1
|
Chang E, Jeon K, Lee N, Park MJ, Song W, Kim HS, Kim HS, Kim JS, Kim J, Jeong S. Clinical performance of the Roche Cobas Liat SARS-CoV-2 & influenza A/B assay: A systematic review and meta-analysis. J Clin Virol 2024; 174:105706. [PMID: 38908267 DOI: 10.1016/j.jcv.2024.105706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 05/17/2024] [Accepted: 06/05/2024] [Indexed: 06/24/2024]
Abstract
Respiratory tract infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses are persistent and critical. The Cobas Liat SARS-CoV-2 & influenza A/B assay (Multiplex Liat), the FDA-authorized point-of-care reverse transcriptase polymerase chain reaction (RT-PCR) assay, has a turnaround time of 20 min and high accuracy. This study evaluates the pooled performance of this assay to provide practical information. This meta-analysis was registered in PROSPERO (registration number: CRD42023467579). A systematic literature search was conducted within PubMed, Ovid-EMBASE, and the Cochrane Library for articles evaluating the accuracy of the Multiplex Liat assay through September 2023. A random-effects model was used to calculate the pooled diagnostic values with real-time RT-PCR (rRT-PCR) as a reference test. A total of 4,705 samples from eight studies were included in the primary meta-analysis. The overall pooled sensitivity and specificity of Multiplex Liat were 100.0 % (95 % confidence interval [CI] = 96.7 %-100.0 %) and 99.7 % (95 % CI = 98.7 %-99.9 %), respectively. The presence of variants of concern or in-house rRT-PCR assays as reference standards did not significantly affect the pooled diagnostic performance of the Multiplex Liat. When 5,333 samples from nine studies were assessed for sensitivity, the pooled sensitivity was 100.0 % (95 % CI = 85.8 %-100.0 %) without a significant difference. This meta-analysis demonstrates the usefulness of Multiplex Liat for the detection of SARS-CoV-2 based on pooled diagnostic values. These practical findings may facilitate appropriate settings for the diagnosis and management of patients with respiratory tract infections.
Collapse
Affiliation(s)
- Eunjin Chang
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Kibum Jeon
- Department of Laboratory Medicine, Hallym University Hangang Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, South Korea
| | - Nuri Lee
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, South Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University Hospital, Hallym University College of Medicine, Anyang, South Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, South Korea
| | - Jimin Kim
- Division of Healthcare Technology Assessment Research, National Evidence-Based Healthcare Collaborating Agency, Seoul, South Korea
| | - Seri Jeong
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea.
| |
Collapse
|
2
|
Al-Emran HM, Rahman F, Sarkar L, Das PK, Mondol P, Yesmin S, Sultana P, Ahammed T, Parvez R, Hasan MS, Sarkar SL, Rahman MS, Hossain A, Rahman M, Islam OK, Islam MT, Nigar S, Akter S, Rubayet Ul Alam ASM, Rahman MM, Jahid IK, Hossain MA. Emergence of SARS-CoV-2 Variants Are Induced by Coinfections With Dengue. Bioinform Biol Insights 2024; 18:11779322241272399. [PMID: 39290577 PMCID: PMC11406487 DOI: 10.1177/11779322241272399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/29/2024] [Indexed: 09/19/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 has accumulated a series of point mutations and evolved into several variants of concern (VOCs), some of which are more transmissible and potentially more severe than the original strain. The most notable VOCs are Alpha, Beta, Gamma, Delta, and Omicron, which have spread to various parts of the world. This study conducted surveillance in Jashore, Bangladesh to identify the prevalence of SARS-CoV-2 coinfected with dengue virus and their genomic effect on the emergence of VOCs. A hospital-based COVID-19 surveillance from June to August, 2021 identified 9 453 positive patients in the surveillance area. The study enrolled 572 randomly selected COVID-19-positive patients, of which 11 (2%) had dengue viral coinfection. Whole genome sequences of SARS-CoV-2 were analyzed and compared between coinfection positive and negative group. In addition, we extracted 185 genome sequences from GISAID to investigate the cross-correlation function between SARS-CoV-2 mutations and VOC; multiple ARIMAX(p,d,q) models were developed to estimate the average number of amino acid (aa) substitution among different SARS-CoV-2 VOCs. The results of the study showed that the coinfection group had an average of 30.6 (±1.7) aa substitutions in SARS-CoV-2, whereas the dengue-negative COVID-19 group had that average of 25.6 (±1.8; P < .01). The coinfection group showed a significant difference of aa substitutions in open reading frame (ORF) and N-protein when compared to dengue-negative group (P = .03). Our ARIMAX models estimated that the emergence of SARS-CoV-2 variants Delta required additional 9 to 12 aa substitutions than Alpha, Beta, or Gamma variant. The emergence of Omicron accumulated additional 19 (95% confidence interval [CI]: 15.74, 21.95) aa substitution than Delta. Increased number of point mutations in SARS-CoV-2 genome identified from coinfected cases could be due to the compromised immune function of host and induced adaptability of pathogens during coinfections. As a result, new variants might be emerged when series of coinfection events occur during concurrent two epidemics.
