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He Y, Yang T, Zhong G, Yu X, Zhao Z, Shi Y, Huang B. Performance evaluation of a newly developed 2019-nCoV nucleic acid detection kit based on Ion Proton sequencing platform and its comparison with the MGI Tech (DNBSEQ-G99) platform. Diagn Microbiol Infect Dis 2024; 109:116323. [PMID: 38703530 DOI: 10.1016/j.diagmicrobio.2024.116323] [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: 02/18/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
PURPOSE To evaluate the performance of a newly developed 2019-nCoV nucleic acid detection kit based on Ion Proton sequencing platform and make comparation with MGI Tech (DNBSEQ-G99) platform. METHODS References and clinical samples were used to evaluate the precision, agreement rate, limit of detection (LOD), anti-interference ability and analytical specificity. Twenty-seven clinical specimens were used to make comparison between two platforms. RESULTS The kit showed good intra-assay, inter-assay, inter-day precision between different operators and laboratories, fine agreement rate with references, a relatively low LOD of 1 × 103 copies/ml, anti-interference capability of 5 % whole blood and 1mg/ml mucin and no cross reaction with twenty-nine common clinical pathogens. Consistency of variant classification was observed between two platforms. The WGS from Ion Proton tended to have higher coverage and less missing data. CONCLUSIONS The newly developed kit has shown satisfactory performances and excellent consistency with DNBSEQ-G99, making it a good alternative choice clinically.
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Affiliation(s)
- Yuting He
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Tingting Yang
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Guosheng Zhong
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Xuegao Yu
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Zhiwei Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Yaling Shi
- Department of Clinical Laboratory, Guangzhou Eighth People's Hospital, Guangzhou Medical University
| | - Bin Huang
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China.
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2
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Campos GRF, Almeida NBF, Filgueiras PS, Corsini CA, Gomes SVC, de Miranda DAP, de Assis JV, Silva TBDS, Alves PA, Fernandes GDR, de Oliveira JG, Rahal P, Grenfell RFQ, Nogueira ML. Second booster dose improves antibody neutralization against BA.1, BA.5 and BQ.1.1 in individuals previously immunized with CoronaVac plus BNT162B2 booster protocol. Front Cell Infect Microbiol 2024; 14:1371695. [PMID: 38638823 PMCID: PMC11024236 DOI: 10.3389/fcimb.2024.1371695] [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: 01/16/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction SARS-CoV-2 vaccines production and distribution enabled the return to normalcy worldwide, but it was not fast enough to avoid the emergence of variants capable of evading immune response induced by prior infections and vaccination. This study evaluated, against Omicron sublineages BA.1, BA.5 and BQ.1.1, the antibody response of a cohort vaccinated with a two doses CoronaVac protocol and followed by two heterologous booster doses. Methods To assess vaccination effectiveness, serum samples were collected from 160 individuals, in 3 different time points (9, 12 and 18 months after CoronaVac protocol). For each time point, individuals were divided into 3 subgroups, based on the number of additional doses received (No booster, 1 booster and 2 boosters), and a viral microneutralization assay was performed to evaluate neutralization titers and seroconvertion rate. Results The findings presented here show that, despite the first booster, at 9m time point, improved neutralization level against omicron ancestor BA.1 (133.1 to 663.3), this trend was significantly lower for BQ.1.1 and BA.5 (132.4 to 199.1, 63.2 to 100.2, respectively). However, at 18m time point, the administration of a second booster dose considerably improved the antibody neutralization, and this was observed not only against BA.1 (2361.5), but also against subvariants BQ.1.1 (726.1) and BA.5 (659.1). Additionally, our data showed that, after first booster, seroconvertion rate for BA.5 decayed over time (93.3% at 12m to 68.4% at 18m), but after the second booster, seroconvertion was completely recovered (95% at 18m). Discussion Our study reinforces the concerns about immunity evasion of the SARS-CoV-2 omicron subvariants, where BA.5 and BQ.1.1 were less neutralized by vaccine induced antibodies than BA.1. On the other hand, the administration of a second booster significantly enhanced antibody neutralization capacity against these subvariants. It is likely that, as new SARS-CoV-2 subvariants continue to emerge, additional immunizations will be needed over time.
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Affiliation(s)
- Guilherme R. F. Campos
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | | | - Priscilla Soares Filgueiras
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Camila Amormino Corsini
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Sarah Vieira Contin Gomes
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Daniel Alvim Pena de Miranda
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Jéssica Vieira de Assis
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Thaís Bárbara de Souza Silva
- Laboratório de Imunologia de Doenças Virais, Instituto Rene Rachou - Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Pedro Augusto Alves
- Laboratório de Imunologia de Doenças Virais, Instituto Rene Rachou - Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Gabriel da Rocha Fernandes
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | | | - 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
| | - Rafaella Fortini Queiroz Grenfell
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
- Hospital de Base, São José do Rio Preto, Brazil
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
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3
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Wang Y, Wang L, Ma W, Zhao H, Han X, Zhao X. Development of a novel dynamic nosocomial infection risk management method for COVID-19 in outpatient settings. BMC Infect Dis 2024; 24:214. [PMID: 38369460 PMCID: PMC10875793 DOI: 10.1186/s12879-024-09058-w] [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: 03/01/2023] [Accepted: 01/25/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Application of accumulated experience and management measures in the prevention and control of coronavirus disease 2019 (COVID-19) has generally depended on the subjective judgment of epidemic intensity, with the quality of prevention and control management being uneven. The present study was designed to develop a novel risk management system for COVID-19 infection in outpatients, with the ability to provide accurate and hierarchical control based on estimated risk of infection. METHODS Infection risk was estimated using an auto regressive integrated moving average model (ARIMA). Weekly surveillance data on influenza-like-illness (ILI) among outpatients at Xuanwu Hospital Capital Medical University and Baidu search data downloaded from the Baidu Index in 2021 and 22 were used to fit the ARIMA model. The ability of this model to estimate infection risk was evaluated by determining the mean absolute percentage error (MAPE), with a Delphi process used to build consensus on hierarchical infection control measures. COVID-19 control measures were selected by reviewing published regulations, papers and guidelines. Recommendations for surface sterilization and personal protection were determined for low and high risk periods, with these recommendations implemented based on predicted results. RESULTS The ARIMA model produced exact estimates for both the ILI and search engine data. The MAPEs of 20-week rolling forecasts for these datasets were 13.65% and 8.04%, respectively. Based on these two risk levels, the hierarchical infection prevention methods provided guidelines for personal protection and disinfection. Criteria were also established for upgrading or downgrading infection prevention strategies based on ARIMA results. CONCLUSION These innovative methods, along with the ARIMA model, showed efficient infection protection for healthcare workers in close contact with COVID-19 infected patients, saving nearly 41% of the cost of maintaining high-level infection prevention measures and enhancing control of respiratory infections.
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Affiliation(s)
- Yuncong Wang
- Hospital Infection Management Division, Xuanwu Hospital Capital Medical University, No. 45 ChangChun Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Lihong Wang
- Hospital Infection Management Division, Xuanwu Hospital Capital Medical University, No. 45 ChangChun Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Wenhui Ma
- Hospital Infection Management Division, Xuanwu Hospital Capital Medical University, No. 45 ChangChun Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Huijie Zhao
- Hospital Infection Management Division, Xuanwu Hospital Capital Medical University, No. 45 ChangChun Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Xu Han
- Hospital Infection Management Division, Xuanwu Hospital Capital Medical University, No. 45 ChangChun Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Xia Zhao
- Hospital Infection Management Division, Xuanwu Hospital Capital Medical University, No. 45 ChangChun Street, Xicheng District, Beijing, 100053, People's Republic of China.
