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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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2
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Lima HS, Tupinambás U, Guimarães FG. Estimating time-varying epidemiological parameters and underreporting of Covid-19 cases in Brazil using a mathematical model with fuzzy transitions between epidemic periods. PLoS One 2024; 19:e0305522. [PMID: 38885221 PMCID: PMC11182538 DOI: 10.1371/journal.pone.0305522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 06/01/2024] [Indexed: 06/20/2024] Open
Abstract
Our study conducts a comprehensive analysis of the Covid-19 pandemic in Brazil, spanning five waves over three years. We employed a novel Susceptible-Infected-Recovered-Dead-Susceptible (SIRDS) model with a fuzzy transition between epidemic periods to estimate time-varying parameters and evaluate case underreporting. The initial basic reproduction number (R0) is identified at 2.44 (95% Confidence Interval (CI): 2.42-2.46), decreasing to 1.00 (95% CI: 0.99-1.01) during the first wave. The model estimates an underreporting factor of 12.9 (95% CI: 12.5-13.2) more infections than officially reported by Brazilian health authorities, with an increasing factor of 5.8 (95% CI: 5.2-6.4), 12.9 (95% CI: 12.5-13.3), and 16.8 (95% CI: 15.8-17.5) in 2020, 2021, and 2022 respectively. Additionally, the Infection Fatality Rate (IFR) is initially 0.88% (95% CI: 0.81%-0.94%) during the initial phase but consistently reduces across subsequent outbreaks, reaching its lowest value of 0.018% (95% CI: 0.011-0.033) in the last outbreak. Regarding the immunity period, the observed uncertainty and low sensitivity indicate that inferring this parameter is particularly challenging. Brazil successfully reduced R0 during the first wave, coinciding with decreased human mobility. Ineffective public health measures during the second wave resulted in the highest mortality rates within the studied period. We attribute lower mortality rates in 2022 to increased vaccination coverage and the lower lethality of the Omicron variant. We demonstrate the model generalization by its application to other countries. Comparative analyses with serological research further validate the accuracy of the model. In forecasting analysis, our model provides reasonable outbreak predictions. In conclusion, our study provides a nuanced understanding of the Covid-19 pandemic in Brazil, employing a novel epidemiological model. The findings contribute to the broader discourse on pandemic dynamics, underreporting, and the effectiveness of health interventions.
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Affiliation(s)
- Hélder Seixas Lima
- Instituto Federal do Norte de Minas Gerais, Januária, MG, Brazil
- Graduate Program in Electrical Engineering, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Unaí Tupinambás
- Department of Medical Clinic, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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3
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Suthar MS. Durability of immune responses to SARS-CoV-2 infection and vaccination. Semin Immunol 2024; 73:101884. [PMID: 38861769 DOI: 10.1016/j.smim.2024.101884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
Infection with SARS-CoV-2 in humans has caused a pandemic of unprecedented dimensions. SARS-CoV-2 is primarily transmitted through respiratory droplets and targets ciliated epithelial cells in the nasal cavity, trachea, and lungs by utilizing the cellular receptor angiotensin-converting enzyme 2 (ACE2). The innate immune response, including type I and III interferons, inflammatory cytokines (IL-6, TNF-α, IL-1β), innate immune cells (monocytes, DCs, neutrophils, natural killer cells), antibodies (IgG, sIgA, neutralizing antibodies), and adaptive immune cells (B cells, CD8+ and CD4+ T cells) play pivotal roles in mitigating COVID-19 disease. Broad and durable B-cell- and T-cell immunity elicited by infection and vaccination is essential for protection against severe disease, hospitalization and death. However, the emergence of SARS-CoV-2 variants that evade neutralizing antibodies continue to jeopardize vaccine efficacy. In this review, we highlight our understanding the infection- and vaccine-mediated humoral, B and T cell responses, the durability of the immune responses, and how variants continue to threaten the efficacy of SARS-CoV-2 vaccines.
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Affiliation(s)
- Mehul S Suthar
- Emory Vaccine Center, Emory National Primate Research Center, Emory Vaccine Center, Emory University, Atlanta, GA, USA; Emory Center of Excellence of Influenza Research and Response (CEIRR), Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA; Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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He X, Chen H, Zhu X, Gao W. Non-pharmaceutical interventions in containing COVID-19 pandemic after the roll-out of coronavirus vaccines: a systematic review. BMC Public Health 2024; 24:1524. [PMID: 38844867 PMCID: PMC11157849 DOI: 10.1186/s12889-024-18980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Non-pharmaceutical interventions (NPIs) have been widely utilised to control the COVID-19 pandemic. However, it is unclear what the optimal strategies are for implementing NPIs in the context of coronavirus vaccines. This study aims to systematically identify, describe, and evaluate existing ecological studies on the real-world impact of NPIs in containing COVID-19 pandemic following the roll-out of coronavirus vaccines. METHODS We conducted a comprehensive search of relevant studies from January 1, 2021, to June 4, 2023 in PubMed, Embase, Web of science and MedRxiv. Two authors independently assessed the eligibility of the studies and extracted the data. A risk of bias assessment tool, derived from a bibliometric review of ecological studies, was applied to evaluate the study design, statistical methodology, and the quality of reporting. Data were collected, synthesised and analysed using qualitative and quantitative methods. The results were presented using summary tables and figures, including information on the target countries and regions of the studies, types of NPIs, and the quality of evidence. RESULTS The review included a total of 17 studies that examined the real-world impact of NPIs in containing the COVID-19 pandemic after the vaccine roll-out. These studies used five composite indicators that combined multiple NPIs, and examined 14 individual NPIs. The studies had an average quality assessment score of 13 (range: 10-16), indicating moderately high quality. NPIs had a larger impact than vaccination in mitigating the spread of COVID-19 during the early stage of the vaccination implementation and in the context of the Omicron variant. Testing policies, workplace closures, and restrictions on gatherings were the most effective NPIs in containing the COVID-19 pandemic, following the roll-out of vaccines. The impact of NPIs varied across different time frames, countries and regions. CONCLUSION NPIs had a larger contribution to the control of the pandemic as compared to vaccination during the early stage of vaccine implementation and in the context of the omicron variant. The impact of NPIs in containing the COVID-19 pandemic exhibited variability in diverse contexts. Policy- and decision-makers need to focus on the impact of different NPIs in diverse contexts. Further research is needed to understand the policy mechanisms and address potential future challenges.
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Affiliation(s)
- Xiaona He
- Department of Epidemiology and Health Statistics, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine and Public Health, Nanchang University, No. 461, Bayi Ave,, Nanchang, 330006, PR China
| | - Huiting Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine and Public Health, Nanchang University, No. 461, Bayi Ave,, Nanchang, 330006, PR China
| | - Xinyu Zhu
- Department of Epidemiology and Health Statistics, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine and Public Health, Nanchang University, No. 461, Bayi Ave,, Nanchang, 330006, PR China
| | - Wei Gao
- Department of Epidemiology and Health Statistics, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China.
- Jiangxi Provincial Key Laboratory of Preventive Medicine and Public Health, Nanchang University, No. 461, Bayi Ave,, Nanchang, 330006, PR China.
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Favresse J, Gillot C, Cabo J, David C, Dogné JM, Douxfils J. Neutralizing antibody response to XBB.1.5, BA.2.86, FL.1.5.1, and JN.1 six months after the BNT162b2 bivalent booster. Int J Infect Dis 2024; 143:107028. [PMID: 38583825 DOI: 10.1016/j.ijid.2024.107028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
OBJECTIVES An increase evasion of the SARS-CoV-2 virus toward vaccination strategies and natural immunity has been rapidly described notably because of the mutations in the spike receptor binding domain and the N-terminal domain. METHODS Participants of the CRO-VAX HCP study who received the bivalent booster were followed up at 6 months. A pseudovirus-neutralization test was used to assess the neutralization potency of antibodies against D614G, Delta, BA.1, BA.5, XBB.1.5, BA.2.86, FL.1.5.1, and JN-1. RESULTS The neutralizing capacity of antibodies against the Omicron variant or its subvariants was significantly reduced compared with D614G and Delta (P <0.0001). The lowest neutralizing response that was observed with JN-1 (geometric mean titers [GMTs] = 22.1) was also significantly lower than XBB.1.5 (GMT = 29.5, P <0.0001), BA.2.86 (GMT = 29.6, P <0.0001), and FL.1.5.1 (GMT = 25.2, P <0.0001). Participants who contracted a breakthrough infection because of XBB.1.5 had significantly higher neutralizing antibodies against all variants than uninfected participants, especially against the Omicron variant and its subvariants. CONCLUSIONS Our results confirm that JN.1 is one of the most immune-evading variants to date and that the BA.2.86 subvariant did not show an increased immunity escape compared with XBB.1.5. The stronger response in breakthrough infection cases with the Omicron variant and its subvariants supports the need to use vaccine antigens that target circulating variants.
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Affiliation(s)
- Julien Favresse
- Clinical Pharmacology and Toxicology Research Unit, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium; Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Constant Gillot
- Clinical Pharmacology and Toxicology Research Unit, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium.
| | - Julien Cabo
- Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Clara David
- Qualiblood s.a., Research and Development Department, Namur, Belgium
| | - Jean-Michel Dogné
- Clinical Pharmacology and Toxicology Research Unit, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium
| | - Jonathan Douxfils
- Clinical Pharmacology and Toxicology Research Unit, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium; Qualiblood s.a., Research and Development Department, Namur, Belgium; Department of Biological Hematology, Centre Hospitalier Universitaire Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
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6
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Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Heliyon 2024; 10:e30208. [PMID: 38707429 PMCID: PMC11066641 DOI: 10.1016/j.heliyon.2024.e30208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.