Collapse
Affiliation(s)
- Hassan M Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fazlur Rahman
- Department of Accounting and Information Systems, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Laxmi Sarkar
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Prosanto Kumar Das
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Provakar Mondol
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Suriya Yesmin
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Pipasha Sultana
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Toukir Ahammed
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Rasel Parvez
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shazid Hasan
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Shovon Lal Sarkar
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Anamica Hossain
- Department of Microbiology, Dhaka University, Dhaka, Bangladesh
| | | | - Ovinu Kibria Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Tanvir Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Shireen Nigar
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Selina Akter
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mohammad Mahfuzur Rahman
- Department of Climate and Disaster Management, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
- Genome Centre, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M Anwar Hossain
- Genome Centre, Jashore University of Science and Technology, Jashore, Bangladesh
| |
Collapse
|
3
|
Barrera A, Martínez-Valdebenito C, Angulo J, Palma C, Hormazábal J, Vial C, Aguilera X, Castillo-Torres P, Pardo-Roa C, Balcells ME, Nervi B, Corre NL, Ferrés M. SARS-CoV-2 infectivity and antigenic evasion: spotlight on isolated Omicron sub-lineages. Front Med (Lausanne) 2024; 11:1414331. [PMID: 39267969 PMCID: PMC11390582 DOI: 10.3389/fmed.2024.1414331] [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: 04/08/2024] [Accepted: 07/16/2024] [Indexed: 09/15/2024] Open
Abstract
Since the SARS-CoV-2 outbreak in 2019, a diversity of viral genomic variants has emerged and spread globally due to increased transmissibility, pathogenicity, and immune evasion. By the first trimester of 2023 in Chile, as in most countries, BQ and XBB were the predominant circulating sub-lineages of Omicron. The molecular and antigenic characteristics of these variants have been mainly determined using non-authentic spike pseudoviruses, which is often described as a limitation. Additionally, few comparative studies using isolates from recent Omicron sub-lineages have been conducted. In this study, we isolated SARS-CoV-2 variants from clinical samples, including the ancestral B.1.1, Delta, Omicron BA.1, and sub-lineages of BA.2 and BA.5. We assessed their infectivity through cell culture infections and their antibody evasion using neutralization assays. We observed variations in viral plaque size, cell morphology, and cytotoxicity upon infection in Vero E6-TMPRSS2 cells for each variant compared to the ancestral B.1.1 virus. BA.2-derived sub-variants, such as XBB.1.5, showed attenuated viral replication, while BA.5-derived variants, such as BQ.1.1, exhibited replication rates similar to the ancestral SARS-CoV-2 virus. Similar trends were observed in intestinal Caco-2 cells, except for Delta. Antibody neutralization experiments using sera from individuals infected during the first COVID-19 wave (FWI) showed a consistent but moderate reduction in neutralization against Omicron sub-lineages. Interestingly, despite being less prevalent, BQ.1.1 showed a 6.1-fold greater escape from neutralization than XBB.1.5. Neutralization patterns were similar when tested against sera from individuals vaccinated with 3xBNT162b2 (PPP) or Coronavac-Coronavac-BNT162b2 (CCP) schedules. However, CCP sera showed 2.3-fold higher neutralization against XBB.1.5 than FWI and PPP sera. This study provides new insights into the differences between BA.2 and BA.5-derived variants, leading to their eventual outcompetition. Our analysis offers important evidence regarding the balance between infectivity and antigenic escape that drives the evolution of second-generation SARS-CoV-2 variants in the population.