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4
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Espinoza B, Adiga A, Venkatramanan S, Warren AS, Chen J, Lewis BL, Vullikanti A, Swarup S, Moon S, Barrett CL, Athreya S, Sundaresan R, Chandru V, Laxminarayan R, Schaffer B, Poor HV, Levin SA, Marathe MV. Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions. Proc Natl Acad Sci U S A 2023; 120:e2305227120. [PMID: 37983514 PMCID: PMC10691339 DOI: 10.1073/pnas.2305227120] [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: 04/04/2023] [Accepted: 10/13/2023] [Indexed: 11/22/2023] Open
Abstract
Disease surveillance systems provide early warnings of disease outbreaks before they become public health emergencies. However, pandemics containment would be challenging due to the complex immunity landscape created by multiple variants. Genomic surveillance is critical for detecting novel variants with diverse characteristics and importation/emergence times. Yet, a systematic study incorporating genomic monitoring, situation assessment, and intervention strategies is lacking in the literature. We formulate an integrated computational modeling framework to study a realistic course of action based on sequencing, analysis, and response. We study the effects of the second variant's importation time, its infectiousness advantage and, its cross-infection on the novel variant's detection time, and the resulting intervention scenarios to contain epidemics driven by two-variants dynamics. Our results illustrate the limitation in the intervention's effectiveness due to the variants' competing dynamics and provide the following insights: i) There is a set of importation times that yields the worst detection time for the second variant, which depends on the first variant's basic reproductive number; ii) When the second variant is imported relatively early with respect to the first variant, the cross-infection level does not impact the detection time of the second variant. We found that depending on the target metric, the best outcomes are attained under different interventions' regimes. Our results emphasize the importance of sustained enforcement of Non-Pharmaceutical Interventions on preventing epidemic resurgence due to importation/emergence of novel variants. We also discuss how our methods can be used to study when a novel variant emerges within a population.
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Affiliation(s)
- Baltazar Espinoza
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Aniruddha Adiga
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Srinivasan Venkatramanan
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Andrew Scott Warren
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Jiangzhuo Chen
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Bryan Leroy Lewis
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Anil Vullikanti
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
- Department of Computer Science, University of Virginia, Charlottesville, VA22904
| | - Samarth Swarup
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Sifat Moon
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
| | - Christopher Louis Barrett
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
- Department of Computer Science, University of Virginia, Charlottesville, VA22904
| | - Siva Athreya
- Indian Statistical Institute, Bengaluru, Karnataka560059, India
- International Centre for Theoretical Sciences, Bengaluru, Karnataka560089, India
| | - Rajesh Sundaresan
- Department of Electrical and Communication Engineering, Indian Institute of Science, Bengaluru, Karnataka560012, India
- Robert Bosch Centre for Cyber-Physical Systems, Indian Institute of Science, Bengaluru, Karnataka560012, India
- Centre for Networked Intelligence, Indian Institute of Science, Bengaluru, Karnataka560012, India
| | - Vijay Chandru
- Strand Life Sciences, Bengaluru, Karnataka560024, India
- BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka560012, India
| | | | - Benjamin Schaffer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ08544
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ08544
| | - H. Vincent Poor
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ08544
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ08544
| | - Madhav V. Marathe
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, VA22904
- Department of Computer Science, University of Virginia, Charlottesville, VA22904
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5
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Gupta A, Basu R, Bashyam MD. Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations. Access Microbiol 2023; 5:acmi000513.v3. [PMID: 37601437 PMCID: PMC10436015 DOI: 10.1099/acmi.0.000513.v3] [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: 09/24/2022] [Accepted: 02/20/2023] [Indexed: 08/22/2023] Open
Abstract
Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.
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Affiliation(s)
- Asmita Gupta
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Reelina Basu
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
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6
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Andrews KR, New DD, Gour DS, Francetich K, Minnich SA, Robison BD, Hovde CJ. Genomic surveillance identifies potential risk factors for SARS-CoV-2 transmission at a mid-sized university in a small rural town. Sci Rep 2023; 13:7902. [PMID: 37193760 PMCID: PMC10185956 DOI: 10.1038/s41598-023-34625-7] [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: 11/03/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
Understanding transmission dynamics of SARS-CoV-2 in institutions of higher education (IHEs) is important because these settings have potential for rapid viral spread. Here, we used genomic surveillance to retrospectively investigate transmission dynamics throughout the 2020-2021 academic year for the University of Idaho ("University"), a mid-sized IHE in a small rural town. We generated genome assemblies for 1168 SARS-CoV-2 samples collected during the academic year, representing 46.8% of positive samples collected from the University population and 49.8% of positive samples collected from the surrounding community ("Community") at the local hospital during this time. Transmission dynamics differed for the University when compared to the Community, with more infection waves that lasted shorter lengths of time, potentially resulting from high-transmission congregate settings along with mitigation efforts implemented by the University to combat outbreaks. We found evidence for low transmission rates between the University and Community, with approximately 8% of transmissions into the Community originating from the University, and approximately 6% of transmissions into the University originating from the Community. Potential transmission risk factors identified for the University included congregate settings such as sorority and fraternity events and residences, holiday travel, and high caseloads in the surrounding community. Knowledge of these risk factors can help the University and other IHEs develop effective mitigation measures for SARS-CoV-2 and similar pathogens.
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Affiliation(s)
- Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA.
| | - Daniel D New
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Digpal S Gour
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | | | - Scott A Minnich
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, 83844, USA
| | - Barrie D Robison
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Carolyn J Hovde
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, 83844, USA
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7
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Mahboob A, Samuel SM, Mohamed A, Wani MY, Ghorbel S, Miled N, Büsselberg D, Chaari A. Role of flavonoids in controlling obesity: molecular targets and mechanisms. Front Nutr 2023; 10:1177897. [PMID: 37252233 PMCID: PMC10213274 DOI: 10.3389/fnut.2023.1177897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Obesity presents a major health challenge that increases the risk of several non-communicable illnesses, such as but not limited to diabetes, hypertension, cardiovascular diseases, musculoskeletal and neurological disorders, sleep disorders, and cancers. Accounting for nearly 8% of global deaths (4.7 million) in 2017, obesity leads to diminishing quality of life and a higher premature mortality rate among affected individuals. Although essentially dubbed as a modifiable and preventable health concern, prevention, and treatment strategies against obesity, such as calorie intake restriction and increasing calorie burning, have gained little long-term success. In this manuscript, we detail the pathophysiology of obesity as a multifactorial, oxidative stress-dependent inflammatory disease. Current anti-obesity treatment strategies, and the effect of flavonoid-based therapeutic interventions on digestion and absorption, macronutrient metabolism, inflammation and oxidative stress and gut microbiota has been evaluated. The use of several naturally occurring flavonoids to prevent and treat obesity with a long-term efficacy, is also described.
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Affiliation(s)
- Anns Mahboob
- Department of Pre-medical Education, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Samson Mathews Samuel
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Arif Mohamed
- College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | - Sofiane Ghorbel
- Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabil Miled
- College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Ali Chaari
- Department of Pre-medical Education, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
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8
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Zhang Y, Wang Q, Zhu Z, Wang S, Tu S, Zhang Y, Zou Y, Liu Y, Liu C, Ren W, Zheng D, Zhao Y, Hu Y, Li L, Shi C, Ge S, Lin P, Xu F, Ma J, Wu X, Ma H, Wang Z, Bao J. Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/4820809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.