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Affiliation(s)
- Niloofar Faraji
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Sadat Aleali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Narges Eslami
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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7
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Di H, Pusch EA, Jones J, Kovacs NA, Hassell N, Sheth M, Lynn KS, Keller MW, Wilson MM, Keong LM, Cui D, Park SH, Chau R, Lacek KA, Liddell JD, Kirby MK, Yang G, Johnson M, Thor S, Zanders N, Feng C, Surie D, DeCuir J, Lester SN, Atherton L, Hicks H, Tamin A, Harcourt JL, Coughlin MM, Self WH, Rhoads JP, Gibbs KW, Hager DN, Shapiro NI, Exline MC, Lauring AS, Rambo-Martin B, Paden CR, Kondor RJ, Lee JS, Barnes JR, Thornburg NJ, Zhou B, Wentworth DE, Davis CT. Antigenic Characterization of Circulating and Emerging SARS-CoV-2 Variants in the U.S. throughout the Delta to Omicron Waves. Vaccines (Basel) 2024; 12:505. [PMID: 38793756 PMCID: PMC11125585 DOI: 10.3390/vaccines12050505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into numerous lineages with unique spike mutations and caused multiple epidemics domestically and globally. Although COVID-19 vaccines are available, new variants with the capacity for immune evasion continue to emerge. To understand and characterize the evolution of circulating SARS-CoV-2 variants in the U.S., the Centers for Disease Control and Prevention (CDC) initiated the National SARS-CoV-2 Strain Surveillance (NS3) program and has received thousands of SARS-CoV-2 clinical specimens from across the nation as part of a genotype to phenotype characterization process. Focus reduction neutralization with various antisera was used to antigenically characterize 143 SARS-CoV-2 Delta, Mu and Omicron subvariants from selected clinical specimens received between May 2021 and February 2023, representing a total of 59 unique spike protein sequences. BA.4/5 subvariants BU.1, BQ.1.1, CR.1.1, CQ.2 and BA.4/5 + D420N + K444T; BA.2.75 subvariants BM.4.1.1, BA.2.75.2, CV.1; and recombinant Omicron variants XBF, XBB.1, XBB.1.5 showed the greatest escape from neutralizing antibodies when analyzed against post third-dose original monovalent vaccinee sera. Post fourth-dose bivalent vaccinee sera provided better protection against those subvariants, but substantial reductions in neutralization titers were still observed, especially among BA.4/5 subvariants with both an N-terminal domain (NTD) deletion and receptor binding domain (RBD) substitutions K444M + N460K and recombinant Omicron variants. This analysis demonstrated a framework for long-term systematic genotype to antigenic characterization of circulating and emerging SARS-CoV-2 variants in the U.S., which is critical to assessing their potential impact on the effectiveness of current vaccines and antigen recommendations for future updates.
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Affiliation(s)
- Han Di
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Elizabeth A. Pusch
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Nicholas A. Kovacs
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Norman Hassell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Mili Sheth
- Division of Core Laboratory Services and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kelly Sabrina Lynn
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Matthew W. Keller
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Malania M. Wilson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lisa M. Keong
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Dan Cui
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - So Hee Park
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Eagle Global Scientific, Inc., Atlanta, GA 30341, USA
| | - Reina Chau
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kristine A. Lacek
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jimma D. Liddell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Marie K. Kirby
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Genyan Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Monique Johnson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Sharmi Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Natosha Zanders
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Chenchen Feng
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Diya Surie
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jennifer DeCuir
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Sandra N. Lester
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lydia Atherton
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Heather Hicks
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Synergy America, Inc., Duluth, GA 30329, USA
| | - Azaibi Tamin
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jennifer L. Harcourt
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Melissa M. Coughlin
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wesley H. Self
- Vanderbilt Institute for Clinical & Translational Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jillian P. Rhoads
- Vanderbilt Institute for Clinical & Translational Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kevin W. Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - David N. Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Matthew C. Exline
- Department of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Adam S. Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin Rambo-Martin
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Clinton R. Paden
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Rebecca J. Kondor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Justin S. Lee
- Division of Core Laboratory Services and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Natalie J. Thornburg
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Bin Zhou
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - David E. Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Charles Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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8
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Deida J, Papa Mze N, Beye M, Ahmed SM, El Bara A, Bollahi MA, Basco L, Ould Mohamed Salem Boukhary A, Fournier PE. Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania. Genes (Basel) 2024; 15:361. [PMID: 38540420 PMCID: PMC10970642 DOI: 10.3390/genes15030361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024] Open
Abstract
The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.
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Affiliation(s)
- Jemila Deida
- UR-Génomes et Milieux, Université de Nouakchott, Nouakchott BP 880, Mauritania; (J.D.); (A.O.M.S.B.)
- Institut National de Recherche en Santé Publique, Nouakchott BP 695, Mauritania; (S.M.A.); (A.E.B.); (M.A.B.)
| | - Nasserdine Papa Mze
- Aix Marseille University, AP-HM, SSA, VITROME, 13005 Marseille, France; (N.P.M.); (M.B.); (L.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Mamadou Beye
- Aix Marseille University, AP-HM, SSA, VITROME, 13005 Marseille, France; (N.P.M.); (M.B.); (L.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Sidi Mohamed Ahmed
- Institut National de Recherche en Santé Publique, Nouakchott BP 695, Mauritania; (S.M.A.); (A.E.B.); (M.A.B.)
| | - Ahmed El Bara
- Institut National de Recherche en Santé Publique, Nouakchott BP 695, Mauritania; (S.M.A.); (A.E.B.); (M.A.B.)
| | - Mohamed Abdallahi Bollahi
- Institut National de Recherche en Santé Publique, Nouakchott BP 695, Mauritania; (S.M.A.); (A.E.B.); (M.A.B.)
| | - Leonardo Basco
- Aix Marseille University, AP-HM, SSA, VITROME, 13005 Marseille, France; (N.P.M.); (M.B.); (L.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Ali Ould Mohamed Salem Boukhary
- UR-Génomes et Milieux, Université de Nouakchott, Nouakchott BP 880, Mauritania; (J.D.); (A.O.M.S.B.)
- Aix Marseille University, AP-HM, SSA, VITROME, 13005 Marseille, France; (N.P.M.); (M.B.); (L.B.)
| | - Pierre-Edouard Fournier
- Aix Marseille University, AP-HM, SSA, VITROME, 13005 Marseille, France; (N.P.M.); (M.B.); (L.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
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9
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Zhang RG, Liu XJ, Guo YL, Chen CL. SARS-CoV-2 spike protein receptor binding domain promotes IL-6 and IL-8 release via ATP/P2Y 2 and ERK1/2 signaling pathways in human bronchial epithelia. Mol Immunol 2024; 167:53-61. [PMID: 38359646 DOI: 10.1016/j.molimm.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
The spike protein of SARS-CoV-2 as well as its receptor binding domain (RBD) has been demonstrated to be capable of activating the release of pro-inflammatory mediators in endothelial cells and immune cells such as monocytes. However, the effects of spike protein or its RBD on airway epithelial cells and mechanisms underlying these effects have not been adequately characterized. Here, we show that the RBD of spike protein alone can induce bronchial epithelial inflammation in a manner of ATP/P2Y2 dependence. Incubation of human bronchial epithelia with RBD induced IL-6 and IL-8 release, which could be inhibited by antibody. The incubation of RBD also up-regulated the expression of inflammatory indicators such as ho-1 and mkp-1. Furthermore, ATP secretion was observed after RBD treatment, P2Y2 receptor knock down by siRNA significantly suppressed the IL-6 and IL-8 release evoked by RBD. Additionally, S-RBD elevated the phosphorylation level of ERK1/2, and the effect that PD98059 can inhibit the pro-inflammatory cytokine release suggested the participation of ERK1/2. These novel findings provide new evidence of SARS-CoV-2 on airway inflammation and introduce purinergic signaling as promising treatment target.
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Affiliation(s)
- Rui-Gang Zhang
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China.
| | - Xing-Jian Liu
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China
| | - Yu-Ling Guo
- First Clinical School, Guangdong Medical University, Zhanjiang, China
| | - Chun-Ling Chen
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China
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10
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Aguayo-Acosta A, Oyervides-Muñoz MA, Rodriguez-Aguillón KO, Ovalle-Carcaño A, Romero-Castillo KD, Robles-Zamora A, Johnson M, Parra-Saldívar R, Sosa-Hernández JE. Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology. IJID REGIONS 2024; 10:44-51. [PMID: 38149263 PMCID: PMC10750064 DOI: 10.1016/j.ijregi.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/28/2023]
Abstract
Objectives To identify the SARS-CoV-2 variants Delta and Omicron during the fourth wave of the COVID-19 pandemic in Mexico using samples taken from 19 locations in 18 out of the 32 states. Methods The genetic material concentration was done with PEG/NaCl precipitation, SARS-CoV-2 presence was confirmed by reverse transcriptase-quantitative polymerase chain reaction assay, the variant detection was carried out using a commercial mutation detection panel kit, and variant/mutation confirmation was done by amplicon sequencing of receptor-binding domain target region. The study used 41 samples. Results The Delta variant was confirmed in two samples during August 2021 (Querétaro and CDMX) and in three samples during November 2021 (Aguascalientes, Ciudad Juárez campuses, and Nuevo Leon). In December 2021, another sample with the Delta variant was confirmed in Nuevo Leon. Between January to March 2022 only the presence of Omicron was confirmed, (variant BA.1). Additionally, in this period six samples were identified with the status "Variant Not Determined". Conclusion To our knowledge, this study is one of the first to identify Omicron and Delta variants with polymerase chain reaction in Mexico and Latin America and its distribution across the country with 56% Mexican states making it a viable alternative for variant detection without conducting a large quantity of sequencing of clinical tests.
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Affiliation(s)
- Alberto Aguayo-Acosta
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Kassandra O. Rodriguez-Aguillón
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Antonio Ovalle-Carcaño
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | | | | | - Marc Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, USA
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
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11
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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12
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Teixeira DG, Rodrigues-Neto JF, da Cunha DCS, Jeronimo SMB. Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105556. [PMID: 38242186 DOI: 10.1016/j.meegid.2024.105556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and to correlate with circulating variants. From March 2020 to June 2022, the state of Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across the three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta (AY.*), which circulated in Brazil in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma (P.1 + P.1.*)) dominated the first half of 2021. Late 2021 had two new clusters, Cluster 2 (Omicron, (B.1.1.529 + BA.*)), and Cluster 3 (BA.*) with the most unique epitopes, in addition to Cluster 4 (Delta sub lineages) which emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.
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Affiliation(s)
- Diego Gomes Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - João Firmino Rodrigues-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Escola Multicampi de Ciências Médicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Caicó, Rio Grande do Norte, Brazil
| | - Dayse Caroline Severiano da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil; Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil.
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13
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Maliha ST, Fatemi R, Araf Y. COVID-19 and the brain: understanding the pathogenesis and consequences of neurological damage. Mol Biol Rep 2024; 51:318. [PMID: 38386201 DOI: 10.1007/s11033-024-09279-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
SARS-CoV-2 has been known remarkably since December 2019 as a strain of pathogenic coronavirus. Starting from the earlier stages of the COVID-19 pandemic until now, we have witnessed many cases of neurological damage caused by SARS-CoV-2. There are many studies and research conducted on COVID-19-positive-patients that have found brain-related abnormalities with clear neurological symptoms, ranging from simple headaches to life-threatening strokes. For treating neurological damage, knowing the actual pathway or mechanism of causing brain damage via SARS-CoV-2 is very important. For this reason, we have tried to explain the possible pathways of brain damage due to SARS-CoV-2 with mechanisms and illustrations. The SARS-CoV-2 virus enters the human body by binding to specific ACE2 receptors in the targeted cells, which are present in the glial cells and CNS neurons of the human brain. It is found that direct and indirect infections with SARS-CoV-2 in the brain result in endothelial cell death, which alters the BBB tight junctions. These probable alterations can be the reason for the excessive transmission and pathogenicity of SARS-CoV-2 in the human brain. In this precise review, we have tried to demonstrate the neurological symptoms in the case of COVID-19-positive-patients and the possible mechanisms of neurological damage, along with the treatment options for brain-related abnormalities. Knowing the transmission mechanism of SARS-CoV-2 in the human brain can assist us in generating novel treatments associated with neuroinflammation in other brain diseases.
