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1.
Food Research International ; 162, 2022.
Article in English | Web of Science | ID: covidwho-2104926

ABSTRACT

The COVID-19 pandemic caused by SARS-CoV-2 has had a major impact on human health and the global economy. Various transmission possibilities of SARS-CoV-2 have been proposed, such as the surface of food in the cold chain and food packaging, as well as the fecal-oral route, although person-to-person contact via droplets and aerosols has been confirmed as the main route of transmission. This study evaluated the survivability of HCoV-229E, a SARS-CoV-2 surrogate, in suspension, on food-contact surfaces and on food at various temperatures, and in simulated digestive fluids by TCID50 assay. In suspension, HCoV-229E survived after 5 days at 20 degrees C with a 3.69 log reduction, after 28 days at 4 degrees C with a 3.07 log reduction, and after 12 weeks at -20 degrees C with a 1.18 log reduction. On food-contact surfaces, HCoV-229E was not detected on day 3 on stainless steel (SS), plastic (LDPE), and silicone rubber (SR) at 20 degrees C with a 3.28, 3.24 and 3.28 log reduction, respectively, and survived after 28 days on SS and LDPE at 4 degrees C with a 3.13 and 2.88 log reduction, respectively, and survived after 12 weeks on SS, LDPE, and SR at -20 degrees C with a 1.92, 1.32 and 1.99 log reduction, respectively. On food, HCoV-229E was not detected on day 3 on lettuce and day 4 on chicken breast and salmon at 20 degrees C with a 3.61, 3.26 and 3.08 log reduction, respectively, and on day 14 on lettuce and day 21 on chicken breast and salmon at 4 degrees C with a 3.88, 3.44 and 3.56 log reduction, respectively. The virus remained viable for 12 weeks in all foods at -20 degrees C with 2-2.47 log reduction. In addition, in simulated digestive fluid experiments, HCoV-229E was relatively resistant in simulated salivary fluid (SSF;pH 7, 5), fed state simulated gastric fluid (FeSSGF;pH 3, 5, 7), and fasted state simulated intestinal fluid (FaSSIF;pH 7). However, the virus was less tolerant in fasted state simulated gastric fluid (FaSSGF;pH 1.6) and fed state simulated intestinal fluid (FeSSIF;pH 5). Therefore, this study suggested that HCoV-229E remained infectious on various food-contact surfaces and foods;in particular, it survived longer at lower temperatures and survived depending on the pH of the simulated digestive fluid.

2.
35th Conference on Neural Information Processing Systems, NeurIPS 2021 ; 20:16346-16357, 2021.
Article in English | Scopus | ID: covidwho-1898354

ABSTRACT

Molecular representation learning is the first yet vital step in combining deep learning and molecular science. To push the boundaries of molecular representation learning, we present PhysChem, a novel neural architecture that learns molecular representations via fusing physical and chemical information of molecules. PhysChem is composed of a physicist network (PhysNet) and a chemist network (ChemNet). PhysNet is a neural physical engine that learns molecular conformations through simulating molecular dynamics with parameterized forces;ChemNet implements geometry-aware deep message-passing to learn chemical/biomedical properties of molecules. Two networks specialize in their own tasks and cooperate by providing expertise to each other. By fusing physical and chemical information, PhysChem achieved state-of-the-art performances on MoleculeNet, a standard molecular machine learning benchmark. The effectiveness of PhysChem was further corroborated on cutting-edge datasets of SARS-CoV-2. © 2021 Neural information processing systems foundation. All rights reserved.

