccines to prevent hospital admissions related to each variant.

          Design

          Case-control study.

          Setting

          21 hospitals across the United States.

          Participants

          11 690 adults (≥18 years) admitted to hospital: 5728 with covid-19 (cases) and 5962 without covid-19 (controls). Patients were classified into SARS-CoV-2 variant groups based on viral whole genome sequencing, and, if sequencing did not reveal a lineage, by the predominant circulating variant at the time of hospital admission: alpha (11 March to 3 July 2021), delta (4 July to 25 December 2021), and omicron (26 December 2021 to 14 January 2022).

          Main outcome measures

          Vaccine effectiveness calculated using a test negative design for mRNA vaccines to prevent covid-19 related hospital admissions by each variant (alpha, delta, omicron). Among patients admitted to hospital with covid-19, disease severity on the World Health Organization’s clinical progression scale was compared among variants using proportional odds regression.

          Results

          Effectiveness of the mRNA vaccines to prevent covid-19 associated hospital admissions was 85% (95% confidence interval 82% to 88%) for two vaccine doses against the alpha variant, 85% (83% to 87%) for two doses against the delta variant, 94% (92% to 95%) for three doses against the delta variant, 65% (51% to 75%) for two doses against the omicron variant; and 86% (77% to 91%) for three doses against the omicron variant. In-hospital mortality was 7.6% (81/1060) for alpha, 12.2% (461/3788) for delta, and 7.1% (40/565) for omicron. Among unvaccinated patients with covid-19 admitted to hospital, severity on the WHO clinical progression scale was higher for the delta versus alpha variant (adjusted proportional odds ratio 1.28, 95% confidence interval 1.11 to 1.46), and lower for the omicron versus delta variant (0.61, 0.49 to 0.77). Compared with unvaccinated patients, severity was lower for vaccinated patients for each variant, including alpha (adjusted proportional odds ratio 0.33, 0.23 to 0.49), delta (0.44, 0.37 to 0.51), and omicron (0.61, 0.44 to 0.85).

          Conclusions

          mRNA vaccines were found to be highly effective in preventing covid-19 associated hospital admissions related to the alpha, delta, and omicron variants, but three vaccine doses were required to achieve protection against omicron similar to the protection that two doses provided against the delta and alpha variants. Among adults admitted to hospital with covid-19, the omicron variant was associated with less severe disease than the delta variant but still resulted in substantial morbidity and mortality. Vaccinated patients admitted to hospital with covid-19 had significantly lower disease severity than unvaccinated patients for all the variants.

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          Most cited references24

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          A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

          The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. We present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and de-labelling virus lineages that become unobserved and hence are likely inactive. By focusing on active virus lineages and those spreading to new locations this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.
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            A minimal common outcome measure set for COVID-19 clinical research

            Summary Clinical research is necessary for an effective response to an emerging infectious disease outbreak. However, research efforts are often hastily organised and done using various research tools, with the result that pooling data across studies is challenging. In response to the needs of the rapidly evolving COVID-19 outbreak, the Clinical Characterisation and Management Working Group of the WHO Research and Development Blueprint programme, the International Forum for Acute Care Trialists, and the International Severe Acute Respiratory and Emerging Infections Consortium have developed a minimum set of common outcome measures for studies of COVID-19. This set includes three elements: a measure of viral burden (quantitative PCR or cycle threshold), a measure of patient survival (mortality at hospital discharge or at 60 days), and a measure of patient progression through the health-care system by use of the WHO Clinical Progression Scale, which reflects patient trajectory and resource use over the course of clinical illness. We urge investigators to include these key data elements in ongoing and future studies to expedite the pooling of data during this immediate threat, and to hone a tool for future needs.
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              Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

              The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function 4 . Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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                Author and article information

                Contributors
                Role: associate professor
                Role: CDC scientist
                Role: associate professor
                Role: professor
                Role: professor
                Role: interim chair
                Role: pulmonologist
                Role: assistant professor
                Role: associate professor
                Role: assistant professor
                Role: professor
                Role: pharmacist
                Role: professor
                Role: assistant professor
                Role: associate professor
                Role: associate professor
                Role: research specialist
                Role: associate professor
                Role: assistant professor
                Role: professor
                Role: professor
                Role: assistant professor
                Role: associate professor
                Role: assistant professor
                Role: professor
                Role: associate professor
                Role: professor
                Role: associate professor
                Role: professor
                Role: associate professor
                Role: professor
                Role: assistant professor
                Role: research specialist
                Role: associate professor
                Role: associate professor
                Role: research specialist
                Role: associate professor
                Role: professor
                Role: pulmonologist
                Role: research specialist
                Role: professor
                Role: assistant professor
                Role: professor
                Role: associate professor
                Role: associate professor
                Role: assistant professor
                Role: research specialist
                Role: research specialist
                Role: research specialist
                Role: professor
                Role: research specialist
                Role: statistician
                Role: CDC scientist
                Role: CDC scientist
                Role: CDC scientist
                Role: CDC scientist
                Role: CDC scientist
                Role: CDC scientist
                Role: vice president
                Journal
                BMJ
                BMJ
                BMJ-US
                bmj
                The BMJ
                BMJ Publishing Group Ltd.
                0959-8138
                1756-1833
                2022
                09 March 2022
                09 March 2022
                : 376
                : e069761
                Affiliations
                [1 ]Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
                [2 ]CDC COVID-19 Response Team, Atlanta, GA, USA
                [3 ]Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
                [4 ]Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, TX, USA
                [5 ]Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, CO, USA
                [6 ]Department of Anesthesiology, University of Colorado School of Medicine, Aurora, CO, USA
                [7 ]Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
                [8 ]Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
                [9 ]Department of Emergency Medicine, University of Iowa, Iowa City, IA, USA
                [10 ]Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
                [11 ]Department of Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
                [12 ]Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
                [13 ]Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
                [14 ]Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
                [15 ]Department of Medicine, The Ohio State University, Columbus, OH, USA
                [16 ]Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York, NY, USA
                [17 ]Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
                [18 ]Department of Emergency Medicine, University of Washington, Seattle, WA, USA
                [19 ]Department of Medicine, Baystate Medical Center, Springfield, MA, USA
                [20 ]Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City, UT, USA
                [21 ]School of Public Health, University of Michigan, Ann Arbor, MI, USA
                [22 ]Department of Medicine, Oregon Health and Sciences University, Portland, OR, USA
                [23 ]Department of Medicine, Emory University, Atlanta, GA, USA
                [24 ]Emory Critical Care Center, Emory Healthcare, Atlanta, GA, USA
                [25 ]Department of Medicine, Cleveland Clinic, Cleveland, OH, USA
                [26 ]Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
                [27 ]Department of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
                [28 ]Department of Medicine, University of Miami, Miami, FL, USA
                [29 ]Department of Medicine, Washington University, St Louis, MI, USA
                [30 ]Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
                [31 ]Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
                [32 ]Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
                Author notes
                Correspondence to: W H Self wesley.self@ 123456vumc.org
                Author information
                https://orcid.org/0000-0002-9300-3045
                Article
                bmj-2021-069761.R1 laua069761
                10.1136/bmj-2021-069761
                8905308
                35264324
                2b524dbb-3862-4571-af46-7e68a2c28b1a
                © Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

                This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

                History
                : 24 February 2022
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