Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Variants on Inpatient Clinical Outcome
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Abstract
Background
Prior observation has shown differences in COVID-19 hospitalization risk between SARS-CoV-2 variants, but limited information describes hospitalization outcomes.
Methods
Inpatients with COVID-19 at 5 hospitals in the eastern United States were included if they had hypoxia, tachypnea, tachycardia, or fever, and SARS-CoV-2 variant data, determined from whole-genome sequencing or local surveillance inference. Analyses were stratified by history of SARS-CoV-2 vaccination or infection. The average effect of SARS-CoV-2 variant on 28-day risk of severe disease, defined by advanced respiratory support needs, or death was evaluated using models weighted on propensity scores derived from baseline clinical features.
Results
Severe disease or death within 28 days occurred for 977 (29%) of 3369 unvaccinated patients and 269 (22%) of 1230 patients with history of vaccination or prior SARS-CoV-2 infection. Among unvaccinated patients, the relative risk of severe disease or death for Delta variant compared with ancestral lineages was 1.30 (95% confidence interval [CI]: 1.11–1.49). Compared with Delta, the risk for Omicron patients was .72 (95% CI: .59–.88) and compared with ancestral lineages was .94 (.78–1.1). Among Omicron and Delta infections, patients with history of vaccination or prior SARS-CoV-2 infection had half the risk of severe disease or death (adjusted hazard ratio: .40; 95% CI: .30–.54), but no significant outcome difference by variant.
Conclusions
Although risk of severe disease or death for unvaccinated inpatients with Omicron was lower than with Delta, it was similar to ancestral lineages. Severe outcomes were less common in vaccinated inpatients, with no difference between Delta and Omicron infections.
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SciScore for 10.1101/2022.02.02.22270337: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical considerations and data availability: Research was conducted under Johns Hopkins institutional review board protocol IRB00300364 with a waiver of consent. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources WGS was performed on the Oxford Nanopore GridION using either the V3 primer ARTIC SARS-CoV-2 sequencing protocol or the NEBNext® ARTIC SARS-CoV-2 Companion Kit (VarSkip Short SARS-CoV-2 # E7660-L). WGSsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when …
SciScore for 10.1101/2022.02.02.22270337: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical considerations and data availability: Research was conducted under Johns Hopkins institutional review board protocol IRB00300364 with a waiver of consent. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources WGS was performed on the Oxford Nanopore GridION using either the V3 primer ARTIC SARS-CoV-2 sequencing protocol or the NEBNext® ARTIC SARS-CoV-2 Companion Kit (VarSkip Short SARS-CoV-2 # E7660-L). WGSsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Study limitations include reliance on community prevalence to infer SARS-CoV-2 lineage for most patients. However, surveillance was performed locally with 96% concordance of inferred to confirmed variant. Model estimates from sensitivity analyses limited to confirmed variants were similar to primary analyses. Co-circulation of the comparatively severe Delta variant at low levels during Omicron-dominant transmission may overrepresent Delta among hospitalized patients, especially the severely ill. Although inferred-confirmed variant concordance decreased to 87% during Omicron-dominant transmission, this misclassification biases against finding a severity difference between Omicron and Delta. Differences in patient characteristics and care patterns may limit the generalizability of estimates of severe disease risk. Reliance on vital sign abnormalities likely includes patients whose hospitalization may be due to exacerbation of chronic medical conditions temporally related to a positive SARS-CoV-2 test and misses others with more subtle COVID-19 symptoms. Study strengths include strict, objective inclusion criteria for symptomatic COVID-19, detailed clinical information from the EMR, extensive WGS results, and robust causal inference methods. Our findings show that for vaccinated patients who are hospitalized with COVID-19, their risk of severe disease or death is low–reduced by half compared to unvaccinated patients - and equally low for both Omicron and Delta infections. Despit...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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