Collapse
Affiliation(s)
- Aldo Barrera
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Martínez-Valdebenito
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jenniffer Angulo
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Palma
- Laboratorio de Infectología y Virología Molecular, Facultad de Medicina y Red de Salud UC CHRISTUS, Santiago, Chile
| | - Juan Hormazábal
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Ximena Aguilera
- Centro de Epidemiología y Políticas de Salud, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Pablo Castillo-Torres
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Salud del Niño y el Adolescente, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Pardo-Roa
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Salud del Niño y el Adolescente, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Elvira Balcells
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bruno Nervi
- Departamento de Hematología y Oncología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Facultad de Medicina y Red de Salud UC CHRISTUS, Santiago, Chile
| | - Marcela Ferrés
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Facultad de Medicina y Red de Salud UC CHRISTUS, Santiago, Chile
| |
Collapse
|
4
|
Tatsing Foka FE, Tumelo Mufhandu H. Predictive Assessment of the Antiviral Properties of Imperata cylindrica against SARS-CoV-2. Adv Virol 2024; 2024:8598708. [PMID: 39135917 PMCID: PMC11317227 DOI: 10.1155/2024/8598708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 06/26/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
The omicron variant and its sublineages are highly contagious, and they still constitute a global source of concern despite vaccinations. Hospitalizations and mortality rates resulting from infections by these variants of concern are still common. The existing therapeutic alternatives have presented various setbacks such as low potency, poor pharmacokinetic profiles, and drug resistance. The need for alternative therapeutic options cannot be overemphasized. Plants and their phytochemicals present interesting characteristics that make them suitable candidates for the development of antiviral therapeutic agents. This study aimed to investigate the antiviral potential of Imperata cylindrica (I. cylindrica). Specifically, the objective of this study was to identify I. cylindrica phytochemicals that display inhibitory effects against SARS-CoV-2 main protease (Mpro), a highly conserved protein among coronaviruses. Molecular docking and in silico pharmacokinetic assays were used to assess 72 phytocompounds that are found in I. cylindrica as ligands and Mpro (6LU7) as the target. Only eight phytochemicals (bifendate, cylindrene, tabanone, siderin, 5-hydroxy-2-[2-(2-hydroxyphenyl)ethyl]-4H-1-benzopyran-4-one, maritimin, 5-methoxyflavone, and flavone) displayed high binding affinities with Mpro with docking scores ranging from -5.6 kcal/mol to -9.1 kcal/mol. The in silico pharmacokinetic and toxicological assays revealed that tabanone was the best and safest phytochemical for the development of an inhibitory agent against coronavirus main protease. Thus, the study served as a baseline for further in vitro and in vivo assessment of this phytochemical against Mpro of SARS-CoV-2 variants of concern to validate these in silico findings.
Collapse
Affiliation(s)
- Frank Eric Tatsing Foka
- Department of MicrobiologyVirology LaboratorySchool of Biological SciencesFaculty of Natural and Agricultural SciencesNorth West University, Mafikeng, Private Bag X2046, Mmabatho, South Africa
| | - Hazel Tumelo Mufhandu
- Department of MicrobiologyVirology LaboratorySchool of Biological SciencesFaculty of Natural and Agricultural SciencesNorth West University, Mafikeng, Private Bag X2046, Mmabatho, South Africa
| |
Collapse
|
5
|
Shempela DM, Chambaro HM, Sikalima J, Cham F, Njuguna M, Morrison L, Mudenda S, Chanda D, Kasanga M, Daka V, Kwenda G, Musonda K, Munsaka S, Chilengi R, Sichinga K, Simulundu E. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study. Int J Mol Sci 2024; 25:6338. [PMID: 38928045 PMCID: PMC11203853 DOI: 10.3390/ijms25126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.
Collapse
Affiliation(s)
| | - Herman M. Chambaro
- Virology Unit, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka 10101, Zambia;
| | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Fatim Cham
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Michael Njuguna
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Linden Morrison
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Duncan Chanda
- University Teaching Hospital, Ministry of Health, Lusaka 10101, Zambia;
| | - Maisa Kasanga
- Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
| | - Victor Daka
- Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia;
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Karen Sichinga
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Macha Research Trust, Choma 20100, Zambia
| |
Collapse
|
6
|
Hyun H, Nham E, Seong H, Yoon JG, Noh JY, Cheong HJ, Kim WJ, Yoon SK, Park SJ, Gwak W, Lee JW, Kim B, Song JY. Long-term humoral and cellular immunity against vaccine strains and Omicron subvariants (BQ.1.1, BN.1, XBB.1, and EG.5) after bivalent COVID-19 vaccination. Front Immunol 2024; 15:1385135. [PMID: 38756783 PMCID: PMC11096540 DOI: 10.3389/fimmu.2024.1385135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Background The assessment of long-term humoral and cellular immunity post-vaccination is crucial for establishing an optimal vaccination strategy. Methods This prospective cohort study evaluated adults (≥18 years) who received a BA.4/5 bivalent vaccine. We measured the anti-receptor binding domain immunoglobulin G antibody and neutralizing antibodies (NAb) against wild-type and Omicron subvariants (BA.5, BQ.1.1, BN.1, XBB.1 and EG.5) up to 9 months post-vaccination. T-cell immune responses were measured before and 4 weeks after vaccination. Results A total of 108 (28 SARS-CoV-2-naïve and 80 previously infected) participants were enrolled. Anti-receptor binding domain immunoglobulin G (U/mL) levels were higher at 9 months post-vaccination than baseline in SAR-CoV-2-naïve individuals (8,339 vs. 1,834, p<0.001). NAb titers against BQ.1.1, BN.1, and XBB.1 were significantly higher at 9 months post-vaccination than baseline in both groups, whereas NAb against EG.5 was negligible at all time points. The T-cell immune response (median spot forming unit/106 cells) was highly cross-reactive at both baseline (wild-type/BA.5/XBB.1.5, 38.3/52.5/45.0 in SARS-CoV-2-naïve individuals; 51.6/54.9/54.9 in SARS-CoV-2-infected individuals) and 4 weeks post-vaccination, with insignificant boosting post-vaccination. Conclusion Remarkable cross-reactive neutralization was observed against BQ.1.1, BN.1, and XBB.1 up to 9 months after BA.4/5 bivalent vaccination, but not against EG.5. The T-cell immune response was highly cross-reactive.