3.
Embase; 2021.
Preprint in English | EMBASE | ID: ppcovidwho-335918

ABSTRACT

Introduction The infection-fatality rate (IFR) of COVID-19 has been carefully measured and analyzed in high-income countries, whereas there has been no systematic analysis of age-specific seroprevalence or IFR for developing countries. Methods We systematically reviewed the literature to identify all COVID-19 serology studies in developing countries that were conducted using population representative samples collected by early 2021. For each of the antibody assays used in these serology studies, we identified data on assay characteristics, including the extent of seroreversion over time. We analyzed the serology data using a Bayesian model that incorporates conventional sampling uncertainty as well as uncertainties about assay sensitivity and specificity. We then calculated IFRs using individual case reports or aggregated public health updates, including age-specific estimates whenever feasible. Results Seroprevalence in many developing country locations was markedly higher than in high-income countries. In most locations, seroprevalence among older adults was similar to that of younger age cohorts, underscoring the limited capacity that these nations have to protect older age groups. Age-specific IFRs were roughly 2x higher than in high-income countries. The median value of the population IFR was about 0.5%, similar to that of high-income countries, because disparities in healthcare access were roughly offset by differences in population age structure. Conclusion The burden of COVID-19 is far higher in developing countries than in high-income countries, reflecting a combination of elevated transmission to middle-aged and older adults as well as limited access to adequate healthcare. These results underscore the critical need to accelerate the provision of vaccine doses to populations in developing countries.

4.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326836

ABSTRACT

Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally and functionally characterized a potent human antibody ADI-62113 that also neutralizes SARS-CoV-2 variants of concern and cross-reacts with many other sarbecoviruses. A YYDRxG motif encoded by IGHD3-22 in CDR H3 facilitates targeting to a highly conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences identified many antibodies with broad neutralization activity against SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to counteract sarbecoviruses. These findings also suggest an epitope targeting strategy to identify potent and broadly neutralizing antibodies that can aid in the design of pan-sarbecovirus vaccines and antibody therapeutics.

5.
MEDLINE;
Preprint in English | MEDLINE | ID: ppcovidwho-326687

ABSTRACT

The emergence of current SARS-CoV-2 variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy 1-7 . Development of broadly effective coronavirus vaccines that can mitigate these threats is needed 8, 9 . Notably, several recent studies have revealed that vaccination of recovered COVID-19 donors results in enhanced nAb responses compared to SARS-CoV-2 infection or vaccination alone 10-13 . Here, we utilized a targeted donor selection strategy to isolate a large panel of broadly neutralizing antibodies (bnAbs) to sarbecoviruses from two such donors. Many of the bnAbs are remarkably effective in neutralization against sarbecoviruses that use ACE2 for viral entry and a substantial fraction also show notable binding to non-ACE2-using sarbecoviruses. The bnAbs are equally effective against most SARS-CoV-2 VOCs and many neutralize the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor binding domain (RBD) as opposed to strain-specific nAbs to the receptor binding site that are commonly elicited in SARS-CoV-2 infection and vaccination 14-18 . Consistent with targeting of conserved sites, select RBD bnAbs exhibited in vivo protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model. The generation of a large panel of potent bnAbs provides new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and, importantly, provides a molecular basis for effective design of pan-sarbecovirus vaccines.

6.
MEDLINE;
Preprint in English | MEDLINE | ID: ppcovidwho-326636

ABSTRACT

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and, importantly, as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a coronavirus disease 2019 (COVID-19)-convalescent donor that exhibits broad reactivity with human beta-coronaviruses (beta-CoVs). Here, we showed that CC40.8 targets the conserved S2 stem-helix region of the coronavirus spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem-peptide at 1.6 A resolution and found that the peptide adopted a mainly helical structure. Conserved residues in beta-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted CC40.8-like bnAbs are relatively rare in human COVID-19 infection and therefore their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on beta-CoV spike proteins for protective antibodies that may facilitate the development of pan-beta-CoV vaccines. SUMMARY: A human mAb isolated from a COVID-19 donor defines a protective cross-neutralizing epitope for pan-beta-CoV vaccine design strategies.