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Affiliation(s)
- Sumaiya Tasnim Maliha
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Rabeya Fatemi
- Department of Genetic Engineering and Biotechnology, East West University, Dhaka, 1212, Bangladesh
| | - Yusha Araf
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, Bangladesh.
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14
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Kim D, Kim M, Kim J, Baek K, Park H, Park S, Kang BM, Kim S, Kim MJ, Mostafa MN, Maharjan S, Shin HE, Lee MH, Il Kim J, Park MS, Kim YS, Choi EK, Lee Y, Kwon HJ. A mouse xenograft long-term replication yields a SARS-CoV-2 Delta mutant with increased lethality. J Med Virol 2024; 96:e29459. [PMID: 38345153 DOI: 10.1002/jmv.29459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
We recently established a long-term SARS-CoV-2 infection model using lung-cancer xenograft mice and identified mutations that arose in the SARS-CoV-2 genome during long-term propagation. Here, we applied our model to the SARS-CoV-2 Delta variant, which has increased transmissibility and immune escape compared with ancestral SARS-CoV-2. We observed limited mutations in SARS-CoV-2 Delta during long-term propagation, including two predominant mutations: R682W in the spike protein and L330W in the nucleocapsid protein. We analyzed two representative isolates, Delta-10 and Delta-12, with both predominant mutations and some additional mutations. Delta-10 and Delta-12 showed lower replication capacity compared with SARS-CoV-2 Delta in cultured cells; however, Delta-12 was more lethal in K18-hACE2 mice compared with SARS-CoV-2 Delta and Delta-10. Mice infected with Delta-12 had higher viral titers, more severe histopathology in the lungs, higher chemokine expression, increased astrocyte and microglia activation, and extensive neutrophil infiltration in the brain. Brain tissue hemorrhage and mild vacuolation were also observed, suggesting that the high lethality of Delta-12 was associated with lung and brain pathology. Our long-term infection model can provide mutant viruses derived from SARS-CoV-2 Delta and knowledge about the possible contributions of emergent mutations to the properties of new variants.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Mo-Jong Kim
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Mohd Najib Mostafa
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Yong-Sun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Eun-Kyoung Choi
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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15
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Banho CA, de Carvalho Marques B, Sacchetto L, Sepedro Lima AK, Pereira Parra MC, Jeronimo Lima AR, Ribeiro G, Jorge Martins A, dos Santos Barros CR, Carolina Elias M, Coccuzzo Sampaio S, Nanev Slavov S, Strazza Rodrigues E, Vieira Santos E, Tadeu Covas D, Kashima S, Augusto Brassaloti R, Petry B, Gaspar Clemente L, Lehmann Coutinho L, Akemi Assato P, da Silva da Costa FA, Souza-Neto JA, Maria Tommasini Grotto R, Daiana Poleti M, Cristina Chagas Lesbon J, Chicaroni Mattos E, Fukumasu H, Giovanetti M, Carlos Junior Alcantara L, Rahal P, Pessoa Araújo JF, Althouse BM, Vasilakis N, Lacerda Nogueira M. Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil. RESEARCH SQUARE 2024:rs.3.rs-3788142. [PMID: 38343798 PMCID: PMC10854302 DOI: 10.21203/rs.3.rs-3788142/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.
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Affiliation(s)
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
| | - Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Fernando Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Benjamin M. Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM
- Information School, University of Washington, Seattle, WA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
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16
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Mir S, Mir M. The mRNA vaccine, a swift warhead against a moving infectious disease target. Expert Rev Vaccines 2024; 23:336-348. [PMID: 38369742 DOI: 10.1080/14760584.2024.2320327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION The rapid development of mRNA vaccines against SARS-CoV-2 has revolutionized vaccinology, offering hope for swift responses to emerging infectious diseases. Initially met with skepticism, mRNA vaccines have proven effective and safe, reducing vaccine hesitancy amid the evolving COVID-19 pandemic. The COVID-19 pandemic has demonstrated that the time required to modify mRNA vaccines to counter new mutant strains is significantly shorter than the time it takes for pathogens to mutate and generate new variants that can thrive in vaccinated populations. This highlights the notion that mRNA vaccine technology appears to be outpacing viruses in the ongoing evolutionary race. AREAS COVERED This review article offers valuable insights into several crucial aspects of mRNA vaccine development and deployment, including the fundamentals of mRNA vaccine design and synthesis, the utilization of delivery systems, considerations regarding vaccine safety, the longevity of the immune response, strategies for modifying the original mRNA vaccine to address emerging mutant strains, as well as addressing vaccine hesitancy and potential approaches to mitigate reluctance. EXPERT OPINION Challenges such as stability, storage, manufacturing complexities, production capacity, allergic reactions, long-term effects, accessibility, and misinformation must be addressed. Despite these hurdles, mRNA vaccine technology holds promise for revolutionizing future vaccination strategies.
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Affiliation(s)
- Sheema Mir
- College of Veterinary Sciences, Western University of Health Sciences, Pomona, CA, USA
| | - Mohammad Mir
- College of Veterinary Sciences, Western University of Health Sciences, Pomona, CA, USA
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17
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Jurlina Bs A, Maul T, Hunsaker Bs P, Steffen Bs M, Gawaskar Bs S, Sarandria J, Glass TF, Blake K, Alexander K, Rivera-Sepulveda A. Changes in Bronchiolitis Characteristics During the COVID-19 Pandemic: A Description of Pediatric Emergency Department Visits in a Community Hospital, 2019-2021. Clin Pediatr (Phila) 2024; 63:73-79. [PMID: 37872735 PMCID: PMC11061886 DOI: 10.1177/00099228231208941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A retrospective, cross-sectional study of children with bronchiolitis aged 1 to 24 months during an ED visit between 2019 and 2021 was performed. Chi-square or Kruskal-Wallis was used to compare groups. The gamma coefficient was used to measure the association of variables through time. Bronchiolitis cases decreased by 75% from 2019 to 2020 and rose back to prepandemic levels by 2021. Radiographs (gamma -0.443), steroids (gamma -0.298), and bronchodilators (gamma -0.414) decreased during the study period (P < .001). Laboratory studies (gamma 0.032), viral testing (gamma 0.097), antibiotic use (gamma -0.069), and respiratory support (gamma 0.166) were unchanged. The decrease in steroids and bronchodilators was related to a clinical pathway that discouraged their use. Respiratory support remained unchanged. The COVID-19 pandemic (2019-2021) seems to have had little effect on the severity or resource utilization associated with bronchiolitis but may have unraveled a potential bronchiolitis phenotype that may have been more prominent during the pandemic.
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Affiliation(s)
- Anna Jurlina Bs
- College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Timothy Maul
- Department of Cardiac Surgery, Nemours Children's Hospital, Orlando, FL, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | - John Sarandria
- Division of Hospitalist Medicine, Nemours Children's Health, Orlando, FL, USA
| | - Todd F Glass
- Division of Emergency Medicine and Urgent Care, Nemours Children's Health, Orlando, FL, USA
| | | | - Kenneth Alexander
- Division of Infectious Diseases, Nemours Children's Hospital, Orlando, FL, USA
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18
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Banada PP, Green R, Streck D, Kurvathi R, Reiss R, Banik S, Daivaa N, Montalvan I, Jones R, Marras SAE, Chakravorty S, Alland D. An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern. Sci Rep 2023; 13:21927. [PMID: 38081834 PMCID: PMC10713575 DOI: 10.1038/s41598-023-48647-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The continued emergence of vaccine-resistant SARS-CoV-2 variants of concern (VOC) requires specific identification of each VOC as it arises. Here, we report an expanded version of our previously described sloppy molecular beacon (SMB) melting temperature (Tm) signature-based assay for VOCs, now modified to include detection of Delta (B.1.617.2) and Omicron (B.1.1.529) sub-variants. The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). The limit of detection (LOD) of the assay was 20, 22 and 36 genomic equivalents (GE) per reaction with the Delta, Omicron BA.1 and BA.2 respectively. Clinical validation of the 3-codon assay in the LC480 instrument showed the assay detected 94% (81/86) of the specimens as WT or VOCs and 6% (5/86) of the tests producing indeterminate results compared to sequencing. Sanger sequencing also failed for four samples. None of the specimens were incorrectly identified as WT or as a different VOC by our assay. Thus, excluding specimens with indeterminant results, the assay was 100% sensitive and 100% specific compared to Sanger sequencing for variant identification. This new assay concept can be easily expanded to add newer variants and can serve as a robust diagnostic tool for selecting appropriate monoclonal antibody therapy and rapid VOC surveillance.
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Affiliation(s)
- Padmapriya P Banada
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA.
| | - Raquel Green
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | - Deanna Streck
- Institute of Genomic Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Rohini Kurvathi
- Institute of Genomic Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Robert Reiss
- Division of Infectious Diseases, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Sukalyani Banik
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | - Naranjargal Daivaa
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | | | | | - Salvatore A E Marras
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | - Soumitesh Chakravorty
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
- Cepheid, Sunnyvale, CA, USA
| | - David Alland
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA.
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19
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Lipskij A, Arbeitman C, Rojas P, Ojeda-May P, Garcia ME. Dramatic Differences between the Structural Susceptibility of the S1 Pre- and S2 Postfusion States of the SARS-CoV-2 Spike Protein to External Electric Fields Revealed by Molecular Dynamics Simulations. Viruses 2023; 15:2405. [PMID: 38140646 PMCID: PMC10748067 DOI: 10.3390/v15122405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In its prefusion state, the SARS-CoV-2 spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating its functions. After the binding process of its S1 subunit (S1) with ACE2, the spike protein (S) undergoes a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed-using large-scale molecular dynamics simulations-that the application of external electric fields (EFs) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild-type spike protein, as well of the Alpha, Beta, and Gamma variants, leaving a structure which cannot be recognized anymore by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of the RBD of the prefusion state of S to moderate EF (as weak as 104 V/m), but, more importantly, we also show that, in contrast, the S2 subunit of the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the connection between the prefusion-state metastability of the SARS-CoV-2 spike protein and its susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V/m) like most globular proteins.