Collapse
Affiliation(s)
- Hakjun Hyun
- Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Eliel Nham
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hye Seong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Gu Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo Joo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sun Kyung Yoon
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Se-Jin Park
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - WonSeok Gwak
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - June-Woo Lee
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Byoungguk Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
7
|
Sharma D, Rawat P, Greiff V, Janakiraman V, Gromiha MM. Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166959. [PMID: 37967796 DOI: 10.1016/j.bbadis.2023.166959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
COVID-19 has resulted in millions of deaths and severe impact on economies worldwide. Moreover, the emergence of SARS-CoV-2 variants presented significant challenges in controlling the pandemic, particularly their potential to avoid the immune system and evade vaccine immunity. This has led to a growing need for research to predict how mutations in SARS-CoV-2 reduces the ability of antibodies to neutralize the virus. In this study, we assembled a set of 1813 mutations from the interface of SARS-CoV-2 spike protein's receptor binding domain (RBD) and neutralizing antibody complexes and developed a machine learning model to classify high or low escape mutations using interaction energy, inter-residue contacts and predicted binding free energy change. Our approach achieved an Area under the Receiver Operating Characteristics (ROC) Curve (AUC) of 0.91 using the Random Forest classifier on the test dataset with 217 mutations. The model was further utilized to predict the escape mutations on a dataset of 29,165 mutations located at the interface of 83 RBD-neutralizing antibody complexes. A small subset of this dataset was also validated based on available experimental data. We found that top 10 % high escape mutations were dominated by charged to nonpolar mutations whereas low escape mutations were dominated by polar to nonpolar mutations. We believe that the present method will allow prioritization of high/low escape mutations in the context of neutralizing antibodies targeting SARS-CoV-2 RBD region and assist antibody design for current and emerging variants.
Collapse
Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Puneet Rawat
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vani Janakiraman
- Infection Biology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Department of Computer Science, National University of Singapore, Singapore.
| |
Collapse
|
8
|
Choi BY, Grace AR, Tsai J. Heterogeneity of COVID-19 symptoms and associated factors: Longitudinal analysis of laboratory-confirmed COVID-19 cases in San Antonio. PLoS One 2023; 18:e0295418. [PMID: 38064447 PMCID: PMC10707584 DOI: 10.1371/journal.pone.0295418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Few studies have examined heterogeneous associations of risk factors with Coronavirus Disease-2019 (COVID-19) symptoms by type. The objectives of this study were to estimate the prevalence of and risk factors associated with COVID-19 symptoms and to investigate whether the associations differ by the type of symptoms. This study obtained longitudinal data over 6 months from laboratory-confirmed COVID-19 cases in a citywide sample in San Antonio. Sixteen symptoms of COVID-19 infection, measured at baseline and three follow-up times (1, 3, and 6 months), were analyzed using generalized estimating equations (GEE) to investigate potential risk factors while accounting for the repeated measurements. The risk factors included time in months, sociodemographic characteristics, and past or current medical and psychiatric conditions. To obtain interpretable results, we categorized these sixteen symptoms into five categories (cardiopulmonary, neuro-psychological, naso-oropharyngeal, musculoskeletal, and miscellaneous). We fitted GEE models with a logit link using each category as the outcome variable. Our study demonstrated that the associations were heterogeneous by the categories of symptoms. The time effects were the strongest for naso-oropharyngeal symptoms but the weakest for neuro-psychological symptoms. Female gender was associated with increased odds of most of the symptoms. Hispanic ethnicity was also associated with higher odds of neuro-psychological, musculoskeletal, and miscellaneous symptoms. Depression was the most robust psychiatric condition contributing to most of the symptoms. Different medical conditions seemed to contribute to different symptom expressions of COVID-19 infection.