7.
Zhongguo Huanjing Kexue/China Environmental Science ; 41(7):3106-3114, 2021.
Article in Chinese | Scopus | ID: covidwho-1355437

ABSTRACT

Using a Machine Learning Model (MLM) to decouple meteorological parameters, this paper quantified true impacts of emission reduction by pollution sources resulting from COVID-19 on air quality in Xianyang. Compared with the non-epidemic scenario, the results showed that concentrations of PM2.5, PM10, SO2, NO2, and CO in Xianyang had significantly decreased by 19.3%, 26.0%, 13.4%, 60.1% and 9.1%, respectively, with NO2 decreasing the most, SO2 and CO decreasing slightly, and O3 increased by 50.9% conversely. Under the condition that both primary emission and precursors of secondary particulate matter decreased, the concentration of PM2.5 dropped lower than expected, and O3 increased though, showing the complexity of PM2.5 and O3 control, in the meanwhile implying that the impact of operating pollution sources during the epidemic on air quality was greater than malfunctioned sources, and official regulations to restrict and suspend production in factories (similar to the impact of the pandemic) had limited improvement on air quality. In the future, emphases should be put on the treatment of operating pollution sources during the pandemic such as scattered coal and biomass combustion, heat production and supply, and crude oil processing and petroleum product manufacturing. © 2021, Editorial Board of China Environmental Science. All right reserved.

8.
ACM Int. Conf. Proc. Ser. ; : 52-56, 2020.
Article in English | Scopus | ID: covidwho-1166588
9.
Chinese Journal of New Drugs ; 29(21):2496-2501, 2020.
Article in Chinese | EMBASE | ID: covidwho-984680

ABSTRACT

Objective: To establish and verify a competitive ELISA method for the detection of blocking activity of monoclonal antibody against SARS-CoV-2 RBD, and to compare the results by correlation analysis with that of live virus neutralization activity measured by the plaque reduction neutralization test (PRNT). Methods: Using RBD-Fc as coating antigen, ACE2-His and anti-SARS-CoV-2 RBD monoclonal antibodies were added to competitively bind to RBD. Anti-6×his antibody labeled with horseradish peroxidase was used as the secondary antibody. The competitive ELISA method detecting the ability of McAb to block the binding of RBD to ACE2 was established. The specificity, relative accuracy, precision, linearity and range of the method were verified. Seven monoclonal antibodies against SARS-CoV-2 RBD were detected by this method. The results were compared with PRNT method, and correlation analysis was performed. Results: The blocking activity of the relevant anti-SARS-CoV-2 RBD monoclonal antibody on RBD and ACE2 protein can be effectively detected using the established competitive ELISA method. The blocking ability of McAb was dose-dependent and conformed to the four-parameter equation. The samples with theoretical titers of 64%, 80%, 100%, 125% and 156% were determined for 10 times, and the relative bias was within ±20%. The logarithm (abscissa) of theoretical potency value was used for linear regression to the logarithm (ordinate) of the corresponding titer determination value. The regression equation was y=1.156x-0.021 3, in which the slope was between 0.8 and 1.25, meaning good relative accuracy. The geometric coefficient of variation (GCV%) of the relative titers of each titer level were 2.6%, 5.2%, 3.6%, 3.4% and 10.2%, respectively, all of which were less than 20% with good precision. The correlation coefficient of linear regression equation was 0.985, meeting the requirements. The relative accuracy, intermediate precision and linearity of the method all met the requirements of the titer level range was 64%~156%. The detection results of the blocking activity of the 7 RBD monoclonal antibodies showed good correlation with the results of the live virus neutralization activity measured by the PRNT method. Conclusion: A competitive ELISA method for the detection of anti-SARS-CoV-2 RBD monoclonal antibody has been successfully established. The method has satisfied specificity, accuracy, precision and linearity. The results had a good correlation with that by PRNT method. It can be used to indirectly evaluate the neutralizing activity of related SARS-CoV-2 monoclonal antibodies against the live viruses.

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