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Affiliation(s)
- Alexander Lipskij
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Claudia Arbeitman
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Buenos Aires C1425FQB, Argentina
- GIBIO-Universidad Tecnológica Nacional-Facultad Regional Buenos Aires, Medrano 951, Buenos Aires C1179AAQ, Argentina
| | - Pablo Rojas
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Pedro Ojeda-May
- High Performance Computing Center North (HPC2N), Umeå University, S-90187 Umeå, Sweden;
| | - Martin E. Garcia
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
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20
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Ealand CS, Gordhan BG, Machowski EE, Kana BD. Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages. Front Cell Infect Microbiol 2023; 13:1283328. [PMID: 38130775 PMCID: PMC10733533 DOI: 10.3389/fcimb.2023.1283328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Ongoing SARS-CoV-2 infections are driven by the emergence of various variants, with differential propensities to escape immune containment. Single nucleotide polymorphisms (SNPs) in the RNA genome result in altered protein structures and when these changes occur in the S-gene, encoding the spike protein, the ability of the virus to penetrate host cells to initiate an infection can be significantly altered. As a result, vaccine efficacy and prior immunity may be diminished, potentially leading to new waves of infection. Early detection of SARS-CoV-2 variants using a rapid and scalable approach will be paramount for continued monitoring of new infections. In this study, we developed minor groove-binding (MGB) probe-based qPCR assays targeted to specific SNPs in the S-gene, which are present in variants of concern (VOC), namely the E484K, N501Y, G446S and D405N mutations. A total of 95 archived SARS-CoV-2 positive clinical specimens collected in Johannesburg, South Africa between February 2021 and March 2022 were assessed using these qPCR assays. To independently confirm SNP detection, Sanger sequencing of the relevant region in the S-gene were performed. Where a PCR product could be generated and sequenced, qPCR assays were 100% concordant highlighting the robustness of the approach. These assays, and the approach described, offer the opportunity for easy detection and scaling of targeted detection of variant-defining SNPs in the clinical setting.
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Affiliation(s)
| | | | | | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and The National Health Laboratory Service, Johannesburg, South Africa
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21
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Wei D, Xie Y, Liu X, Chen R, Zhou M, Zhang X, Qu J. Pathogen evolution, prevention/control strategy and clinical features of COVID-19: experiences from China. Front Med 2023; 17:1030-1046. [PMID: 38157194 DOI: 10.1007/s11684-023-1043-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported at the end of 2019 as a worldwide health concern causing a pandemic of unusual viral pneumonia and many other organ damages, which was defined by the World Health Organization as coronavirus disease 2019 (COVID-19). The pandemic is considered a significant threat to global public health till now. In this review, we have summarized the lessons learnt during the emergence and spread of SARS-CoV-2, including its prototype and variants. The overall clinical features of variants of concern (VOC), heterogeneity in the clinical manifestations, radiology and pathology of COVID-19 patients are also discussed, along with advances in therapeutic agents.
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Affiliation(s)
- Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yusang Xie
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Rong Chen
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China.
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22
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Ahmadi AS, Shafiei-Jandaghi NZ, Sadeghi K, Nejati A, Zadheidar S, Mokhtari-Azad T, Yavarian J. Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:2621-2629. [PMID: 38435775 PMCID: PMC10903313 DOI: 10.18502/ijph.v52i12.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/11/2023] [Indexed: 03/05/2024]
Abstract
Background Whole viral genome sequencing with next generation sequencing (NGS) technique is useful tool for determining the diversity of variants and mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study we have attempted to characterize the mutations and circulating variants of the SARSCoV-2 genome during the 4th wave of COVID-19 pandemic in Tehran, Iran in 2021. Methods We performed complete genome sequencing of 15 SARS-CoV-2 detected from 15 COVID-19 patients during the 4th wave of COVID-19 pandemic with NGS. Three groups of the patients at the beginning, middle and the end of the 4th wave were compared together. Results We detected alpha and delta variants during the 4th wave of the pandemic. The results illustrated a dominance of amino acid substitution D614G in spike, and the most frequent mutants were N-R203K, G204R, S235F, nsp12-P323L, nsp6-G106del, G107del and F108del. Conclusion The detection of the virus mutations is a useful procedure for identifying the virus behavior and its genetic evolution in order to improve the efficacy of the monitoring strategies and therapeutic measures.
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Affiliation(s)
- Akram Sadat Ahmadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sevrin Zadheidar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Tehran University of Medical Sciences, Tehran, Iran
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23
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Giardina F, Ferrari G, Zavaglio F, Paolucci S, Rovida F, Campanini G, Pellegrinelli L, Galli C, Pariani E, Bergami F, Nava A, Matarazzo E, Renica S, Fanti D, Cento V, Alteri C, Scaglione F, Vismara C, Perno CF, Piralla A, Baldanti F. An overview of SARS-CoV-2 variants circulating in the 2020-2022 period in Lombardy. Diagn Microbiol Infect Dis 2023; 107:116070. [PMID: 37714081 DOI: 10.1016/j.diagmicrobio.2023.116070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
Since the beginning of the pandemic, SARS-CoV-2 has shown genetic variability. All the variants that have sustained pandemic waves have shown several mutations, especially in the Spike protein that could affect viral pathogenesis. A total of 15,729 respiratory samples, collected between December 2020 and August 2022, have been included in this study. We report the circulation of SARS-CoV-2 variants in the Lombardy region, Italy, in a 2-year study period. Alpha, Delta, and Omicron variants became predominant causing the majority of cases whereas Beta or Gamma variants mostly caused local outbreaks. Next-generation sequencing revealed several mutations and few deletions in all of the main variants. For example, 147 mutations were observed in the Spike protein of Omicron sublineages; 20% of these mutations occurred in the receptor-binding domain region.
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Affiliation(s)
- Federica Giardina
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Zavaglio
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefania Paolucci
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Rovida
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giulia Campanini
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Federica Bergami
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alice Nava
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Elisa Matarazzo
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Diana Fanti
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Valeria Cento
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Francesco Scaglione
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Chiara Vismara
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Multimodal Research Area, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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24
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Biagini D, Oliveri P, Baj A, Gasperina DD, Ferrante FD, Lomonaco T, Ghimenti S, Lenzi A, Bonini A, Vivaldi F, Oger C, Galano JM, Balas L, Durand T, Maggi F, Di Francesco F. The effect of SARS-CoV-2 variants on the plasma oxylipins and PUFAs of COVID-19 patients. Prostaglandins Other Lipid Mediat 2023; 169:106770. [PMID: 37633481 DOI: 10.1016/j.prostaglandins.2023.106770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
Oxylipins are important signalling compounds that are significantly involved in the regulation of the immune system and the resolution of inflammation. Lipid metabolism is strongly activated upon SARS-CoV-2 infection, however the modulating effects of oxylipins induced by different variants remain unexplored. Here, we compare the plasma profiles of thirty-seven oxylipins and four PUFAs in subjects infected with Wild-type, Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. The results suggest that oxidative stress and inflammation resulting from COVID-19 were highly dependent on the SARS-CoV-2 variant, and that the Wild-type elicited the strongest inflammatory storm. The Alpha and Delta variants induced a comparable lipid profile alteration upon infection, which differed significantly from Omicron. The latter variant increased the levels of pro-inflammatory mediators and decreased the levels of omega-3 PUFA in infected patients. We speculate that changes in therapeutics, vaccination, and prior infections may have a role in the alteration of the oxylipin profile besides viral mutations. The results shed new light on the evolution of the inflammatory response in COVID-19.
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Affiliation(s)
- Denise Biagini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy.
| | | | - Andreina Baj
- Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy
| | | | | | - Tommaso Lomonaco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy
| | - Silvia Ghimenti
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy
| | - Alessio Lenzi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy
| | - Andrea Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy
| | - Federico Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy
| | - Camille Oger
- Institut des Biomolécules Max Mousseron (IBMM), Pôle Chimie Balard Recherche, University of Montpellier, ENSCN, UMR 5247 CNRS, France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron (IBMM), Pôle Chimie Balard Recherche, University of Montpellier, ENSCN, UMR 5247 CNRS, France
| | - Laurence Balas
- Institut des Biomolécules Max Mousseron (IBMM), Pôle Chimie Balard Recherche, University of Montpellier, ENSCN, UMR 5247 CNRS, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), Pôle Chimie Balard Recherche, University of Montpellier, ENSCN, UMR 5247 CNRS, France
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, Italy.
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25
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Chen C, Wang X, Zhang Z. Humoral and cellular immunity against diverse SARS-CoV-2 variants. J Genet Genomics 2023; 50:934-947. [PMID: 37865193 DOI: 10.1016/j.jgg.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has rapidly spread worldwide. This has led to an unprecedented global pandemic, marked by millions of COVID-19 cases and a significant number of fatalities. Over a relatively short period, several different vaccine platforms are developed and deployed for use globally to curb the pandemic. However, the genome of SARS-CoV-2 continuously undergoes mutation and/or recombination, resulting in the emergence of several variants of concern (VOC). These VOCs can elevate viral transmission and evade the neutralizing antibodies induced by vaccines, leading to reinfections. Understanding the impact of the SARS-CoV-2 genomic mutation on viral pathogenesis and immune escape is crucial for assessing the threat of new variants to public health. This review focuses on the emergence and pathogenesis of VOC, with particular emphasis on their evasion of neutralizing antibodies. Furthermore, the memory B cell, CD4+, and CD8+ T cell memory induced by different COVID-19 vaccines or infections are discussed, along with how these cells recognize VOC. This review summarizes the current knowledge on adaptive immunology regarding SARS-CoV-2 infection and vaccines. Such knowledge may also be applied to vaccine design for other pathogens.
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Affiliation(s)
- Changxu Chen
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Xin Wang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Zeli Zhang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China.
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Ashraf J, Bukhari SARS, Kanji A, Iqbal T, Yameen M, Nisar MI, Khan W, Hasan Z. Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic. Sci Rep 2023; 13:20955. [PMID: 38017265 PMCID: PMC10684861 DOI: 10.1038/s41598-023-48272-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. In period A, G clades were predominant, and substitution rate was 5.25 × 10-4 per site per year. In B, Delta variants dominated, and substitution rates increased to 9.74 × 10-4. In C, Omicron variants led to substitution rates of 5.02 × 10-4. Genome-wide entropy was the highest during B particularly, at Spike E484K and K417N. During C, genome-wide mutations increased whilst entropy was reduced. Enhanced SARS-CoV-2 genome substitution rates were associated with a period when more virulent SARS-CoV-2 variants were prevalent. Reduced substitution rates and stabilization of genome entropy was subsequently evident when vaccinations were introduced. Whole genome entropy analysis can help predict virus evolution to guide public health interventions.