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9
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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10
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Tartaninan AC, Mulroney N, Poselenzny K, Akroush M, Unger T, Helseth DL, Sabatini LM, Bouma M, Larkin PM. NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges. Front Public Health 2023; 11:1177695. [PMID: 37151582 PMCID: PMC10157391 DOI: 10.3389/fpubh.2023.1177695] [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: 03/01/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits provide institutions with an expectation of high informational upside with little insight in regards to practicality with implementation and execution of such high complexity testing in the midst of a pandemic. This article details our institution's experience implementing and using Next Generation Sequencing (NGS) to monitor SARS-CoV-2 lineages in the northern Chicagoland area throughout the pandemic. To date, we have sequenced nearly 7,000 previously known SARS-CoV-2 positive samples from various patient populations (e.g., outpatient, inpatient, and outreach sites) to reduce bias in sampling. As a result, our hospital was guided while making crucial decisions about staffing, masking, and other infection control measures during the pandemic. While beneficial, establishing this NGS procedure was challenging, with countless considerations at every stage of assay development and validation. Reduced staffing prompted transition from a manual to automated high throughput workflow, requiring further validation, lab space, and instrumentation. Data management and IT security were additional considerations that delayed implementation and dictated our bioinformatic capabilities. Taken together, our experience highlights the obstacles and triumphs of SARS-CoV-2 sequencing.
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Affiliation(s)
| | - Nicole Mulroney
- NorthShore University HealthSystem, Evanston, IL, United States
| | | | - Michael Akroush
- NorthShore University HealthSystem, Evanston, IL, United States
| | - Trevor Unger
- NorthShore University HealthSystem, Evanston, IL, United States
| | | | - Linda M. Sabatini
- NorthShore University HealthSystem, Evanston, IL, United States
- Pritzker School of Medicine, The University of Chicago, Chicago, IL, United States
| | - Michael Bouma
- NorthShore University HealthSystem, Evanston, IL, United States
| | - Paige M.K. Larkin
- NorthShore University HealthSystem, Evanston, IL, United States
- Pritzker School of Medicine, The University of Chicago, Chicago, IL, United States
- *Correspondence: Paige M.K. Larkin,
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11
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Capraru ID, Romanescu M, Anghel FM, Oancea C, Marian C, Sirbu IO, Chis AR, Ciordas PD. Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:1841. [PMID: 36557043 PMCID: PMC9788413 DOI: 10.3390/medicina58121841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Background and Objectives: SARS-CoV-2 is the first global threat and life-changing event of the twenty-first century. Although efficient treatments and vaccines have been developed, due to the virus's ability to mutate in key regions of the genome, whole viral genome sequencing is needed for efficient monitoring, evaluation of the spread, and even the adjustment of the molecular diagnostic assays. Materials and Methods: In this study, Nanopore and Ion Torrent sequencing technologies were used to detect the main SARS-CoV-2 circulating strains in Timis County, Romania, between February 2021 and May 2022. Results: We identified 22 virus lineages belonging to seven clades: 20A, 20I (Alpha, V1), 21B (Kappa), 21I (Delta), 21J (Delta), 21K (Omicron), and 21L (Omicron). Conclusions: Results obtained with both methods are comparable, and we confirm the utility of Nanopore sequencing in large-scale epidemiological surveillance due to the lower cost and reduced time for library preparation.
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Affiliation(s)
- Ionut Dragos Capraru
- Discipline of Epidemiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Public Health Authority Timiș County, 300029 Timișoara, Romania
| | - Mirabela Romanescu
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Discipline of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Center for Complex Network Science, “Victor Babes” University of Medicine and Pharmacy, 300041 Timişoara, Romania
| | - Flavia Medana Anghel
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Discipline of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Cristian Oancea
- Discipline of Pulmonology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Catalin Marian
- Discipline of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Center for Complex Network Science, “Victor Babes” University of Medicine and Pharmacy, 300041 Timişoara, Romania
| | - Ioan Ovidiu Sirbu
- Discipline of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Center for Complex Network Science, “Victor Babes” University of Medicine and Pharmacy, 300041 Timişoara, Romania
| | - Aimee Rodica Chis
- Discipline of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Center for Complex Network Science, “Victor Babes” University of Medicine and Pharmacy, 300041 Timişoara, Romania
| | - Paula Diana Ciordas
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Discipline of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Center for Complex Network Science, “Victor Babes” University of Medicine and Pharmacy, 300041 Timişoara, Romania
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12
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Fernandes Q, Inchakalody VP, Merhi M, Mestiri S, Taib N, Moustafa Abo El-Ella D, Bedhiafi T, Raza A, Al-Zaidan L, Mohsen MO, Yousuf Al-Nesf MA, Hssain AA, Yassine HM, Bachmann MF, Uddin S, Dermime S. Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines. Ann Med 2022; 54:524-540. [PMID: 35132910 PMCID: PMC8843115 DOI: 10.1080/07853890.2022.2031274] [Citation(s) in RCA: 218] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The emergence of novel and evolving variants of SARS-CoV-2 has fostered the need for change in the form of newer and more adaptive diagnostic methods for the detection of SARS-CoV-2 infections. On the other hand, developing rapid and sensitive diagnostic technologies is now more challenging due to emerging variants and varying symptoms exhibited among the infected individuals. In addition to this, vaccines remain the major mainstay of prevention and protection against infection. Novel vaccines and drugs are constantly being developed to unleash an immune response for the robust targeting of SARS-CoV-2 and its associated variants. In this review, we provide an updated perspective on the current challenges posed by the emergence of novel SARS-CoV-2 mutants/variants and the evolution of diagnostic techniques to enable their detection. In addition, we also discuss the development, formulation, working mechanisms, advantages, and drawbacks of some of the most used vaccines/therapeutic drugs and their subsequent immunological impact.Key messageThe emergence of novel variants of the SARS-CoV-2 in the past couple of months, highlights one of the primary challenges in the diagnostics, treatment, as well as vaccine development against the virus.Advancements in SARS-CoV-2 detection include nucleic acid based, antigen and immuno- assay-based and antibody-based detection methodologies for efficient, robust, and quick testing; while advancements in COVID-19 preventive and therapeutic strategies include novel antiviral and immunomodulatory drugs and SARS-CoV-2 targeted vaccines.The varied COVID-19 vaccine platforms and the immune responses induced by each one of them as well as their ability to battle post-vaccination infections have all been discussed in this review.
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Affiliation(s)
- Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar
| | - Varghese Philipose Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa Abo El-Ella
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Takwa Bedhiafi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Mona O Mohsen
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Department of Biomedical Research, Immunology RIA, University of Bern, Bern, Switzerland
| | | | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | | | - Martin F Bachmann
- Department of Biomedical Research, Immunology RIA, University of Bern, Bern, Switzerland.,Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
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13
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Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Since the beginning of the pandemic, SARS-CoV-2 has caused problems for all of world’s population, not only in terms of deaths but also in terms of overloading healthcare facilities in all countries. Diagnosis is one of the key aspects of controlling the spread of SARS-CoV-2, and among the current molecular techniques, real-time PCR is considered as the gold standard. The availability of tests that allow for the rapid and accurate identification of SARS-CoV-2 is therefore of considerable importance. Moreover, if these tests allow for even minimal intervention by the operator, any risk of contamination is reduced. In this study, the performances of the new STANDARDTM M10 SARS-CoV-2 (SD Biosensor Inc., Suwon, Korea) rapid molecular test, which incorporates the above-mentioned features, were characterized. The clinical and analytical performances measured by testing different variants circulating in Italy of STANDARDTM M10 SARS-CoV-2 were compared to the test already on the market and recognized as the gold standard: Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, CA, USA). The results obtained between the two tests are largely comparable, suggesting that STANDARDTM M10 SARS-CoV-2 can be used with excellent results in the fight against the global spread of SARS-CoV-2.
