GISAID’s Role in Pandemic Response

Khare, Shruti; Gurry, Céline; Freitas, Lucas; Schultz, Mark B.; Bach, Gunter; Diallo, Amadou; Akite, Nancy; Ho, Joses; Lee, Raphael Tc; Yeo, Winston; Team, Gisaid Core Curation; Maurer‐Stroh, Sebastian

doi:10.46234/ccdcw2021.255

Cited by 676 publications

(672 citation statements)

References 6 publications

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“…As shown in Tables 1 and 2, we concluded that the weighted average risk of reinfection and breakthrough infection decreased by 90. 39 [7,8], stringency index, vaccine coverage [9], and variant proportions [10][11][12][13] Iwasaki [14] detailed a case of SARS-CoV-2 reinfection in the US. However, the risk of reinfection in the US has been reported relatively rarely.…”

Section: Introductionmentioning

confidence: 99%

Multiple COVID-19 Waves and Vaccination Effectiveness in the United States

Lin

Zhao

Chen

et al. 2022

IJERPH

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(1) Background: The coronavirus 2019 (COVID-19) pandemic has caused multiple waves of cases and deaths in the United States (US). The wild strain, the Alpha variant (B.1.1.7) and the Delta variant (B.1.617.2) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were the principal culprits behind these waves. To mitigate the pandemic, the vaccination campaign was started in January 2021. While the vaccine efficacy is less than 1, breakthrough infections were reported. This work aims to examine the effects of the vaccination across 50 US states and the District of Columbia. (2) Methods: Based on the classic Susceptible—Exposed—Infectious–Recovered (SEIR) model, we add a delay class between infectious and death, a death class and a vaccinated class. We compare two special cases of our new model to simulate the effects of the vaccination. The first case expounds the vaccinated individuals with full protection or not, compared to the second case where all vaccinated individuals have the same level of protection. (3) Results: Through fitting the two approaches to reported COVID-19 deaths in all 50 US states and the District of Columbia, we found that these two approaches are equivalent. We calculate that the death toll could be 1.67–3.33 fold in most states if the vaccine was not available. The median and mean infection fatality ratio are estimated to be approximately 0.6 and 0.7%. (4) Conclusions: The two approaches we compared were equivalent in evaluating the effectiveness of the vaccination campaign in the US. In addition, the effect of the vaccination campaign was significant, with a large number of deaths averted.

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Section: Introductionmentioning

confidence: 99%

Multiple COVID-19 Waves and Vaccination Effectiveness in the United States

Lin

Zhao

Chen

et al. 2022

IJERPH

View full text Add to dashboard Cite

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“…Infections have increased dramatically in recent weeks, coinciding with the global detection of the omicron B.1.1.529 variant. Globally, the number of countries registering SARS-CoV-2 omicron B.1.1.529 infections keeps climbing, with 117 countries reporting 354 million confirmed cases as of 15 January 2022 [3]. Due to the widely altered omicron variant, many nations have imposed travel restrictions or border closures, and extensive research is desperately required for medical examinations and border closure advantages [4].…”

Section: Introductionmentioning

confidence: 99%

In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer

et al. 2022

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Omicron is an emerging SARS-CoV-2 variant, evolved from the Indian delta variant B.1.617.2, which is currently infecting worldwide. The spike glycoprotein, an important molecule in the pathogenesis and transmissions of SARS-CoV-2 variants, especially omicron B.1.1.529, shows 37 mutations distributed over the trimeric protein domains. Notably, fifteen of these mutations reside in the receptor-binding domain of the spike glycoprotein, which may alter transmissibility and infectivity. Additionally, the omicron spike evades neutralization more efficiently than the delta spike. Most of the therapeutic antibodies are ineffective against the omicron variant, and double immunization with BioNTech-Pfizer (BNT162b2) might not adequately protect against severe disease induced by omicron B.1.1.529. So far, no efficient antiviral drugs are available against omicron. The present study identified the promising inhibitors from seaweed’s bioactive compounds to inhibit the omicron variant B.1.1.529. We have also compared the seaweed’s compounds with the standard drugs ceftriaxone and cefuroxime, which were suggested as beneficial antiviral drugs in COVID-19 treatment. Our molecular docking analysis revealed that caffeic acid hexoside (−6.4 kcal/mol; RMSD = 2.382 Å) and phloretin (−6.3 kcal/mol; RMSD = 0.061 Å) from Sargassum wightii (S. wightii) showed the inhibitory effect against the crucial residues ASN417, SER496, TYR501, and HIS505, which are supported for the inviolable omicron and angiotensin-converting enzyme II (ACE2) receptor interaction. Cholestan-3-ol, 2-methylene-, (3beta, 5 alpha) (CMBA) (−6.0 kcal/mol; RMSD = 3.074 Å) from Corallina officinalis (C. officinalis) manifested the strong inhibitory effect against the omicron RBD mutated residues LEU452 and ALA484, was magnificently observed as the essential residues in Indian delta variant B.1.617.2 previously. The standard drugs (ceftriaxone and cefuroxime) showed no or less inhibitory effect against RBD of omicron B.1.1.529. The present study also emphasized the pharmacological properties of the considered chemical compounds. The results could be used to develop potent seaweed-based antiviral drugs and/or dietary supplements to treat omicron B.1.1529-infected patients.

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“…The N gene of the studied variants was aligned with the ClustalOmega pipeline at the Ugene (Unipro) software suite ( Unipro UGENE, 2021 ). The mutations found on each variant were checked with other sequences of the same variant at the GISAID database ( Khare et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%