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Affiliation(s)
- Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Sayed Ali Raza Shah Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Tulaib Iqbal
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, CITRIC Center for Bioinformatics and Computational Biology, Aga Khan University, Karachi, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, CITRIC Center for Bioinformatics and Computational Biology, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan.
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Niedre-Otomere B, Kampenusa I, Trofimova J, Bodrenko J, Vangravs R, Skenders G, Nikisins S, Savicka O. Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia. Diagnostics (Basel) 2023; 13:3467. [PMID: 37998603 PMCID: PMC10670528 DOI: 10.3390/diagnostics13223467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain's quality threshold for "good". We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2.
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Pitsillou E, Yu Y, Beh RC, Liang JJ, Hung A, Karagiannis TC. Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity. Clin Exp Med 2023; 23:3277-3298. [PMID: 37615803 DOI: 10.1007/s10238-023-01168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Yiping Yu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Cunningham CL, Frye CJ, Makowski JA, Kensinger AH, Shine M, Milback EJ, Lackey PE, Evanseck JD, Mihailescu MR. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p. RNA (NEW YORK, N.Y.) 2023; 29:1754-1771. [PMID: 37604684 PMCID: PMC10578481 DOI: 10.1261/rna.079627.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/30/2023] [Indexed: 08/23/2023]
Abstract
The s2m, a highly conserved 41-nt hairpin structure in the SARS-CoV-2 genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and the subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a >99% correlation of a single nucleotide mutation at the 15th position (G15U) in Delta SARS-CoV-2. Based on 1H NMR spectroscopy assignments comparing the imino proton resonance region of s2m and the s2m G15U at 19°C, we show that the U15-A29 base pair closes, resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we show that the s2m G15U mutation drastically impacts the binding of host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on immune responses.
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Affiliation(s)
- Caylee L Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Caleb J Frye
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Joseph A Makowski
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Adam H Kensinger
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Morgan Shine
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, Pennsylvania 16172, USA
| | - Ella J Milback
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Patrick E Lackey
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, Pennsylvania 16172, USA
| | - Jeffrey D Evanseck
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Mihaela-Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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Totolian AA, Smirnov VS, Krasnov AA, Ramsay ES, Dedkov VG, Popova AY. COVID-19 Incidence Proportion as a Function of Regional Testing Strategy, Vaccination Coverage, and Vaccine Type. Viruses 2023; 15:2181. [PMID: 38005859 PMCID: PMC10675075 DOI: 10.3390/v15112181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Introduction: The COVID-19 pandemic has become a serious challenge for humanity almost everywhere globally. Despite active vaccination around the world, the incidence proportion in different countries varies significantly as of May 2022. The reason may be a combination of demographic, immunological, and epidemiological factors. The purpose of this study was to analyze possible relationships between COVID-19 incidence proportion in the population and the types of SARS-CoV-2 vaccines used in different countries globally, taking into account demographic and epidemiological factors. Materials and methods: An initial database was created of demographic and immunoepidemiological information about the COVID-19 situation in 104 countries collected from published official sources and repository data. The baseline included, for each country, population size and density; SARS-CoV-2 testing coverage; vaccination coverage; incidence proportion; and a list of vaccines that were used, including their relative share among all vaccinations. Subsequently, the initial data set was stratified by population and vaccination coverage. The final data set was subjected to statistical processing both in general and taking into account population testing coverage. Results: After formation of the final data set (including 53 countries), it turned out that reported COVID-19 case numbers correlated most strongly with testing coverage and the proportions of vaccine types used, specifically, mRNA (V1); vector (V2); peptide/protein (V3); and whole-virion/inactivated (V4). Due to the fact that an inverse correlation was found between 'reported COVID-19 case numbers' with V2, V3, and V4, these three vaccine types were also combined into one analytic group, 'non-mRNA group' vaccines (Vnmg). When the relationship between vaccine type and incidence proportion was examined, minimum incidence proportion was noted at V1:Vnmg ratios (%:%) from 0:100 to 30:70. Maximum incidence proportion was seen with V1:Vnmg from 80:20 to 100:0. On the other hand, we have shown that the number of reported COVID-19 cases in different countries largely depends on testing coverage. To offset this factor, countries with low and extremely high levels of testing were excluded from the data set; it was then confirmed that the largest number of reported COVID-19 cases occurred in countries with a dominance of V1 vaccines. The fewest reported cases were seen in countries with a dominance of Vnmg vaccines. Conclusion: In this paper, we have shown for the first time that the level of reported COVID-19 incidence proportion depends not only on SARS-CoV-2 testing and vaccination coverage, which is quite logical, but probably also on the vaccine types used. With the same vaccination level and testing coverage, those countries that predominantly use vector and whole-virion vaccines feature incidence proportion that is significantly lower than countries that predominantly use mRNA vaccines.
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Affiliation(s)
- Areg A. Totolian
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Viacheslav S. Smirnov
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Alexei A. Krasnov
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Edward S. Ramsay
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Vladimir G. Dedkov
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Anna Y. Popova
- Federal Service for Supervision of Consumer Rights Protection and Human Welfare, 127994 Moscow, Russia;
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Lo Presti A, Di Martino A, Ambrosio L, De Sabato L, Knijn A, Vaccari G, Di Bartolo I, Morabito S, Terregino C, Fusaro A, Monne I, Giussani E, Tramuto F, Maida CM, Mazzucco W, Costantino C, Rueca M, Giombini E, Gruber CEM, Capobianchi MR, Palamara AT, Stefanelli P. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions. Microorganisms 2023; 11:2644. [PMID: 38004656 PMCID: PMC10673055 DOI: 10.3390/microorganisms11112644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Isabella Monne
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Fabio Tramuto
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Carmelo Massimo Maida
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Claudio Costantino
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
- Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
- Department of Infectious Tropical Diseases and Microbiology, Sacro Cuore Don Calabria Hospital I.R.C.C.S., Via Don A. Sempreboni 5, 37024 Negrar di Valpolicella, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
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Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B 2023; 127:8586-8602. [PMID: 37775095 PMCID: PMC10578311 DOI: 10.1021/acs.jpcb.3c01467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Indexed: 10/01/2023]
Abstract
SARS-CoV-2 strains have made an appearance across the globe, causing over 757 million cases and over 6.85 million deaths at the time of writing. The emergence of these variants shows the amplitude of genetic variation to which the wild-type strains have been subjected. The rise of the different SARS-CoV-2 variants resulting from such genetic modification has significantly affected COVD-19's major impact on proliferation, virulence, and clinics. With the emergence of the variants of concern, the spike protein has been identified as a possible therapeutic target due to its critical role in binding to human cells and pathogenesis. These mutations could be linked to functional heterogeneity and use a different infection strategy. For example, the Omicron variant's multiple mutations should be carefully examined, as they represent one of the most widely spread strains and hint to us that there may be more genetic changes in the virus. As a result, we applied a common protocol where we reconstructed SARS-CoV-2 variants of concern and performed molecular dynamics simulations to study the stability of the ACE2-RBD complex in each variant. We also carried out free energy calculations to compare the binding and biophysical properties of the different SARS-CoV-2 variants when they interact with ACE2. Therefore, we were able to obtain consistent results and uncover new crucial residues that were essential for preserving a balance between maintaining a high affinity for ACE2 and the capacity to evade RBD-targeted antibodies. Our detailed structural analysis showed that SARS-CoV-2 variants of concern show a higher affinity for ACE2 compared to the Wuhan strain. Additionally, residues K417N and E484K/A might play a crucial role in antibody evasion, whereas Q498R and N501Y are specifically mutated to strengthen RBD affinity to ACE2 and, thereby, increase the viral effect of the COVID-19 virus.
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Affiliation(s)
- Mariem Ghoula
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Audrey Deyawe Kongmeneck
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Rita Eid
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Anne-Claude Camproux
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Gautier Moroy
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
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Pondé RADA. Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants. Virology 2023; 587:109850. [PMID: 37562286 DOI: 10.1016/j.virol.2023.109850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Emerging in South Africa, SARS-CoV-2 Omicron variant was marked by the expression of an exaggerated number of mutations throughout its genome and by the emergence of subvariants, whose attributes developed by them have been associated with amino acid exchanges that occur mainly in the RBM region of the spike protein. The RBM comprises a region within the RBD and is directly involved in the SARS-CoV-2 spike protein interaction with the host cell ACE2 receptor, during the infection mechanism and viral transmission. Defined as the region from aa 437 to aa 508, there are several residues in certain positions that interact directly with the human ACE-2 receptor during these processes. The occurrence of amino acid exchanges in these positions causes physicochemical alterations in the SARS-CoV-2 spike protein, which confer additional advantages and attributes to the agent. In addition, these exchanges serve as a basis for the characterization of new variants and subvariants of SARS-CoV-2. In this review, the amino acid exchanges that have occurred in the RBM of the subvariants BA.1 to BA.5 of SARS-CoV-2 that emerged from the Omicron are described. The physicochemical effects caused by them on spike protein are also described, as well as their influence on the biological properties and attributes developed by the subvariants BA.1, BA.2, BA.3, BA.4 and BA.5.
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Affiliation(s)
- Robério Amorim de Almeida Pondé
- Secretaria de Estado da Saúde -SES/Superintendência de Vigilância em Saúde-SUVISA/GO, Gerência de Vigilância Epidemiológica de Doenças Transmissíveis-GVEDT/Coordenação de Análises e Pesquisas-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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Ning P, Han Y, Liu Y, Liu S, Sun Z, Wang X, Wang B, Gao F, Wang Y, Wang Y, Gao X, Chen G, Li X. Study on disinfection effect of a 222-nm UVC excimer lamp on object surface. AMB Express 2023; 13:102. [PMID: 37752386 PMCID: PMC10522550 DOI: 10.1186/s13568-023-01611-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
Effective disinfection of contaminated surfaces is essential for preventing the transmission of pathogens. In this study, we investigated the UV irradiance and wavelength distribution of a 222-nm ultraviolet C (UVC) excimer lamp and its disinfection efficacy against microorganisms in laboratory conditions. By using a carrier quantitative germicidal test with stainless steel sheets as carriers, we examined the disinfection effect of the 222-nm UVC lamp on three standard strains-Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. We tested the disinfection efficacy under different conditions by adjusting irradiation time, as well as the state and temperature of the stainless steel carriers. Our results indicated that a bacterial suspension in PBS and not-dried stainless steel carriers yielded better disinfection than in TSB and dried carriers. Additionally, carrier temperature had no significant impact on disinfection efficacy. When utilizing a bacterial suspension in PBS and non-dried carriers at a temperature of 20 °C, the three bacteria were eliminated by 222-nm UVC excimer lamp irradiation in just 15 s. In contrast, when using a bacterial suspension in TSB and dried carriers at temperatures of 20 °C, 4 °C, or - 20 °C, the three bacteria were eradicated by 222-nm UVC excimer lamp irradiation in 60 s. Comparatively, the LPM lamp required more than 10 min to achieve the same disinfection effect. Our data demonstrate that the 222-nm UVC excimer lamp has higher irradiance and a more potent microbial disinfection effect than the LPM lamp, requiring significantly less irradiation time to achieve the same disinfection effect under identical conditions. Furthermore, the 222-nm UVC excimer lamp exhibited a substantial disinfection effect on bacterial propagules at low temperatures. Our findings support the optimization of "tunnel-type" cold-chain goods disinfection devices, providing an alternative, highly efficient, and practical tool to combat the spread of SARS-CoV-2 through cold-chain systems.