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14
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Gu SH, Song DH, Yun H, Kim J, Lee S, Lee H, Lee TH, Kang SM, Jung YS, Hur G, Lee D. Molecular characterization of SARS-CoV-2 from the saliva of patients in the Republic of Korea in 2020. Health Sci Rep 2022; 5:e856. [PMID: 36210871 PMCID: PMC9528954 DOI: 10.1002/hsr2.856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background and aims Despite global vaccination efforts, the number of confirmed cases of coronavirus disease 2019 (COVID-19) remains high. To overcome the crisis precipitated by the ongoing pandemic, characteristic studies such as virus diagnosis, isolation, and genome analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary. Herein, we report the isolation and molecular characterization of SARS-CoV-2 from the saliva of patients who had tested positive for COVID-19 at Proving Ground in Taean County, Republic of Korea, in 2020. Methods We analyzed the whole-genome sequence of SARS-CoV-2 isolated from the saliva samples of patients through next-generation sequencing. We also successfully isolated SARS-CoV-2 from the saliva samples of two patients by using cell culture, which was used to study the cytopathic effects and viral replication in Vero E6 cells. Results Whole-genome sequences of the isolates, SARS-CoV-2 ADD-2 and ADD-4, obtained from saliva were identical, and phylogenetic analysis using Bayesian inference methods showed SARS-CoV-2 GH clade (B.1.497) genome-specific clustering. Typical coronavirus-like particles, with diameters of 70-120 nm, were observed in the SARS-CoV-2 infected Vero E6 cells using transmission electron microscopy. Conclusion In conclusion, this report provides insights into the molecular diagnosis, isolation, genetic characteristics, and diversity of SARS-CoV-2 isolated from the saliva of patients. Further studies are needed to explore and monitor the evolution and characteristics of SARS-CoV-2 variants.
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Affiliation(s)
- Se Hun Gu
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Dong Hyun Song
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Hyeongseok Yun
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Jung‐Eun Kim
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Seung‐Ho Lee
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Hyunjin Lee
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Tae Ho Lee
- Institute of Health and EnvironmentDaejeonRepublic of Korea
| | - Seol Muk Kang
- Defense Test and Evaluation Research InstituteAgency for Defense DevelopmentTaeanRepublic of Korea
| | - Yu Sub Jung
- Defense Test and Evaluation Research InstituteAgency for Defense DevelopmentTaeanRepublic of Korea
| | - Gyeunghaeng Hur
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Daesang Lee
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
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15
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Cuypers L, Dellicour S, Hong SL, Potter BI, Verhasselt B, Vereecke N, Lambrechts L, Durkin K, Bours V, Klamer S, Bayon-Vicente G, Vael C, Ariën KK, De Mendonca R, Soetens O, Michel C, Bearzatto B, Naesens R, Gras J, Vankeerberghen A, Matheeussen V, Martens G, Obbels D, Lemmens A, Van den Poel B, Van Even E, De Rauw K, Waumans L, Reynders M, Degosserie J, Maes P, André E, Baele G. Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants. Viruses 2022; 14:2301. [PMID: 36298856 PMCID: PMC9612291 DOI: 10.3390/v14102301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022] Open
Abstract
An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country's genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.
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Affiliation(s)
- Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1000 Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Barney I. Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Nick Vereecke
- PathoSense BV, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA Research Institute, 4000 Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA Research Institute, 4000 Liège, Belgium
- Department of Human Genetics, University Hospital of Liège, 4000 Liège, Belgium
| | - Sofieke Klamer
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Guillaume Bayon-Vicente
- Department of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, 7000 Mons, Belgium
| | - Carl Vael
- Clinical Laboratory, AZ Klina, 2930 Brasschaat, Belgium
| | - Kevin K. Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium
| | - Ricardo De Mendonca
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), 1000 Brussels, Belgium
| | - Bertrand Bearzatto
- Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1000 Brussels, Belgium
| | - Reinout Naesens
- Department of Medical Microbiology, Ziekenhuis Netwerk Antwerpen, 2020 Antwerp, Belgium
| | - Jeremie Gras
- Institute of Pathology and Genetics (IPG), 6041 Gosselies, Belgium
| | - Anne Vankeerberghen
- Laboratory of Molecular Biology, Campus Aalst-Asse-Ninove, Onze-Lieve-Vrouwziekenhuis, 9300 Aalst, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, Department of Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium
| | - Geert Martens
- Department of Laboratory Medicine, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Dagmar Obbels
- Clinical Laboratory, Imelda Hospital, 2820 Bonheiden, Belgium
| | - Ann Lemmens
- Laboratory of Clinical Biology, AZ Sint-Maarten Hospital, 2800 Mechelen, Belgium
| | - Bea Van den Poel
- Clinical Laboratory, General Hospital Jan Portaels, 1800 Vilvoorde, Belgium
| | - Ellen Van Even
- Clinical Laboratory of Microbiology, HH Hospital Lier, 2500 Lier, Belgium
| | - Klara De Rauw
- Laboratory of Clinical Biology, AZ Sint Lucas Hospital, 9000 Ghent, Belgium
| | - Luc Waumans
- Clinical Laboratory, Jessa Hospital, 3500 Hasselt, Belgium
| | - Marijke Reynders
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Bruges-Ostend AV, 8000 Bruges, Belgium
| | - Jonathan Degosserie
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530 Yvoir, Belgium
- Next Generation Sequencing Platform, Molecular Diagnostic Center, CHU UCL Namur, 5530 Yvoir, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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16
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Zeng HL, Liu Y, Dichio V, Aurell E. Temporal epistasis inference from more than 3 500 000 SARS-CoV-2 genomic sequences. Phys Rev E 2022; 106:044409. [PMID: 36397507 DOI: 10.1103/physreve.106.044409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
We use direct coupling analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling. We use full-length, high-quality genomes from the GISAID repository up to October 2021 for a total of over 3 500 000 genomes. We find that DCA terms are more stable over time than correlations but nevertheless change over time as mutations disappear from the global population or reach fixation. Correlations are enriched for phylogenetic effects, and in particularly statistical dependencies at short genomic distances, while DCA brings out links at longer genomic distance. We discuss the validity of a DCA analysis under these conditions in terms of a transient auasilinkage equilibrium state. We identify putative epistatic interaction mutations involving loci in spike.
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Affiliation(s)
- Hong-Li Zeng
- School of Science, Nanjing University of Posts and Telecommunications, New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing 210023, China
| | - Yue Liu
- School of Science, Nanjing University of Posts and Telecommunications, New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing 210023, China
| | - Vito Dichio
- Inria Paris, Aramis Project Team, Paris 75013, France
- Institut du Cerveau, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Paris, France
| | - Erik Aurell
- Department of Computational Science and Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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17
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Prandi IG, Mavian C, Giombini E, Gruber CEM, Pietrucci D, Borocci S, Abid N, Beccari AR, Talarico C, Chillemi G. Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins. Int J Mol Sci 2022; 23:ijms23158680. [PMID: 35955815 PMCID: PMC9369368 DOI: 10.3390/ijms23158680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023] Open
Abstract
The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on the spike (S) glycoprotein, which mediates virus entry into the host cell by binding to the human ACE2 receptor. Herein, we carry out an investigation into the dynamic properties of the S glycoprotein, focusing on the much more transmissible Delta and Omicron variants. Notwithstanding the great number of mutations that have accumulated, particularly in the Omicron S glycoprotein, our data clearly showed the conservation of some structural and dynamic elements, such as the global motion of the receptor binding domain (RBD). However, our studies also revealed structural and dynamic alterations that were concentrated in the aa 627–635 region, on a small region of the receptor binding motif (aa 483–485), and the so-called “fusion-peptide proximal region”. In particular, these last two S regions are known to be involved in the human receptor ACE2 recognition and membrane fusion. Our structural evidence, therefore, is likely involved in the observed different transmissibility of these S mutants. Finally, we highlighted the role of glycans in the increased RBD flexibility of the monomer in the up conformation of Omicron.