Collapse
Affiliation(s)
- Byeong Yeob Choi
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Abigail R. Grace
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Jack Tsai
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| |
Collapse
|
9
|
Petcharat S, Supataragul A, Hirunpatrawong P, Torvorapanit P, Klungthong C, Chinnawirotpisan P, Ninwattana S, Thippamom N, Paitoonpong L, Suwanpimolkul G, Jantarabenjakul W, Buathong R, Joonlasak K, Manasatienkij W, Rattanatumhi K, Chantasrisawad N, Chumpa N, Cotrone TS, Fernandez S, Sriswasdi S, Wacharapluesadee S, Putcharoen O. High Transmission Rates of Early Omicron Subvariant BA.2 in Bangkok, Thailand. Adv Virol 2023; 2023:4940767. [PMID: 38094619 PMCID: PMC10719011 DOI: 10.1155/2023/4940767] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/01/2023] [Accepted: 11/24/2023] [Indexed: 02/01/2024] Open
Abstract
The emergence of Omicron as the fifth variant of concern within the SARS-CoV-2 pandemic in late 2021, characterized by its rapid transmission and distinct spike gene mutations, underscored the pressing need for cost-effective and efficient methods to detect viral variants, especially given their evolving nature. This study sought to address this need by assessing the effectiveness of two SARS-CoV-2 variant classification platforms based on RT-PCR and mass spectrometry. The primary aim was to differentiate between Delta, Omicron BA.1, and Omicron BA.2 variants using 618 COVID-19-positive samples collected from Bangkok patients between November 2011 and March 2022. The analysis revealed that both BA.1 and BA.2 variants exhibited significantly higher transmission rates, up to 2-3 times, when compared to the Delta variant. This research presents a cost-efficient approach to virus surveillance, enabling a quantitative evaluation of variant-specific public health implications, crucial for informing and adapting public health strategies.
Collapse
Affiliation(s)
- Sininat Petcharat
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Ananporn Supataragul
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Piyapha Hirunpatrawong
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattama Torvorapanit
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Piyawan Chinnawirotpisan
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Sasiprapa Ninwattana
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nattakarn Thippamom
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Leilani Paitoonpong
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Gompol Suwanpimolkul
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Watsamon Jantarabenjakul
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Rome Buathong
- Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Khajohn Joonlasak
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Khwankamon Rattanatumhi
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Napaporn Chantasrisawad
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nuntana Chumpa
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thomas S Cotrone
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Sira Sriswasdi
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Artificial Intelligence in Medicine, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
10
|
Banjac J, Vuković V, Pustahija T, Bohucki N, Berić DK, Medić S, Petrović V, Ristić M. Epidemiological Characteristics of COVID-19 during Seven Consecutive Epidemiological Waves (2020-2022) in the North Bačka District, Serbia. Viruses 2023; 15:2221. [PMID: 38005898 PMCID: PMC10674962 DOI: 10.3390/v15112221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The COVID-19 pandemic continues to pose a threat to global public health. The purpose of this research was to determine the epidemiological characteristics of COVID-19 in the North Bačka district while observing seven pandemic waves. The cross-sectional study was based on data from the COVID-19 surveillance database of the Institute for Public Health of Vojvodina during the period from March 2020 to December 2022. A total of 38,685 primary infections and 4067 reinfections caused by SARS-CoV-2 were notified. Pandemic waves caused by the Delta variant (cumulative incidence rate of 2482.37/100,000) and by the Omicron variant (cumulative incidence rate of 2994.45/100,000) emerged as significant focal points during the surveillance period. Over the course of three consecutive years (2020-2022), women were more affected (50.11%, 54.03%, and 55.68%, respectively). The highest incidence rates in age-specific categories were recorded in 2021 for the age group 40-49 (1345.32 per 10,000 inhabitants), while in 2022, they shifted towards the elderly population. Regarding vaccination status at the time of diagnosis, in 2021, around 15% of patients were vaccinated, while in 2022, the number increased to 37%. The most widely received vaccine was BBIBP-CorV (67.45%), followed by BNT162b2 (19.81%), Gam-COVID-Vac (9.31%), and ChAdOx1 nCoV-19 (3.42%) vaccine. The implementation of stringent public health measures and their mitigation, together with the emergence of new variants, influenced the dynamics of COVID-19 pandemic waves in the North Bačka district. Notably, throughout the study period, the working-age population was the most affected, along with females, with a mild clinical presentation dominating. Reinfections were most frequently recorded during the latter pandemic waves. Dealing with this pandemic has provided some valuable lessons for the development of future strategies in the case of a similar public health crisis.