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Affiliation(s)
- Peiyong Ning
- Tianjin Centers for Disease Control and Prevention-Institute of Microbiology, Tianjin, 300011, China.
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China.
| | - Yanzhen Han
- Tianjin Centers for Disease Control and Prevention-Institute of Microbiology, Tianjin, 300011, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Yang Liu
- Animal, Plant and Foodstuffs Inspection Centre of Tianjin Customs, Tianjin, 300457, China
| | - Shengchun Liu
- Tianjin University of Commerce, Tianjin, 300134, China
| | - Zhili Sun
- Tianjin University of Commerce, Tianjin, 300134, China
| | - Xinru Wang
- Tianjin University of Commerce, Tianjin, 300134, China
| | - Baiqi Wang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, 300070, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin, 300070, China
| | - Feng Gao
- Tianjin Bureau of Commerce, Tianjin, 300040, China
| | - Ying Wang
- Tianjin Centers for Disease Control and Prevention-Institute of Microbiology, Tianjin, 300011, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Yuan Wang
- Tianjin Centers for Disease Control and Prevention-Institute of Microbiology, Tianjin, 300011, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Xin Gao
- Tianjin Centers for Disease Control and Prevention-Institute of Microbiology, Tianjin, 300011, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Guanyi Chen
- Tianjin University of Commerce, Tianjin, 300134, China
| | - Xiaoyan Li
- Tianjin Centers for Disease Control and Prevention-Institute of Microbiology, Tianjin, 300011, China.
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China.
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36
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Häring C, Jungwirth J, Schroeder J, Löffler B, Engert B, Ehrhardt C. The Local Anaesthetic Procaine Prodrugs ProcCluster ® and Procaine Hydrochloride Impair SARS-CoV-2 Replication and Egress In Vitro. Int J Mol Sci 2023; 24:14584. [PMID: 37834031 PMCID: PMC10572566 DOI: 10.3390/ijms241914584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
As vaccination efforts against SARS-CoV-2 progress in many countries, there is still an urgent need for efficient antiviral treatment strategies for those with severer disease courses, and lately, considerable efforts have been undertaken to repurpose existing drugs as antivirals. The local anaesthetic procaine has been investigated for antiviral properties against several viruses over the past decades. Here, we present data on the inhibitory effect of the procaine prodrugs ProcCluster® and procaine hydrochloride on SARS-CoV-2 infection in vitro. Both procaine prodrugs limit SARS-CoV-2 progeny virus titres as well as reduce interferon and cytokine responses in a proportional manner to the virus load. The addition of procaine during the early stages of the SARS-CoV-2 replication cycle in a cell culture first limits the production of subgenomic RNA transcripts, and later affects the replication of the viral genomic RNA. Interestingly, procaine additionally exerts a prominent effect on SARS-CoV-2 progeny virus release when added late during the replication cycle, when viral RNA production and protein production are already largely completed.
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Affiliation(s)
- Clio Häring
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Johannes Jungwirth
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Josefine Schroeder
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany;
| | | | - Christina Ehrhardt
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
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Maldonado-Cabrera A, Colin-Vilchis JA, Haque U, Velazquez C, Alvarez Villaseñor AS, Magdaleno-Márquez LE, Calleros-Muñoz CI, Figueroa-Enríquez KF, Angulo-Molina A, Gallego-Hernández AL. SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population. Infect Dis Rep 2023; 15:535-548. [PMID: 37737000 PMCID: PMC10514801 DOI: 10.3390/idr15050053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) presents global heterogeneity, and their relative effect on pediatric severity is still limited. In this study, we associate VOCs with pediatric clinical severity outcomes in Mexico. Bioinformatics methods were used to characterize VOCs and single amino acid (aa) mutations in 75,348 SARS-CoV-2 genetic sequences from February 2020 to October 2022. High-predominance VOCs groups were calculated and subsequently associated with 372,989 COVID-19 clinical pediatric outcomes. We identified 21 high-frequency mutations related to Omicron lineages with an increased prevalence in pediatric sequences compared to adults. Alpha and the other lineages had a significant increase in case fatality rate (CFR), intensive critical unit (ICU) admission, and automated mechanical ventilation (AMV). Furthermore, a logistic model with age-adjusted variables estimated an increased risk of hospitalization, ICU/AMV, and death in Gamma and Alpha, in contrast to the other lineages. We found that, regardless of the VOCs lineage, infant patients presented the worst severity prognoses. Our findings improve the understanding of the impact of VOCs on pediatric patients across time, regions, and clinical outcomes. Enhanced understanding of the pediatric severity for VOCs would enable the development and improvement of public health strategies worldwide.
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Affiliation(s)
- Anahí Maldonado-Cabrera
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
- Department of Epidemiology, Family Medicine Unit No. 37, Mexican Social Security Institute (IMSS), Hermosillo 83260, Mexico
| | | | - Ubydul Haque
- Rutgers Global Health Institute, New Brunswick, NJ 08901, USA;
- Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ 08854, USA
| | - Carlos Velazquez
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
| | | | | | | | | | - Aracely Angulo-Molina
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Ana Lucía Gallego-Hernández
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
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38
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Zhan Y, Ye L, Ouyang Q, Yin J, Cui J, Liu K, Guo C, Zhang H, Zhai J, Zheng C, Guo A, Sun B. The binding profile of SARS-CoV-2 with human leukocyte antigen polymorphisms reveals critical alleles involved in immune evasion. J Med Virol 2023; 95:e29113. [PMID: 37750416 DOI: 10.1002/jmv.29113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), astonished the world and led to millions of deaths. Due to viral new mutations and immune evasion, SARS-CoV-2 ranked first in transmission and influence. The binding affinity of human leukocyte antigen (HLA) polymorphisms to SARS-CoV-2 might be related to immune escape, but the mechanisms remained unclear. In this study, we obtained the binding affinity of SARS-CoV-2 strains with different HLA proteins and identified 31 risk alleles. Subsequent structural predictions identified 10 active binding sites in these HLA proteins that may promote immune evasion. Particularly, we also found that the weak binding ability with HLA class I polymorphisms could contribute to the immune evasion of Omicron. These findings suggest important implications for preventing the immune evasion of SARS-CoV-2 and providing new insights for the vaccine design.
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Affiliation(s)
- Yan Zhan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Ling Ye
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qianying Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Jiye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Jiajia Cui
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ke Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Chengxian Guo
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | | | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Aoxiang Guo
- Department of Pharmacy, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory of Chinese Medicine Active substance screening and Translational Research, Shenzhen, China
| | - Bao Sun
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
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Salvetat ML, Musa M, Pellegrini F, Salati C, Spadea L, Zeppieri M. Considerations of COVID-19 in Ophthalmology. Microorganisms 2023; 11:2220. [PMID: 37764064 PMCID: PMC10538084 DOI: 10.3390/microorganisms11092220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Since its emergence in early 2020, the SARS-CoV-2 infection has had a significant impact on the entire eye care system. Ophthalmologists have been categorized as a high-risk group for contracting the virus due to the belief that the eye may be a site of inoculation and transmission of the SARS-CoV-2 infection. As a result, clinical ophthalmologists, optometrists, and eyecare professionals have had to familiarize themselves with the ocular manifestations of COVID-19, as well as its treatments and vaccines. The implementation of measures to prevent the transmission of the virus, such as restrictions, lockdowns, telemedicine, and artificial intelligence (AI), have led to substantial and potentially irreversible changes in routine clinical practice, education, and research. This has resulted in the emergence of a new mode of managing patients in a routine clinical setting. This brief review aims to provide an overview of various aspects of COVID-19 in ophthalmology, including the ocular manifestations related to the disease, the modes of transmission of SARS-CoV-2 infection, precautions taken in ophthalmic practice to prevent the spread of the virus, drugs, and vaccines used in the treatment of COVID-19, the impact of the pandemic on patients, clinicians, and the eye care system as a whole, and the future of ophthalmology conditioned by this global pandemic experience.
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Affiliation(s)
- Maria Letizia Salvetat
- Department of Ophthalmology, Azienda Sanitaria Friuli Occidentale, 33170 Pordenone, Italy
| | - Mutali Musa
- Department of Optometry, University of Benin, Benin City 300238, Edo State, Nigeria
| | - Francesco Pellegrini
- Department of Ophthalmology, Azienda Sanitaria Friuli Occidentale, 33170 Pordenone, Italy
| | - Carlo Salati
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
| | - Leopoldo Spadea
- Eye Clinic, Policlinico Umberto I, “Sapienza” University of Rome, 00142 Rome, Italy
| | - Marco Zeppieri
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
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40
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Li K, Melnychuk S, Sandstrom P, Ji H. Tracking the evolution of the SARS-CoV-2 Delta variant of concern: analysis of genetic diversity and selection across the whole viral genome. Front Microbiol 2023; 14:1222301. [PMID: 37614597 PMCID: PMC10443222 DOI: 10.3389/fmicb.2023.1222301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023] Open
Abstract
Background Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has diversified extensively, producing five highly virulent lineages designated as variants of concern (VOCs). The Delta VOC emerged in India with increased transmission, immune evasion, and mortality, causing a massive global case surge in 2021. This study aims to understand how the Delta VOC evolved by characterizing mutation patterns in the viral population before and after its emergence. Furthermore, we aim to identify the influence of positive and negative selection on VOC evolution and understand the prevalence of different mutation types in the viral genome. Methods Three groups of whole viral genomes were retrieved from GISAID, sourced from India, with collection periods as follows: Group A-during the initial appearance of SARS-CoV-2; Group B-just before the emergence of the Delta variant; Group C-after the establishment of the Delta variant in India. Mutations in >1% of each group were identified with BioEdit to reveal differences in mutation quantity and type. Sites under positive or negative selection were identified with FUBAR. The results were compared to determine how mutations correspond with selective pressures and how viral mutation profiles changed to reflect genetic diversity before and after VOC emergence. Results The number of mutations increased progressively in Groups A-C, with Group C reporting a 2.2- and 1.9-fold increase from Groups A and B, respectively. Among all the observed mutations, Group C had the highest percentage of deletions (22.7%; vs. 4.2% and 2.6% in Groups A and B, respectively), and most mutations altered the final amino acid code, such as non-synonymous substitutions and deletions. Conversely, Group B had the most synonymous substitutions that are effectively silent. The number of sites experiencing positive selection increased in Groups A-C, but Group B had 2.4- and 2.6 times more sites under negative selection compared to Groups A and C, respectively. Conclusion Our findings demonstrated that viral genetic diversity continuously increased during and after the emergence of the Delta VOC. Despite this, Group B reports heightened negative selection, which potentially preserves important gene regions during evolution. Group C contains an unprecedented quantity of mutations and positively selected sites, providing strong evidence of active viral adaptation in the population.