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Affiliation(s)
- Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
| | - Carla Mavian
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Emanuela Giombini
- Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
| | - Cesare E. M. Gruber
- Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
| | - Daniele Pietrucci
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies—IBIOM, CNR, 70126 Bari, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Institute for Biological Systems—ISB, CNR, Area della Ricerca di Roma 1, SP35d 9, 00010 Montelibretti, Italy
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
- High Institute of Biotechnology of Monastir, Department of Molecular and Cellular Biology, University of Monastir, Monastir 5000, Tunisia
| | | | - Carmine Talarico
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy
- Correspondence: (C.T.); (G.C.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Correspondence: (C.T.); (G.C.)
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18
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SARS-CoV-2-Specific T Cell Immunity in HIV-Associated Kaposi Sarcoma Patients in Zambia. J Immunol Res 2022; 2022:2114285. [PMID: 35935575 PMCID: PMC9352483 DOI: 10.1155/2022/2114285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) virus is the cause of coronavirus disease 2019 (COVID-19). It has caused millions of infections and deaths globally over a 2-year period. Some populations including those living with HIV and/or cancer are reported to be at a higher risk of infection and severe disease. HIV infection leads to a depletion of CD4+ T cells which impairs cell-mediated immunity and increases the risk of malignancies such as Kaposi sarcoma (KS) and viral infections such as SARS-CoV-2. However, several other factors including level of immunosuppression and chemotherapy may also affect the immune response against SARS-CoV-2. In this study, we investigated factors affecting SARS-CoV-2-specific T cell immunity towards the spike, nucleoprotein, membrane protein, and other open reading frame proteins in individuals with HIV-associated KS. The KS patients were SARS-CoV-2 seropositive with detectable T cell responses, but had no history of symptomatic SARS-CoV-2 infection. We observed that the T cell responses increase from baseline levels during follow-up, with responses towards the NMO peptide pool being statistically significant. Low CD4 counts below 200 cells/μl were associated with lower SARS-CoV-2-specific T cell responses. Cancer chemotherapy and KS T staging did not have a significant effect on the T cell responses.
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19
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Bellamkonda N, Lambe UP, Sawant S, Nandi SS, Chakraborty C, Shukla D. Immune Response to SARS-CoV-2 Vaccines. Biomedicines 2022; 10:1464. [PMID: 35884770 PMCID: PMC9312515 DOI: 10.3390/biomedicines10071464] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/21/2022] Open
Abstract
COVID-19 vaccines have been developed to confer immunity against the SARS-CoV-2 infection. Prior to the pandemic of COVID-19 which started in March 2020, there was a well-established understanding about the structure and pathogenesis of previously known Coronaviruses from the SARS and MERS outbreaks. In addition to this, vaccines for various Coronaviruses were available for veterinary use. This knowledge supported the creation of various vaccine platforms for SARS-CoV-2. Before COVID-19 there are no reports of a vaccine being developed in under a year and no vaccine for preventing coronavirus infection in humans had ever been developed. Approximately nine different technologies are being researched and developed at various levels in order to design an effective COVID-19 vaccine. As the spike protein of SARS-CoV-2 is responsible for generating substantial adaptive immune response, mostly all the vaccine candidates have been targeting the whole spike protein or epitopes of spike protein as a vaccine candidate. In this review, we have compiled the immune response to SARS-CoV-2 infection and followed by the mechanism of action of various vaccine platforms such as mRNA vaccines, Adenoviral vectored vaccine, inactivated virus vaccines and subunit vaccines in the market. In the end we have also summarized the various adjuvants used in the COVID-19 vaccine formulation.
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Affiliation(s)
- Navya Bellamkonda
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | | | - Sonali Sawant
- ICMR-NIV, Mumbai Unit, A. D. Road, Parel, Mumbai 400012, India; (U.P.L.); (S.S.)
| | - Shyam Sundar Nandi
- ICMR-NIV, Mumbai Unit, A. D. Road, Parel, Mumbai 400012, India; (U.P.L.); (S.S.)
| | | | - Deepak Shukla
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
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20
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Volkov V. System analysis of the fast global coronavirus disease 2019 (COVID-19) spread. Can we avoid future pandemics under global climate change? Commun Integr Biol 2022; 15:150-157. [PMID: 35656201 PMCID: PMC9154790 DOI: 10.1080/19420889.2022.2082735] [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] [Indexed: 11/19/2022] Open
Abstract
The recent fast global spread of COVID-19 caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) questions why and how the disease managed to be so effective against existing health protection measures. These measures, developed by many countries over centuries and strengthened over the last decades, proved to be ineffective against COVID-19. The sharp increase in human longevity and current transport systems in economically developing countries with the background of persisting cultural frameworks and stable local pools of high bacterial and viral mutations generated the wide gap between the established health protection systems and the new emerging diseases. SARS-CoV-2 targets human populations over the world with long incubation periods, often without symptoms, and serious outcomes. Hence, novel strategies are necessary to meet the demands of developing economic and social environments. Moreover, the ongoing climate change adds extra challenges while altering the existing system of interactions in biological populations and in human society. Climate change may lead to new sources of viral and microbial mutations, new ways of zoonotic disease transmission and to huge social and economic transformations in many countries. The present short Opinion applies a system approach linking biomedical, climate change, social and economic aspects and, accordingly, discusses the measures and more efficient means to avoid future pandemics.
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Affiliation(s)
- Vadim Volkov
- Research Institute of Russian Academy of Sciences, K.A. Timiriazev Institute of Plant Physiology RAS, Moscow, Russia
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21
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Delmotte J, Pelletier C, Morga B, Galinier R, Petton B, Lamy JB, Kaltz O, Avarre JC, Jacquot M, Montagnani C, Escoubas JM. Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: A first attempt to phylogeographic inference for a marine mollusc disease. Virus Evol 2022; 8:veac039. [PMID: 35600094 PMCID: PMC9119428 DOI: 10.1093/ve/veac039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity of viral populations is a key driver of the spatial and temporal diffusion of viruses; yet, studying the diversity of whole genomes from natural populations still remains a challenge. Phylodynamic approaches are commonly used for RNA viruses harboring small genomes but have only rarely been applied to DNA viruses with larger genomes. Here, we used the Pacific oyster mortality syndrome (a disease that affects oyster farms around the world) as a model to study the genetic diversity of its causative agent, the Ostreid herpesvirus 1 (OsHV-1) in the three main French oyster-farming areas. Using ultra-deep sequencing on individual moribund oysters and an innovative combination of bioinformatics tools, we de novo assembled twenty-one OsHV-1 new genomes. Combining quantification of major and minor genetic variations, phylogenetic analysis, and ancestral state reconstruction of discrete traits approaches, we assessed the connectivity of OsHV-1 viral populations between the three oyster-farming areas. Our results suggest that the Marennes-Oléron Bay represents the main source of OsHV-1 diversity, from where the virus has dispersed to other farming areas, a scenario consistent with current practices of oyster transfers in France. We demonstrate that phylodynamic approaches can be applied to aquatic DNA viruses to determine how epidemiological, immunological, and evolutionary processes act and potentially interact to shape their diversity patterns.