Collapse
Affiliation(s)
- Jelena Banjac
- Public Health Institute Subotica, 24000 Subotica, Serbia; (J.B.); (N.B.); (D.K.B.)
| | - Vladimir Vuković
- Institute of Public Health of Vojvodina, 21000 Novi Sad, Serbia; (T.P.); (S.M.); (V.P.); (M.R.)
- Department of Epidemiology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Tatjana Pustahija
- Institute of Public Health of Vojvodina, 21000 Novi Sad, Serbia; (T.P.); (S.M.); (V.P.); (M.R.)
- Department of Epidemiology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Nebojša Bohucki
- Public Health Institute Subotica, 24000 Subotica, Serbia; (J.B.); (N.B.); (D.K.B.)
| | | | - Snežana Medić
- Institute of Public Health of Vojvodina, 21000 Novi Sad, Serbia; (T.P.); (S.M.); (V.P.); (M.R.)
- Department of Epidemiology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Vladimir Petrović
- Institute of Public Health of Vojvodina, 21000 Novi Sad, Serbia; (T.P.); (S.M.); (V.P.); (M.R.)
- Department of Epidemiology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Mioljub Ristić
- Institute of Public Health of Vojvodina, 21000 Novi Sad, Serbia; (T.P.); (S.M.); (V.P.); (M.R.)
- Department of Epidemiology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| |
Collapse
|
11
|
Fomina DS, Lebedkina MS, Iliukhina AA, Kovyrshina AV, Shelkov AY, Andreev SS, Chernov AA, Dolzhikova IV, Kruglova TS, Andrenova GV, Tukhvatulin AI, Shcheblyakov DV, Karaulov AV, Lysenko MA, Logunov DY, Gintsburg AL. Real-world clinical effectiveness of Tixagevimab/Cilgavimab and Regdanvimab monoclonal antibodies for COVID-19 treatment in Omicron variant-dominant period. Front Immunol 2023; 14:1259725. [PMID: 37928549 PMCID: PMC10623550 DOI: 10.3389/fimmu.2023.1259725] [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: 07/16/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
Several virus-neutralizing monoclonal antibodies (mAbs) have become new tools in the treatment of the coronavirus disease (COVID-19), but their effectiveness against the rapidly mutating virus is questionable. The present study investigated the effectiveness of Tixagevimab/Cilgavimab and Regdanvimab for mild and moderate COVID-19 treatment in real-world clinical practice during the Omicron variant-dominant period. Patients with known risk factors for disease progression and increasing disease severity were enrolled in the study within the first 7 days of symptom onset. Seventy-seven patients were divided into four groups: first 15 patients received 300 mg Tixagevimab/Cilgavimab intravenously (IV) and 23 patients got the same drug 300 mg intramuscularly (IM), the next 15 patients was on the same combination in dose of 600 mg IV, and 24 patients were on Regdanvimab at a dose of 40 mg/kg IV. By Day 4, 100% of Tixagevimab/Cilgavimab IV patients showed negative polymerase chain reaction results for SARS-CoV-2 Ribonucleic acid (RNA) regardless of the mAbs dose while in the Regdanvimab group 29% of the patients were positive for SARS-CoV-2 virus RNA. The testing for virus neutralizing antibodies (nAbs) to various Omicron sublineages (BA.1, BA.2, and BA.5) showed that an increase in nAb levels was detected in blood serum immediately after the drug administration only in Tixagevimab/Cilgavimab 300 mg and 600 mg IV groups. In the group of intravenous Regdanvimab, a significant increase in the level of nAbs to the Wuhan variant was detected immediately after the drug administration, while no increase in nAbs to different Omicron sublineages was observed. Clinical trial registration https://clinicaltrials.gov/, identifier NCT05982704.