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Affiliation(s)
- Katherine Li
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Stephanie Melnychuk
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
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41
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Castelán-Sánchez HG, Delaye L, Inward RPD, Dellicour S, Gutierrez B, Martinez de la Vina N, Boukadida C, Pybus OG, de Anda Jáuregui G, Guzmán P, Flores-Garrido M, Fontanelli Ó, Hernández Rosales M, Meneses A, Olmedo-Alvarez G, Herrera-Estrella AH, Sánchez-Flores A, Muñoz-Medina JE, Comas-García A, Gómez-Gil B, Zárate S, Taboada B, López S, Arias CF, Kraemer MUG, Lazcano A, Escalera Zamudio M. Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico. eLife 2023; 12:e82069. [PMID: 37498057 PMCID: PMC10431917 DOI: 10.7554/elife.82069] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/23/2023] [Indexed: 07/28/2023] Open
Abstract
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.
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Affiliation(s)
- Hugo G Castelán-Sánchez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Programa de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y TecnologíaMexico CityMexico
| | - Luis Delaye
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Rhys PD Inward
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de BruxellesBruxellesBelgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU LeuvenLeuvenBelgium
| | - Bernardo Gutierrez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | | | - Celia Boukadida
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades RespiratoriasMexico CityMexico
| | - Oliver G Pybus
- Department of Biology, University of OxfordOxfordUnited Kingdom
- Department of Pathobiology, Royal Veterinary CollegeLondonUnited Kingdom
| | - Guillermo de Anda Jáuregui
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Programa de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y TecnologíaMexico CityMexico
- Instituto Nacional de Medicina GenómicaMexico CityMexico
| | | | - Marisol Flores-Garrido
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Ciencias de la Computación, CINVESTAV-IPNMexico CityMexico
| | - Óscar Fontanelli
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Maribel Hernández Rosales
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Amilcar Meneses
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Ciencias de la Computación, CINVESTAV-IPNMexico CityMexico
| | - Gabriela Olmedo-Alvarez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Alfredo Heriberto Herrera-Estrella
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Laboratorio de expresión génica y desarrollo en hongos, CINVESTAV-Unidad IrapuatoIrapuatoMexico
| | - Alejandro Sánchez-Flores
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoChamilpaMexico
| | - José Esteban Muñoz-Medina
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Andreu Comas-García
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Facultad de Medicina y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis PotosíSan Luis PotosíMexico
| | - Bruno Gómez-Gil
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Centro de Investigación en Alimentación y Desarrollo-CIAD, Unidad Regional Mazatlán en Acuicultura y Manejo AmbientalSinaloaMexico
| | - Selene Zárate
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de MéxicoMexico CityMexico
| | - Blanca Taboada
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Susana López
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Carlos F Arias
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Moritz UG Kraemer
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Antonio Lazcano
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Facultad de Ciencias, Universidad Nacional Autónoma de MéxicMexico CityMexico
| | - Marina Escalera Zamudio
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
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Trigo-Tasende N, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Vaamonde M, López-Oriona Á, Barbeito I, Nasser-Ali M, Reif R, Rodiño-Janeiro BK, Fernández-Álvarez E, Iglesias-Corrás I, Freire B, Tarrío-Saavedra J, Tomás L, Gallego-García P, Posada D, Bou G, López-de-Ullibarri I, Cao R, Ladra S, Poza M. Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27877-3. [PMID: 37286834 DOI: 10.1007/s11356-023-27877-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8-36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.
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Affiliation(s)
- Noelia Trigo-Tasende
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Juan A Vallejo
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Soraya Rumbo-Feal
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Kelly Conde-Pérez
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Manuel Vaamonde
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ángel López-Oriona
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Inés Barbeito
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Mohammed Nasser-Ali
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Rubén Reif
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Bruno K Rodiño-Janeiro
- BFlow, University of Santiago de Compostela (USC) and Health Research Institute of Santiago de Compostela (IDIS), Campus Vida, 15706, Santiago de Compostela, A Coruña, Spain
| | - Elisa Fernández-Álvarez
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Iago Iglesias-Corrás
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Borja Freire
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Javier Tarrío-Saavedra
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Germán Bou
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Ignacio López-de-Ullibarri
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ricardo Cao
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Susana Ladra
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Margarita Poza
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain.
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Swami A, Mohanty A, Jamwal A, Turbadkar D, Baveja S, Shastri J, Chitalia V. A comparative analysis of the second and third wave of the Covid-19 pandemic: an experience from a tertiary care hospital in Western India. J Med Microbiol 2023; 72. [PMID: 37171852 DOI: 10.1099/jmm.0.001685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Introduction. As the world was still recovering from the 2020 pandemic, the devastating impact of Covid-19 driven by the Delta variant shook the world in 2021. As the second wave was declining, there was an unusual surge in Covid-19 positive cases by the end of 2021 which led to global concern about the change in virus characteristics.Hypothesis/gap statement. Whole genome sequencing is critical for understanding a rapidly progressing pandemic.Aim. To provide an insight into the major differences encountered in the changing characteristics between the second and third waves of the pandemic at a tertiary care hospital in India.Methods. A retrospective observational cohort analysis was conducted on Covid-positive patients during the second wave of the Covid-19 pandemic (from March 2021 to April 2021) and the third wave of the Covid-19 pandemic (from December 2021 to January 2022).Results. Out of 303 Covid-19 positive cases, 52 samples were tested by whole genome sequencing during the second wave and 108 during the third wave. A decline of 18.5 % was observed in the case fatality rate from the second wave to the third wave. There was a 5 % decline in the number of patients admitted with ARDS and a 16.3 % decline in the number of patients with co-morbidities.In total, 51.9 percent of cases were due to the Delta variant during the second wave and 95 percent due to the Omicron variant during the third wave. We found that 36.5 % of Covid-positive patients during the second wave had been vaccinated compared to 40 % in the third wave.Conclusion. Whole genome sequencing of clinical samples from a wide range of individuals during a viral epidemic will enable us to develop a more rapid public health response to new variants and identify the required vaccine modifications more quickly.
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Affiliation(s)
- Anjali Swami
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ankita Mohanty
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ashima Jamwal
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Dilip Turbadkar
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Sujata Baveja
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, T.N.Medical college and B.Y.L Nair Charitable Hospital and Lab Director, Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Vidushi Chitalia
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
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Paulino-Ramírez R, López P, Mueses S, Cuevas P, Jabier M, Rivera-Amill V. Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085503. [PMID: 37107785 PMCID: PMC10138544 DOI: 10.3390/ijerph20085503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10-3 (95% HPD: 1.2358 × 10-3, 1.8635 × 10-3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
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Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Correspondence:
| | - Pablo López
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
| | - Sayira Mueses
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Paula Cuevas
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic
| | - Vanessa Rivera-Amill
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
- Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA
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Lawrence Panchali MJ, Kim CM, Lee YM, Seo JW, Kim DY, Yun NR, Kim DM. Diagnostic Sensitivity of Saliva and Other Respiratory Tract Samples of SARS-CoV-2 Variants in Patients with COVID-19. Microbiol Spectr 2023; 11:e0307622. [PMID: 36976007 PMCID: PMC10100734 DOI: 10.1128/spectrum.03076-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge during the ongoing coronavirus disease 2019 (COVID-19) pandemic. Contrasting studies on the omicron variant have demonstrated higher viral loads in different clinical specimens, which is consistent with its high transmissibility. We investigated the viral load in clinical specimens that were infected with the SARS-CoV-2 wild-type, delta, and omicron variants, and we analyzed the diagnostic accuracy of upper and lower respiratory specimens for these variants. We performed nested reverse transcription (RT)-polymerase chain reaction (PCR), targeting the spike gene and sequencing for variant classification. RT-PCR was performed using upper and lower respiratory specimens, including saliva from 78 COVID-19 patients (wild-type, delta, and omicron variants). A comparison of the sensitivity and specificity, using the area under the receiver operating characteristic curve (AUC) values from the N gene, showed that the omicron variant saliva samples had a higher sensitivity (AUC = 1.000) than did the delta (AUC = 0.875) and the wild-type (AUC = 0.878) variant samples. The sensitivity of the omicron saliva samples was greater than that of the wild-type nasopharynx and sputum samples (P < 0.001). The viral loads of the saliva samples containing the wild-type, delta, and omicron variants were 8.18 × 105, 2.77 × 106, and 5.69 × 105, respectively, which did not differ significantly (P = 0.610). Statistically significant differences were not observed in the saliva viral loads between vaccinated and nonvaccinated patients who were infected with the omicron variant (P = 0.120). In conclusion, omicron saliva samples had higher sensitivity than did wild-type and delta samples, and the viral load did not significantly differ between vaccinated and nonvaccinated patients. Further research is necessary to elucidate the mechanisms underlying the sensitivity differences. IMPORTANCE Owing to the vast heterogeneity of the studies focused on the correlation between the SARS-CoV-2 omicron variant and COVID-19, accurate comparisons of the specificity and sensitivity of samples and associated outcomes are still inconclusive. Moreover, limited information is available on the leading causes of infection and the factors that are associated with the conditions that underlie the spread of infection. Although several studies have contributed important knowledge regarding infectious specimens, the impact of saliva samples remains unknown. This study showed that the sensitivity of the omicron variant saliva samples was higher than that of the wild-type nasopharyngeal and sputum samples. Moreover, neither vaccinated nor nonvaccinated patients who were infected with the omicron variant showed any significant differences in SARS-CoV-2 viral loads. Hence, this study is an important step toward understanding how saliva sample results are correlated with other specimen results, regardless of the vaccination status of patients who are infected with the SARS-CoV-2 omicron variant.