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Affiliation(s)
| | - Camille Pelletier
- Ifremer, RBE-ASIM, Station La Tremblade, La Tremblade F-17390, France
| | - Benjamin Morga
- Ifremer, RBE-ASIM, Station La Tremblade, La Tremblade F-17390, France
| | - Richard Galinier
- IHPE, CNRS, Ifremer, UPVD, University of Montpellier, Perpignan F-66000, France
| | - Bruno Petton
- Ifremer, CNRS, IRD, Ifremer, LEMAR UMR 6539 Université de Bretagne Occidentale, Argenton-en-Landunvez F-29840, France
| | | | - Oliver Kaltz
- ISEM, IRD, CNRS, University of Montpellier, Montpellier F-34095, France
| | | | - Maude Jacquot
- Ifremer, RBE-ASIM, Station La Tremblade, La Tremblade F-17390, France
- IHPE, CNRS, Ifremer, UPVD, University of Montpellier, Montpellier F-34095, France
| | - Caroline Montagnani
- IHPE, CNRS, Ifremer, UPVD, University of Montpellier, Montpellier F-34095, France
| | - Jean-Michel Escoubas
- IHPE, CNRS, Ifremer, UPVD, University of Montpellier, Montpellier F-34095, France
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22
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Ruan Y, Wen H, Hou M, He Z, Lu X, Xue Y, He X, Zhang YP, Wu CI. The twin-beginnings of COVID-19 in Asia and Europe-one prevails quickly. Natl Sci Rev 2022; 9:nwab223. [PMID: 35497643 PMCID: PMC9046579 DOI: 10.1093/nsr/nwab223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
In the spread of SARS-CoV-2, there have been multiple waves of replacement between strains, each of which having a distinct set of mutations. The first wave is a group of four mutations (C241T, C3037T, C14408T and A23403G [this being the amino acid change D614G]; all designated 0 to 1 below). This DG (D614G) group, fixed at the start of the pandemic, is the foundation of all subsequent waves of strains. Curiously, the DG group is absent in early Asian samples but present (and likely common) in Europe from the beginning. European data show that the high fitness of DG1111 requires the synergistic effect of all four mutations. However, the European strains would have had no time to evolve the four DG mutations (0 to 1), had they come directly from the early Asian DG0000 strain. Very likely, the European DG1111 strain had acquired the highly adaptive DG mutations in pre-pandemic Europe and had been spreading in parallel with the Asian strains. Two recent reports further support this twin-beginning interpretation. There was a period of two-way spread between Asia and Europe but, by May 2020, the European strains had supplanted the Asian strains globally. This large-scale replacement of one set of mutations for another has since been replayed many times as COVID-19 progresses.
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Mei Hou
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - Yongbiao Xue
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing100101, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing100101, China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL60637, USA
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23
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods 2022; 19:374-380. [PMID: 35396471 PMCID: PMC9467803 DOI: 10.1038/s41592-022-01444-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated development of testing methods, and allowed timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific, and organizational challenges. Here, we discuss the application of genomic and computational methods for the efficient data driven COVID-19 response, advantages of democratization of viral sequencing around the world, and challenges associated with viral genome data collection and processing.
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Affiliation(s)
- Sergey Knyazev
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Translational Biomedical Informatics, University of Southern California, Los Angeles, CA, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Pelin Icer Baykal
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoia Comarova
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Yuri Porozov
- World-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Tetyana I Vasylyeva
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Malak S Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Victoria M Pak
- Emory University, School of Nursing, Atlanta, GA, CA, USA
- Emory University, Rollins School of Public Health, Department of Epidemiology, Atlanta, GA, CA, USA
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrey Komissarov
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Fyodor Kondrashov
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P.R. China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, P.R. China
- Centre for Immunology & Infection Limited, Hong Kong SAR, P.R. China
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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24
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Perbolianachis P, Ferla D, Arce R, Ferreiro I, Costábile A, Paz M, Simón D, Moreno P, Cristina J. Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: genetic relations and vaccine strain match. Virus Res 2022; 311:198688. [PMID: 35074431 PMCID: PMC8779862 DOI: 10.1016/j.virusres.2022.198688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/10/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) is caused by a novel member of the family Coronaviridae, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent studies revealed the emergence of virus variants with substitutions in the spike and/or nucleocapsid and RNA-dependent RNA polymerase proteins that are partly responsible for enhanced transmission and reduced or escaped anti-SARS-CoV-2 antibodies that may reduce the efficacy of antibodies and vaccines against the first identified SARS-CoV-2 strains. In order to gain insight into the emergence and evolution of SARS-CoV-2 variants circulating in the South American region, a comprehensive phylogenetic study of SARS-CoV-2 variants circulating in this region was performed. The results of these studies revealed sharp increase in virus effective population size from March to April of 2020. At least 62 different genotypes were found to circulate in this region. Variants of concern (VOCs) Alpha, Beta, Gamma and Delta co-circulate in the region, together with variants of interest (VOIs) Lambda, Mu and Zeta. Most of SARS-CoV-2 variants circulating in the South American region belongs to B.1 genotypes and have substitutions in the spike and/or nucleocapsid and polymerase proteins that confer high transmissibility and/or immune resistance. 148 amino acid positions of the spike protein and 70 positions of the nucleocapsid were found to have substitutions in different variants isolated in the region by comparison with reference strain Wuhan-Hu-1. Significant differences in codon usage among spike genes of SARS-CoV-2 strains circulating in South America was found, which can be linked to SARS-CoV-2 genotypes.
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Affiliation(s)
- Paula Perbolianachis
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Diego Ferla
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Rodrigo Arce
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Irene Ferreiro
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Alicia Costábile
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Mercedes Paz
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Diego Simón
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay.
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25
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Joshi G, Borah P, Thakur S, Sharma P, Mayank, Poduri R. Exploring the COVID-19 vaccine candidates against SARS-CoV-2 and its variants: where do we stand and where do we go? Hum Vaccin Immunother 2021; 17:4714-4740. [PMID: 34856868 PMCID: PMC8726002 DOI: 10.1080/21645515.2021.1995283] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
As of September 2021, 117 COVID-19 vaccines are in clinical development, and 194 are in preclinical development as per the World Health Organization (WHO) published draft landscape. Among the 117 vaccines undergoing clinical trials, the major platforms include protein subunit; RNA; inactivated virus; viral vector, among others. So far, USFDA recognized to approve the Pfizer-BioNTech (Comirnaty) COVID-19 vaccine for its full use in individuals of 16 years of age and older. Though the approved vaccines are being manufactured at a tremendous pace, the wealthiest countries have about 28% of total vaccines despite possessing only 10.8% of the total world population, suggesting an inequity of vaccine distribution. The review comprehensively summarizes the history of vaccines, mainly focusing on vaccines for SARS-CoV-2. The review also connects relevant topics, including measurement of vaccines efficacy against SARS-CoV-2 and its variants, associated challenges, and limitations, as hurdles in global vaccination are also kept forth.
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Affiliation(s)
- Gaurav Joshi
- School of Pharmacy, Graphic Era Hill University, Dehradun, India
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences, Central University of Punjab, Bathinda, India
| | - Pobitra Borah
- School of Pharmacy, Graphic Era Hill University, Dehradun, India
| | - Shweta Thakur
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneshwar, India
| | - Praveen Sharma
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences, Central University of Punjab, Bathinda, India
| | - Mayank
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Ramarao Poduri
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences, Central University of Punjab, Bathinda, India
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26
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Davis JT, Chinazzi M, Perra N, Mu K, Pastore Y Piontti A, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Longini IM, Halloran ME, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave. Nature 2021; 600:127-132. [PMID: 34695837 PMCID: PMC8636257 DOI: 10.1038/s41586-021-04130-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022]
Abstract
Considerable uncertainty surrounds the timeline of introductions and onsets of local transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) globally1-7. Although a limited number of SARS-CoV-2 introductions were reported in January and February 2020 (refs.8,9), the narrowness of the initial testing criteria, combined with a slow growth in testing capacity and porous travel screening10, left many countries vulnerable to unmitigated, cryptic transmission. Here we use a global metapopulation epidemic model to provide a mechanistic understanding of the early dispersal of infections and the temporal windows of the introduction of SARS-CoV-2 and onset of local transmission in Europe and the USA. We find that community transmission of SARS-CoV-2 was likely to have been present in several areas of Europe and the USA by January 2020, and estimate that by early March, only 1 to 4 in 100 SARS-CoV-2 infections were detected by surveillance systems. The modelling results highlight international travel as the key driver of the introduction of SARS-CoV-2, with possible introductions and transmission events as early as December 2019 to January 2020. We find a heterogeneous geographic distribution of cumulative infection attack rates by 4 July 2020, ranging from 0.78% to 15.2% across US states and 0.19% to 13.2% in European countries. Our approach complements phylogenetic analyses and other surveillance approaches and provides insights that can be used to design innovative, model-driven surveillance systems that guide enhanced testing and response strategies.