Collapse
Affiliation(s)
- Daria S. Fomina
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
- Allergy and Immunology Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Marina S. Lebedkina
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Anna A. Iliukhina
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anna V. Kovyrshina
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Artem Y. Shelkov
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Sergey S. Andreev
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Anton A. Chernov
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Inna V. Dolzhikova
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Tatyana S. Kruglova
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Gerelma V. Andrenova
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Amir I. Tukhvatulin
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry V. Shcheblyakov
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander V. Karaulov
- Allergy and Immunology Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Maryana A. Lysenko
- Department of Allergy and Immunology, City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
- General Therapy Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Denis Y. Logunov
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander L. Gintsburg
- State Virus Collection Laboratory, Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
- Allergy and Immunology Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| |
Collapse
|
12
|
Chen X, Hong J, Deng L, Weng H, Huang T, Wang L, Ou A, Li Y, Yu B, Guo J, Yang J. Association between levels of IgG antibodies from vaccines and Omicron symptomatic infection among children and adolescents in China. Front Med (Lausanne) 2023; 10:1240340. [PMID: 37706028 PMCID: PMC10495586 DOI: 10.3389/fmed.2023.1240340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Background Measurements of IgG antibodies to wild-type SARS-CoV-2 antigens can assess vaccine efficacy, but the absolute risk of Omicron symptomatic infection at different IgG levels for children and adolescents remains uncertain, as well as the minimum effective antibody level. We sought to determine the relationship between the tertiles of IgG antibodies to wild-type SARS-CoV-2 antigens and children with symptomatic infection of the pandemic and duration to negative conversion in China for the first time. Methods A retrospective study was conducted, including 168 participants under 18 years old from the No.2 People's Hospital of Lanzhou, China, diagnosed with Omicron variant BA.2.38 between July 8, 2022, and August 2, 2022. We calculated odds ratios (OR) in univariate and multivariate regression to assess the association of symptomatic infection with the tertiles of IgG, respectively. Kaplan-Meier curves and Cox proportional hazards regression were used to evaluate the relationship between IgG level and negative conversion time. Results The average age of the 168 children included in this study was 7.2 (4.7) years old, 133 (79.2%) were symptomatic patients, and the average negative conversion time was 12.2 (3.5) days. The participants with high IgG levels were less likely to become symptomatic, had a shorter turnaround time, and had higher values of IgM and nucleic acid CT. Compared to those with the lowest tertile of IgG, patients with the highest tertile had a 91% lower risk of developing a symptomatic infection after fully adjusting for confounders (OR = 0.09, 95% CI, 0.02-0.36, p = 0.001). There's no robust relationship between IgG level and negative conversion time in multivariate Cox regression. Conclusion The risk of developing a symptomatic infection can be predicted independently by tertiles of IgG antibodies to wild-type SARS-CoV-2 antigens. High IgG levels can inhibit viral replication, vastly reduce the risk of symptomatic infections and promote a virus-negative conversion, especially when IgG quantitative detection was ≥3.44 S/CO, a potential threshold for protection and booster strategy in the future. More data and research are needed in the future to validate the predictive models.
Collapse
Affiliation(s)
- Xinying Chen
- Department of Pediatrics, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Xiaorong Luo’s Renowned Expert Inheritance Studio, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Junbin Hong
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lijun Deng
- Department of Pediatrics, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Xiaorong Luo’s Renowned Expert Inheritance Studio, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Heng Weng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Teng Huang
- Department of Pediatrics, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Xiaorong Luo’s Renowned Expert Inheritance Studio, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Li Wang
- Department of Lab, The No.2 People's Hospital of Lanzhou, Lanzhou, China
| | - Aihua Ou
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuxia Li
- Department of Pediatrics, The Affiliated Hospital of Gansu University of Chinese Medicine, Lanzhou, China
| | - Bo Yu
- Department of Surgery, The No.2 People's Hospital of Lanzhou, Lanzhou, China
| | - Jianwen Guo
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinghua Yang
- Department of Pediatrics, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Xiaorong Luo’s Renowned Expert Inheritance Studio, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| |
Collapse
|
13
|
Dorta-Gorrín A, Navas-Méndez J, Gozalo-Margüello M, Miralles L, García-Hevia L. Detection of SARS-CoV-2 Based on Nucleic Acid Amplification Tests (NAATs) and Its Integration into Nanomedicine and Microfluidic Devices as Point-of-Care Testing (POCT). Int J Mol Sci 2023; 24:10233. [PMID: 37373381 DOI: 10.3390/ijms241210233] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The coronavirus SARS-CoV-2 has highlighted the criticality of an accurate and rapid diagnosis in order to contain the spread of the virus. Knowledge of the viral structure and its genome is essential for diagnosis development. The virus is still quickly evolving and the global scenario could easily change. Thus, a greater range of diagnostic options is essential to face this threat to public health. In response to the global demand, there has been a rapid advancement in the understanding of current diagnostic methods. In fact, innovative approaches have emerged, leveraging the benefits of nanomedicine and microfluidic technologies. Although this development has been incredibly fast, several key areas require further investigation and optimization, such as sample collection and preparation, assay optimization and sensitivity, cost effectiveness, scalability device miniaturization, and portability and integration with smartphones. Addressing these gaps in the knowledge and these technological challenges will contribute to the development of reliable, sensitive, and user-friendly NAAT-based POCTs for the diagnosis of SARS-CoV-2 and other infectious diseases, facilitating rapid and effective patient management. This review aims to provide an overview of current SARS-CoV-2 detection methods based on nucleic acid detection tests (NAATs). Additionally, it explores promising approaches that combine nanomedicine and microfluidic devices with high sensitivity and relatively fast 'time to answer' for integration into point-of-care testing (POCT).