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Affiliation(s)
| | - Choon-Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Yu-Mi Lee
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Jun-Won Seo
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Da Young Kim
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Na Ra Yun
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Dong-Min Kim
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
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Yin Y, Zeng T, Lai M, Luan Z, Wang K, Ma Y, Hu Z, Wang K, Peng Z. Impact of antibody-level on viral shedding in B.1.617.2 (Delta) variant-infected patients analyzed using a joint model of longitudinal and time-to-event data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:8875-8891. [PMID: 37161226 DOI: 10.3934/mbe.2023390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Knowledge of viral shedding remains limited. Repeated measurement data have been rarely used to explore the influencing factors. In this study, a joint model was developed to explore and validate the factors influencing the duration of viral shedding based on longitudinal data and survival data. We divided 361 patients infected with Delta variant hospitalized in Nanjing Second Hospital into two groups (≤ 21 days group and > 21 days group) according to the duration of viral shedding, and compared their baseline characteristics. Correlation analysis was performed to identify the factors influencing the duration of viral shedding. Further, a joint model was established based on longitudinal data and survival data, and the Markov chain Monte Carlo algorithm was used to explain the influencing factors. In correlation analysis, patients having received vaccination had a higher antibody level at admission than unvaccinated patients, and with the increase of antibody level, the duration of viral shedding shortened. The linear mixed-effects model showed the longitudinal variation of logSARS-COV-2 IgM sample/cutoff (S/CO) values, with a parameter estimate of 0.193 and a standard error of 0.017. Considering gender as an influencing factor, the parameter estimate of the Cox model and their standard error were 0.205 and 0.1093 (P = 0.608), the corresponding OR value was 1.228. The joint model output showed that SARS-COV-2 IgM (S/CO) level was strongly associated with the risk of a composite event at the 95% confidence level, and a doubling of SARS-COV-2 IgM (S/CO) level was associated with a 1.38-fold (95% CI: [1.16, 1.72]) increase in the risk of viral non-shedding. A higher antibody level in vaccinated patients, as well as the presence of IgM antibodies in serum, can accelerate shedding of the mutant virus. This study provides some evidence support for vaccine prevention and control of COVID-19 variants.
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Affiliation(s)
- Yi Yin
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ting Zeng
- College of Public Health, Xinjiang Medical University, Urumqi 830017, China
| | - Miao Lai
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zemin Luan
- College of Public Health, Xinjiang Medical University, Urumqi 830017, China
| | - Kai Wang
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing 211166, China
| | - Yuhang Ma
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiliang Hu
- Department of Infectious Disease, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Kai Wang
- Department of Medical Engineering and Technology, Xinjiang Medical University, Urumqi 830017, China
| | - Zhihang Peng
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Baker FL, Zúñiga TM, Smith KA, Batatinha H, Kulangara TS, Seckeler MD, Burgess SC, Katsanis E, Simpson RJ. Exercise mobilizes diverse antigen specific T-cells and elevates neutralizing antibodies in humans with natural immunity to SARS CoV-2. Brain Behav Immun Health 2023; 28:100600. [PMID: 36743994 PMCID: PMC9886396 DOI: 10.1016/j.bbih.2023.100600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/03/2023] Open
Abstract
Epidemiological data suggest that physical activity protects against severe COVID-19 and improves clinical outcomes, but how exercise augments the SARS-CoV-2 viral immune response has yet to be elucidated. Here we determine the antigen-specific CD4 and CD8 T-cell and humoral immunity to exercise in non-vaccinated individuals with natural immunity to SARS CoV-2, using whole-blood SARS-CoV-2 peptide stimulation assays, IFN-γ ELISPOT assays, 8-color flow cytometry, deep T-cell receptor (TCR) β sequencing, and anti-RBD-1 neutralizing antibody serology. We found that acute exercise reliably mobilized (∼2.5-fold increase) highly functional SARS-CoV-2-specific T-cells to the blood compartment in those with natural immunity to the virus. The mobilized cells reacted with spike protein (including alpha (α) and delta (δ)-variants), membrane, and nucleocapsid peptides in those previously infected but not in controls. Both groups reliably mobilized T-cells reacting with Epstein-Barr viral peptides. Exercise mobilized SARS-CoV-2 specific T-cells maintained broad TCR-β diversity with no impact on CDR3 length or V and J family gene usage. Exercise predominantly mobilized MHC I restricted (i.e. CD8+) SARS-CoV-2 specific T-cells that recognized ORF1ab, surface, ORF7b, nucleocapsid, and membrane proteins. SARS-CoV-2 neutralizing antibodies were transiently elevated ∼1.5-fold during exercise after infection. In conclusion, we provide novel data on a potential mechanism by which exercise could increase SARS-CoV-2 immunosurveillance via the mobilization and redistribution of antigen-specific CD8 T-cells and neutralizing antibodies. Further research is needed to define the tissue specific disease protective effects of exercise as SARS-CoV-2 continues to evolve, as well as the impact of COVID-19 vaccination on this response.
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Affiliation(s)
- Forrest L. Baker
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States,Department of Pediatrics, The University of Arizona, Tucson, AZ, United States,Corresponding author. School of Nutritional Sciences and Wellness, The University of Arizona, 1177 E. Fourth Street Shantz Building Room 308, Tucson, AZ, 85721, United States
| | - Tiffany M. Zúñiga
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Kyle A. Smith
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Helena Batatinha
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Terese S. Kulangara
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Michael D. Seckeler
- Department of Pediatrics (Cardiology), The University of Arizona, Tucson, AZ, United States
| | - Shane C. Burgess
- Department of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, United States,Department of Immunobiology, The University of Arizona, Tucson, AZ, United States
| | - Emmanuel Katsanis
- Department of Pediatrics, The University of Arizona, Tucson, AZ, United States,Department of Immunobiology, The University of Arizona, Tucson, AZ, United States,The University of Arizona Cancer Center, Tucson, AZ, United States,Department of Medicine, The University of Arizona, Tucson, AZ, United States,Department of Pathology, The University of Arizona, Tucson, AZ, United States
| | - Richard J. Simpson
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States,Department of Pediatrics, The University of Arizona, Tucson, AZ, United States,Department of Immunobiology, The University of Arizona, Tucson, AZ, United States,The University of Arizona Cancer Center, Tucson, AZ, United States
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48
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He J, Wei Z, Leng T, Bao J, Gao X, Chen F. Vaccination options for pregnant women during the Omicron period. J Reprod Immunol 2023; 156:103798. [PMID: 36640675 PMCID: PMC9817340 DOI: 10.1016/j.jri.2023.103798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/08/2023]
Abstract
Omicron exhibits reduced pathogenicity in general population than the previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the severity of disease and pregnancy outcomes of Omicron infection among pregnant women have not yet been definitively established. Meanwhile, substantial proportions of this population have doubts about the necessity of vaccination given the reports of declining efficacy of coronavirus disease 2019 (COVID-19) vaccines. Herein, we comprehensively discuss the clinical outcomes of infected pregnant women during the Omicron period and summarize the available data on the safety and efficacy profile of COVID-19 vaccination. The results found that the incidence of moderate and severe disease, maternal mortality, pregnancy loss, preterm delivery, stillbirth, preeclampsia/eclampsia, and gestational hypertension during the Omicron period are similar to those during the Pre-Delta period. In view of the effects of mass vaccination and previous natural infection on disease severity, the virulence of Omicron in pregnant women may be comparable to or even higher than that of the Pre-Delta variant. Moreover, the currently approved COVID-19 vaccines are safe and effective for pregnant women. Particularly, those who received a second or third dose had significantly less severe disease with little progression to critical illness or death compared with those who were unvaccinated or received only one dose. Therefore, in the case of the rapid spread of Omicron, pregnant women should still strictly follow preventive measures to avoid infection and receive the COVID-19 vaccine in a timely manner.
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Affiliation(s)
- Jiarui He
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Zichun Wei
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Taiyang Leng
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Jiaqi Bao
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Xinyao Gao
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Fei Chen
- Jining Medical University, 133 Hehua Rd, Jining 272067, China.
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Wang H, Lan Y. The global dynamic transmissibility of COVID-19 and its influencing factors: an analysis of control measures from 176 countries. BMC Public Health 2023; 23:404. [PMID: 36855085 PMCID: PMC9971674 DOI: 10.1186/s12889-023-15174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
OBJECTIVE To summarise the dynamic characteristics of COVID-19 transmissibility; To analyse and quantify the effect of control measures on controlling the transmissibility of COVID-19; To predict and compare the effectiveness of different control measures. METHODS We used the basic reproduction number ([Formula: see text]) to measure the transmissibility of COVID-19, the transmissibility of COVID-19 and control measures of 176 countries and regions from January 1, 2020 to May 14, 2022 were included in the study. The dynamic characteristics of COVID-19 transmissibility were summarised through descriptive research and a Dynamic Bayesian Network (DBN) model was constructed to quantify the effect of control measures on controlling the transmissibility of COVID-19. RESULTS The results show that the spatial transmissibility of COVID-19 is high in Asia, Europe and Africa, the temporal transmissibility of COVID-19 increases with the epidemic of Beta and Omicron strains. Dynamic Bayesian Network (DBN) model shows that the transmissibility of COVID-19 is negatively correlated with control measures. Restricting population mobility has the strongest effect, nucleic acid testing (NAT) has a strong effect, and vaccination has the weakest effect. CONCLUSION Strict control measures are essential for controlling the COVID-19 outbreak; Restricting population mobility and nucleic acid testing (NAT) have significant impacts on controlling the COVID-19 transmissibility, while vaccination has no significant impact. In light of these findings, future control measures may include the widespread use of new NAT technology and the promotion of booster immunization.
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Affiliation(s)
- Hongjian Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yajia Lan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
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50
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Piranej S, Zhang L, Bazrafshan A, Marin M, Melikyan GB, Salaita K. Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530294. [PMID: 36909543 PMCID: PMC10002644 DOI: 10.1101/2023.02.27.530294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Assays detecting viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here we present Rolosense, a virus sensing platform that transduces the motion of synthetic DNA-based motors transporting 5-micron particles on RNA fuel chips. Motors and chips are modified with virus-binding aptamers that lead to stalling of motion. Therefore, motors perform a "mechanical test" of viral target and stall in the presence of whole virions which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as we demonstrated one-pot detection of influenza A and SARS-CoV-2. As a proof-of-concept, we show readout can be achieved using a smartphone camera in as little as 15 mins without any sample preparation steps. Taken together, mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost, point-of-care screening of circulating viruses.
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Affiliation(s)
- Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
| | - Luona Zhang
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
| | | | - Mariana Marin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322 (USA)
- Children’s Healthcare of Atlanta, Atlanta, Georgia 30322 (USA)
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322 (USA)
- Children’s Healthcare of Atlanta, Atlanta, Georgia 30322 (USA)
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322 (USA)
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