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Affiliation(s)
- Jessica T Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Nicola Perra
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
- Networks and Urban Systems Centre, University of Greenwich, London, UK
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | | | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | | | | | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Xinyue Xiong
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA.
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27
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Valesano AL, Fitzsimmons WJ, Blair CN, Woods RJ, Gilbert J, Rudnik D, Mortenson L, Friedrich TC, O’Connor DH, MacCannell DR, Petrie JG, Martin ET, Lauring AS. SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community. Open Forum Infect Dis 2021; 8:ofab518. [PMID: 34805437 PMCID: PMC8600169 DOI: 10.1093/ofid/ofab518] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has had high incidence rates at institutions of higher education (IHE) in the United States, but the transmission dynamics in these settings are poorly understood. It remains unclear to what extent IHE-associated outbreaks have contributed to transmission in nearby communities. METHODS We implemented high-density prospective genomic surveillance to investigate these dynamics at the University of Michigan and the surrounding community during the Fall 2020 semester (August 16-November 24). We sequenced complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 1659 individuals, including 468 students, representing 20% of cases in students and 25% of total cases in Washtenaw County over the study interval. RESULTS Phylogenetic analysis identified >200 introductions into the student population, most of which were not related to other student cases. There were 2 prolonged student transmission clusters, of 115 and 73 individuals, that spanned multiple on-campus residences. Remarkably, <5% of nonstudent genomes were descended from student clusters, and viral descendants of student cases were rare during a subsequent wave of infections in the community. CONCLUSIONS The largest outbreaks among students at the University of Michigan did not significantly contribute to the rise in community cases in Fall 2020. These results provide valuable insights into SARS-CoV-2 transmission dynamics at the regional level.
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Affiliation(s)
- Andrew L Valesano
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher N Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Julie Gilbert
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dawn Rudnik
- University Health Service, University of Michigan, Ann Arbor, Michigan, USA
| | - Lindsey Mortenson
- University Health Service, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Joshua G Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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Murall CL, Fournier E, Galvez JH, N'Guessan A, Reiling SJ, Quirion PO, Naderi S, Roy AM, Chen SH, Stretenowich P, Bourgey M, Bujold D, Gregoire R, Lepage P, St-Cyr J, Willet P, Dion R, Charest H, Lathrop M, Roger M, Bourque G, Ragoussis J, Shapiro BJ, Moreira S. A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada. Genome Med 2021; 13:169. [PMID: 34706766 PMCID: PMC8550813 DOI: 10.1186/s13073-021-00986-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
Background Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. Methods Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus. Results Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and “snowbird” destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7–12 led to the largest transmission lineages of the first wave (accounting for 52–75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Conclusions Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00986-9.
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Affiliation(s)
- Carmen Lía Murall
- McGill Genome Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada
| | - Jose Hector Galvez
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada
| | - Arnaud N'Guessan
- Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
| | - Sarah J Reiling
- McGill Genome Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Pierre-Olivier Quirion
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada.,Calcul Québec, Montreal, QC, Canada
| | - Sana Naderi
- McGill Genome Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Anne-Marie Roy
- McGill Genome Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Shu-Huang Chen
- McGill Genome Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Paul Stretenowich
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada
| | - David Bujold
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada
| | - Romain Gregoire
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | | | - Réjean Dion
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada.,Ecole de santé publique, Université de Montréal, Montreal, QC, Canada
| | - Hugues Charest
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada
| | - Mark Lathrop
- McGill Genome Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michel Roger
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada.,Département de Microbiologie, infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Guillaume Bourque
- McGill Genome Centre, Montreal, QC, Canada.,Canadian Center for Computational Genomics, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada.,Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - B Jesse Shapiro
- McGill Genome Centre, Montreal, QC, Canada. .,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada. .,Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada.
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada
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29
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Chaintoutis SC, Chassalevris T, Tsiolas G, Balaska S, Vlatakis I, Mouchtaropoulou E, Siarkou VI, Tychala A, Koutsioulis D, Skoura L, Argiriou A, Dovas CI. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. J Virol Methods 2021; 296:114242. [PMID: 34274369 PMCID: PMC8282437 DOI: 10.1016/j.jviromet.2021.114242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
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Affiliation(s)
- Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Ioannis Vlatakis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Victoria I Siarkou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54134, Thessaloniki, Greece
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Dimitris Koutsioulis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece; Department of Food Science and Nutrition, University of the Aegean, 81400, Myrina, Lemnos, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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30
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Li F, He P, Xiong D, Lou Y, Pu Q, Zhang H, Zhang H, Yu J. A Reverse Transcription Recombinase-Aided Amplification Method for Rapid and Point-of-Care Detection of SARS-CoV-2, including Variants. Viruses 2021; 13:1875. [PMID: 34578456 PMCID: PMC8472806 DOI: 10.3390/v13091875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 12/23/2022] Open
Abstract
The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its emergence of variants needs rapid and point-of-care testing methods for a broad diagnosis. The regular RT-qPCR is time-consuming and limited in central laboratories, so a broad and large-scale screening requirement calls for rapid and in situ methods. In this regard, a reverse transcription recombinase-aided amplification (RT-RAA) is proposed here for the rapid and point-of-care detection of SARS-CoV-2. A set of highly conserved primers and probes targeting more than 98% of SARS-CoV-2 strains, including currently circulating variants (four variants of concerns (VOCs) and three variants of interest (VOIs)), was used in this study. With the preferred primers, the RT-RAA assay showed a 100% specificity to SARS-CoV-2 from eight other respiratory RNA viruses. Moreover, the assay here is of a high sensitivity and 0.48 copies/μL can be detected within 25 min at a constant temperature (42 °C), which can be realized on portable equipment. Furthermore, the RT-RAA assay demonstrated its high agreement for the detection of SARS-CoV-2 in clinical specimens compared with RT-qPCR. The rapid, simple and point-of-care RT-RAA method is expected to be an appealing detection tool to detect SARS-CoV-2, including variants, in clinical diagnostic applications.
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Affiliation(s)
- Fengyun Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yakun Lou
- Zhengzhou Zhongdao Biotechnology Co., Ltd., Zhengzhou 450000, China;
| | - Qiaosheng Pu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Haixia Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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31
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Rana R, Tripathi A, Kumar N, Ganguly NK. A Comprehensive Overview on COVID-19: Future Perspectives. Front Cell Infect Microbiol 2021; 11:744903. [PMID: 34595136 PMCID: PMC8476999 DOI: 10.3389/fcimb.2021.744903] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
The outbreak of COVID-19 has proven to be an unprecedented disaster for the whole world. The virus has inflicted billion of lives across the globe in all aspects-physically, psychologically, as well as socially. Compared to the previous strains of β-CoV genera- MERS and SARS, SARS-CoV-2 has significantly higher transmissibility and worst post-recovery implications. A frequent mutation in the initial SARS-CoV-2 strain has been a major cause of mortalities (approx. 3 million deaths) and uncontrolled virulence (approx. 1 billion positive cases). As far as clinical manifestations are concerned, this particular virus has exhibited deleterious impacts on systems other than the respiratory system (primary target organ), such as the brain, hematological system, liver, kidneys, endocrine system, etc. with no promising curatives to date. Lack of emergency treatments and shortage of life-saving drugs has promoted the repurposing of existing therapeutics along with the emergence of vaccines with the combined efforts of scientists and industrial experts in this short span. This review summarizes every detail on COVID-19 and emphasizes undermining the future approaches to minimize its prevalence to the remaining lives.