Collapse
Affiliation(s)
- Alexis Dorta-Gorrín
- Department of Molecular Biology, Faculty of Medicine, University of Cantabria (UC), 39011 Santander, Spain
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
- Environmental Genetics Department, Ecohydros S.L., 39600 Maliaño, Spain
| | - Jesús Navas-Méndez
- Department of Molecular Biology, Faculty of Medicine, University of Cantabria (UC), 39011 Santander, Spain
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Mónica Gozalo-Margüello
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
- Microbiology Service of University Hospital Marqués de Valdecilla (HUMV), 39008 Santander, Spain
- CIBER de Enfermedades Infecciosas-CIBERINFEC (CB21/13/00068), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Miralles
- Environmental Genetics Department, Ecohydros S.L., 39600 Maliaño, Spain
- Department of Functional Biology, Area of Genetics, Faculty of Medicine, University of Oviedo, 33006 Oviedo, Spain
| | - Lorena García-Hevia
- Department of Molecular Biology, Faculty of Medicine, University of Cantabria (UC), 39011 Santander, Spain
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| |
Collapse
|
14
|
Favresse J, Douxfils J, Henry B, Lippi G, Plebani M. Clinical Chemistry and Laboratory Medicine celebrates 60 years – narrative review devoted to the contribution of the journal to the diagnosis of SARS-CoV-2. Clin Chem Lab Med 2022; 61:811-821. [PMID: 36420539 DOI: 10.1515/cclm-2022-1166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022]
Abstract
Abstract
This review is an integral part of the special issue for the 60 years of the journal Clinical Chemistry and Laboratory Medicine (CCLM). The aim of the review is to highlight the role of the clinical laboratory since the emergence of the “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2), which causes Coronavirus disease 2019 (COVID-19), with special focus on the contribution of the journal in generating knowledge in SARS-CoV-2 diagnosis. As of October 30, 2022, a total of 186 CCLM publications were dedicated to COVID-19. Of importance, major International Federation of Clinical Chemistry (IFCC) guidelines related to the diagnosis of COVID-19 were published in CCLM. Between early-2020 and late October 2022, COVID-19 publications represented around 27% of all articles in CCLM, highlighting the willingness of the editorial board to help the field in order to better describe and diagnose this new emerging disease. First launched in 1963 under the name “Zeitschrift für Klinische Chemie”, the Journal was entirely devoted to clinical chemistry in the strict sense. The various topics published in relation to COVID-19 including its diagnosis, its impact on biochemical or hematological measures, as well as biosafety measures, is the perfect example that shows that the journal has greatly diversified over time.
Collapse
Affiliation(s)
- Julien Favresse
- IFCC SARS-CoV-2 Variants Working Group , Verona , Italy
- Department of Laboratory Medicine , Clinique St-Luc Bouge , Namur , Belgium
- Department of Pharmacy , Namur Research Institute for Lifes Sciences, University of Namur , Namur , Belgium
| | - Jonathan Douxfils
- Department of Pharmacy , Namur Research Institute for Lifes Sciences, University of Namur , Namur , Belgium
- Qualiblood s.a. , Namur , Belgium
| | - Brandon Henry
- IFCC SARS-CoV-2 Variants Working Group , Verona , Italy
- Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children’s Hospital Medical Center , Cincinnati , OH , USA
| | - Giuseppe Lippi
- IFCC SARS-CoV-2 Variants Working Group , Verona , Italy
- Section of Clinical Biochemistry and School of Medicine, University of Verona , Verona , Italy
| | - Mario Plebani
- IFCC SARS-CoV-2 Variants Working Group , Verona , Italy
- Department of Laboratory Medicine , University-Hospital of Padova , Padova , Italy
| |
Collapse
|
15
|
Gupta S, Kumar A, Gupta N, Bharti DR, Aggarwal N, Ravi V. A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2. BMC Genomics 2022; 23:755. [DOI: 10.1186/s12864-022-08999-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India.
Results
We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC.
Conclusion
Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.
Collapse
|