SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review

Mendiola-Pastrana, Indira Rocío; López-Ortiz, Eduardo; Loza-Zamora, José G. Río de la; González, Jesús Salvador; Gómez-García, Anel; López-Ortiz, Geovani

doi:10.3390/life12020170

Cited by 57 publications

(53 citation statements)

References 90 publications

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“…Furthermore, the relevance of SARS-CoV-2 variants in clinical outcomes has been addressed but results aren’t homogeneous across studies [ 11 , 12 ]. There could be several reasons for this, from sample size, genetic background of the population, comorbidities, available medical equipment and personnel, and the method employed for variant identification.…”

Section: Discussionmentioning

confidence: 99%

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection

Muñoz‐Valle

Venancio-Landeros

Sánchez³

et al. 2022

IJMS

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SARS-CoV-2 variants surveillance is a worldwide task that has been approached with techniques such as Next Generation Sequencing (NGS); however, this technology is not widely available in developing countries because of the lack of equipment and limited funding in science. An option is to deploy a RT-qPCR screening test which aids in the analysis of a higher number of samples, in a shorter time and at a lower cost. In this study, variants present in samples positive for SARS-CoV-2 were identified with a RT-qPCR mutation screening kit and were later confirmed by NGS. A sample with an abnormal result was found with the screening test, suggesting the simultaneous presence of two viral populations with different mutations. The DRAGEN Lineage analysis identified the Delta variant, but there was no information about the other three mutations previously detected. When the sequenced data was deeply analyzed, there were reads with differential mutation patterns, that could be identified and classified in terms of relative abundance, whereas only the dominant population was reported by DRAGEN software. Since most of the software developed to analyze SARS-CoV-2 sequences was aimed at obtaining the consensus sequence quickly, the information about viral populations within a sample is scarce. Here, we present a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis.

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Section: Discussionmentioning

confidence: 99%

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection

Muñoz‐Valle

Venancio-Landeros

Sánchez³

et al. 2022

IJMS

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“…The clinical manifestation of COVID-19 remains unpredictable and varies from asymptomatic to severe or lethal [ 3 , 4 , 5 ]. Hence, there is an urgent need to introduce a simple and fast triage tool to clinical practice aimed at supporting the decision-making process for the clinicians in terms of appropriate management and optimized use of limited resources.…”

Section: Introductionmentioning

confidence: 99%

Sex-Dependent Differences in Predictive Value of the C2HEST Score in Subjects with COVID-19—A Secondary Analysis of the COLOS Study

Rola¹,

Doroszko

Trocha

et al. 2022

Viruses

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Background: Since the outbreak of the COVID-19 pandemic, a growing number of evidence suggests that COVID-19 presents sex-dependent differences in clinical course and outcomes. Nevertheless, there is still an unmet need to stratify the risk for poor outcome at the beginning of hospitalization. Since individual C2HEST components are similar COVID-19 mortality risk factors, we evaluated sex-related predictive value of the score. Material and Methods: A total of 2183 medical records of consecutive patients hospitalized due to confirmed SARS-CoV-2 infections were analyzed. Subjects were assigned to one of two of the study arms (male vs. female) and afterward allocated to different stratum based on the C2HEST score result. The measured outcomes included: in-hospital-mortality, three-month- and six-month-all-cause-mortality and in-hospital non-fatal adverse clinical events. Results: The C2HEST score predicted the mortality with better sensitivity in female population regarding the short- and mid-term. Among secondary outcomes, C2HEST-score revealed predictive value in both genders for pneumonia, myocardial injury, myocardial infarction, acute heart failure, cardiogenic shock, and acute kidney injury. Additionally in the male cohort, the C2HEST value predicted acute liver dysfunction and all-cause bleeding, whereas in the female arm-stroke/TIA and SIRS. Conclusion: In the present study, we demonstrated the betterC2HEST-score predictive value for mortality in women and illustrated sex-dependent differences predicting non-fatal secondary outcomes.

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“…The LumiraDx SARS-CoV-2 Antigen Test has been designed with antibodies that are raised to capture nucleocapsid (N) proteins in SARS-CoV-2-positive samples. The choice of capturing the N protein over the S protein was made because the N protein is more abundantly present, with fewer reported mutations in common variants [13, 14]. This interim study analysis investigated the performance of the LumiraDx SARS-CoV-2 Antigen Test in samples of patients infected with the SARS-CoV-2 Delta and Omicron variants compared using real-time polymerase chain reaction (RT-PCR) reference testing.…”

Section: Introductionmentioning

confidence: 99%

Performance study of a point-of-care antigen test during the SARS-CoV-2 Delta to Omicron variant transition in the USA

Drain

Chiklis

Guest

et al. 2022

Preprint

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IntroductionConcerns have been raised regarding the accuracy of diagnostic antigen testing for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant. We compared the performance of the LumiraDx SARS-CoV-2 Antigen Test between symptomatic participants recruited prospectively during the Delta to Omicron variant transition in the USA.MethodsTwo paired anterior nasal swabs were collected from each participant (adults and children) within 12 days of symptom onset between November 24th, 2021 and February 1st, 2022, during which time Omicron replaced Delta as the dominant variant in the sample population. Swabs were tested by the LumiraDx SARS-CoV-2 Antigen Test and compared using real-time polymerase chain reaction (RT-PCR) reference testing. Reference samples identified as positive were sequenced to identify the SARS-CoV-2 variant. Positive percent agreement (PPA) was calculated, with results stratified by RT-PCR cycle threshold (Ct).ResultsOf the 38 participants for whom LumiraDx SARS-CoV-2 Antigen Test results were available, 36 were confirmed positive by RT-PCR. Overall, PPA of the LumiraDx SARS-CoV-2 Antigen Test was 94.7% (95% confidence interval: 82.3%, 99.4%) and PPA was 100% for samples with a Ct <33. Sufficient viral load for sequencing was present in nine samples (six Delta, three Omicron), all of which returned a positive result using the LumiraDx SARS-CoV-2 Antigen Test. There were no performance differences observed between participants with the Delta and Omicron variants.ConclusionsSARS-CoV-2 differences between Delta and Omicron variant mutations did not affect the performance of the LumiraDx SARS-CoV-2 Antigen Test which detects the nucleocapsid protein antigen. The LumiraDx SARS-CoV-2 Antigen Test can be a useful antigen test to diagnose emerging variants of coronavirus disease 2019.

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SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review

Cited by 57 publications

References 90 publications

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection

Sex-Dependent Differences in Predictive Value of the C2HEST Score in Subjects with COVID-19—A Secondary Analysis of the COLOS Study

Performance study of a point-of-care antigen test during the SARS-CoV-2 Delta to Omicron variant transition in the USA

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