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32
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Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
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Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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33
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Zhu M, Shen J, Zeng Q, Tan JW, Kleepbua J, Chew I, Law JX, Chew SP, Tangathajinda A, Latthitham N, Li L. Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia. Front Public Health 2021; 9:685315. [PMID: 34395364 PMCID: PMC8363229 DOI: 10.3389/fpubh.2021.685315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region. Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model. Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10-3 (1.292 × 10-3 to 1.613 × 10-3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia. Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.
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Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | | | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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34
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Pérez-Lago L, Aldámiz-Echevarría T, García-Martínez R, Pérez-Latorre L, Herranz M, Sola-Campoy PJ, Suárez-González J, Martínez-Laperche C, Comas I, González-Candelas F, Catalán P, Muñoz P, García de Viedma D. Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2. Biomedicines 2021; 9:808. [PMID: 34356872 PMCID: PMC8301427 DOI: 10.3390/biomedicines9070808] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 01/08/2023] Open
Abstract
A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13-15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1-2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.
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Affiliation(s)
- Laura Pérez-Lago
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Teresa Aldámiz-Echevarría
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Rita García-Martínez
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- Internal Medicine Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Leire Pérez-Latorre
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Marta Herranz
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Pedro J. Sola-Campoy
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Julia Suárez-González
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- Genomics Unit, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Carolina Martínez-Laperche
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- Oncohematology Service, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia-CSIC, 46010 Valencia, Spain;
- CIBER Salud Pública (CIBERESP), 28029 Madrid, Spain;
| | - Fernando González-Candelas
- CIBER Salud Pública (CIBERESP), 28029 Madrid, Spain;
- Joint Research Unit “Infection and Public Health”, Institute for Integrative Systems Biology (I2SysBio), FISABIO-University of Valencia, 46980 Valencia, Spain
| | - Pilar Catalán
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Departamento de Medicina, Universidad Complutense, 28040 Madrid, Spain
| | - Darío García de Viedma
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
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Gozashti L, Corbett-Detig R. Shortcomings of SARS-CoV-2 genomic metadata. BMC Res Notes 2021; 14:189. [PMID: 34001211 PMCID: PMC8128092 DOI: 10.1186/s13104-021-05605-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the lab at which the sample was sequenced, and is integral to epidemiological efforts and public health direction. Here, we interrogate some shortcomings of metadata within the GISAID database to raise awareness of common errors and inconsistencies that may affect data-driven analyses and provide possible avenues for resolutions. RESULTS Our analysis reveals a startling prevalence of spelling errors and inconsistent naming conventions, which together occur in an estimated ~ 9.8% and ~ 11.6% of "originating lab" and "submitting lab" GISAID metadata entries respectively. We also find numerous ambiguous entries which provide very little information about the actual source of a sample and could easily associate with multiple sources worldwide. Importantly, all of these issues can impair the ability and accuracy of association studies by deceptively causing a group of samples to identify with multiple sources when they truly all identify with one source, or vice versa.
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Affiliation(s)
- Landen Gozashti
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA. .,Department of Biomolecular Engineering and Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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Genotyping of the Major SARS-CoV-2 Clade by Short-Amplicon High-Resolution Melting (SA-HRM) Analysis. Genes (Basel) 2021; 12:genes12040531. [PMID: 33916492 PMCID: PMC8067340 DOI: 10.3390/genes12040531] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022] Open
Abstract
The genome of the SARS-CoV-2 virus, the causal agent of the COVID-19 pandemic, has diverged due to multiple mutations since its emergence as a human pathogen in December 2019. Some mutations have defined several SARS-CoV-2 clades that seem to behave differently in terms of regional distribution and other biological features. Next-generation sequencing (NGS) approaches are used to classify the sequence variants in viruses from individual human patients. However, the cost and relative scarcity of NGS equipment and expertise in developing countries prevent studies aimed to associate specific clades and variants to clinical features and outcomes in such territories. As of March 2021, the GR clade and its derivatives, including the B.1.1.7 and B.1.1.28 variants, predominate worldwide. We implemented the post-PCR small-amplicon high-resolution melting analysis to genotype SARS-CoV-2 viruses isolated from the saliva of individual patients. This procedure was able to clearly distinguish two groups of samples of SARS-CoV-2-positive samples predicted, according to their melting profiles, to contain GR and non-GR viruses. This grouping of the samples was validated by means of amplification-refractory mutation system (ARMS) assay as well as Sanger sequencing.
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Di Caro A, Cunha F, Petrosillo N, Beeching NJ, Ergonul O, Petersen E, Koopmans MPG. Severe acute respiratory syndrome coronavirus 2 escape mutants and protective immunity from natural infections or immunizations. Clin Microbiol Infect 2021; 27:823-826. [PMID: 33794345 PMCID: PMC8007194 DOI: 10.1016/j.cmi.2021.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/14/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Antonino Di Caro
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Emerging Infections Task Force, ESCMID, Basel, Switzerland; Laboratory of Microbiology, National Institute for Infectious Diseases 'Lazzaro Spallanzani', Rome, Italy; Department of Molecular Medicine, San Matteo Hospital, University of Pavia, Pavia, Italy
| | - Flavia Cunha
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Emerging Infections Task Force, ESCMID, Basel, Switzerland; Department of Infectious Diseases, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Nicola Petrosillo
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), International Affairs Subcommittee, Basel, Switzerland; Clinical and Research Department, National Institute for Infectious Diseases 'Lazzaro Pallanzani', Rome, Italy
| | - Nicholas J Beeching
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Emerging Infections Task Force, ESCMID, Basel, Switzerland; Tropical and Infectious Disease Unit, Royal Liverpool University Hospital, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Oner Ergonul
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Emerging Infections Task Force, ESCMID, Basel, Switzerland; Koç University Research Centre for Infectious Diseases, Istanbul, Turkey
| | - Eskild Petersen
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Emerging Infections Task Force, ESCMID, Basel, Switzerland; Institute for Clinical Medicine, Faculty of Health Science, University of Aarhus, Denmark.
| | - Marion P G Koopmans
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Emerging Infections Task Force, ESCMID, Basel, Switzerland; Viroscience Department, ErasmusMC, WHO Collaborating Centre, Rotterdam, the Netherlands
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38
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Davis JT, Chinazzi M, Perra N, Mu K, Piontti APY, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Halloran ME, Longini IM, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.24.21254199. [PMID: 33791745 PMCID: PMC8010777 DOI: 10.1101/2021.03.24.21254199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment of the COVID-19 pandemic in Europe and the United States (US). The model is calibrated on international case introductions at the early stage of the pandemic. We find that widespread community transmission of SARS-CoV-2 was likely in several areas of Europe and the US by January 2020, and estimate that by early March, only 1 - 3 in 100 SARS-CoV-2 infections were detected by surveillance systems. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 with possible importation and transmission events as early as December, 2019. We characterize the resulting heterogeneous spatio-temporal spread of SARS-CoV-2 and the burden of the first COVID-19 wave (February-July 2020). We estimate infection attack rates ranging from 0.78%-15.2% in the US and 0.19%-13.2% in Europe. The spatial modeling of SARS-CoV-2 introductions and spreading provides insights into the design of innovative, model-driven surveillance systems and preparedness plans that have a broader initial capacity and indication for testing.
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Affiliation(s)
- Jessica T. Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Nicola Perra
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
- Networks and Urban Systems Centre, University of Greenwich, London, UK
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Ana Pastore y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Marco Ajelli
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health,, Bloomington, IN, USA
| | - Natalie E. Dean
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA
| | | | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health,, Bloomington, IN, USA
| | | | | | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Xinyue Xiong
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA. USA
| | - Ira M. Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
- ISI Foundation, Turin, Italy
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