1
|
You C, Jiang S, Ding Y, Ye S, Zou X, Zhang H, Li Z, Chen F, Li Y, Ge X, Guo X. RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages. Virol Sin 2024; 39:156-168. [PMID: 38253258 PMCID: PMC10877444 DOI: 10.1016/j.virs.2024.01.006] [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: 04/08/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
Collapse
Affiliation(s)
- Changqiao You
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yunyun Ding
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shunxing Ye
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Hongming Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Zeqi Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
| |
Collapse
|
2
|
Ma Y, To D, Zeng J, Shoute LCT, Wu M, Babiuk S, Zhuo R, Charlton C, Kanji JN, Babiuk L, Chen J. Improving immunoassay detection accuracy of anti-SARS-CoV-2 antibodies through dual modality validation. BIOSENSORS & BIOELECTRONICS: X 2022; 11:100176. [PMID: 35692737 PMCID: PMC9167148 DOI: 10.1016/j.biosx.2022.100176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/16/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
A novel test strategy is proposed with dual-modality detection techniques for COVID-19 antibody detection. The full-length S protein of SARS-CoV-2 was chemically immobilized on a glass surface to capture anti-SARS-CoV-2 IgG in patient serum and was detected through either Electrochemical Impedance Spectroscopy (EIS) or fluorescence imaging with labeled secondary antibodies. Gold nanoparticles conjugated with protein G were used as the probe and the bound GNP-G was detected through EIS measurements. Anti-human-IgG conjugated with the fluorescent tag Alexa Fluor 488 was used as the probe for fluorescence imaging. Clinical SARS-CoV-2 IgG positive serum and negative controls were used to validate both modalities. For fluorescence-based detection, a high sensitivity was noticed with a quantification range of 0.01-0.1 A.U.C. and a LOD of 0.004 A.U.C. This study demonstrates the possibility of utilizing different measurement techniques in conjunction for improved COVID-19 serology testing.
Collapse
Affiliation(s)
- Yuhao Ma
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Daniel To
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Jie Zeng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Lian C T Shoute
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Meng Wu
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Ran Zhuo
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
| | - Carmen Charlton
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
- Li Ka Shing Institute for Virology, University of Alberta, Edmonton, AB, Canada
| | - Jamil N Kanji
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
- Division of Infectious Diseases, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Lorne Babiuk
- Vaccine and Infectious Disease Organization, University of Alberta, Edmonton, AB, Canada
| | - Jie Chen
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 2V2, Canada
| |
Collapse
|
3
|
Mattoo SUS, Myoung J. A Promising Vaccination Strategy against COVID-19 on the Horizon: Heterologous Immunization. J Microbiol Biotechnol 2021; 31:1601-1614. [PMID: 34949742 PMCID: PMC9705928 DOI: 10.4014/jmb.2111.11026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/15/2022]
Abstract
To overcome the ongoing COVID-19 pandemic, vaccination campaigns are the highest priority of majority of countries. Limited supply and worldwide disproportionate availability issues for the approved vaccines, together with concerns about rare side-effects have recently initiated the switch to heterologous vaccination, commonly known as mixing of vaccines. The COVID-19 vaccines are highly effective in the general population. However, none of the vaccines is 100% efficacious or effective, with variants posing more challenges, resulting in breakthrough cases. This review summarizes the current knowledge of immune responses to variants of concern (VOC) and breakthrough infections. Furthermore, we discuss the scope of heterologous vaccination and future strategies to tackle the COVID-19 pandemic, including fractionation of vaccine doses and alternative route of vaccination.
Collapse
Affiliation(s)
- Sameer-ul-Salam Mattoo
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Jinjong Myoung
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea,Corresponding author Phone: +82-63-9004055 Fax: +82-63-9004012 E-mail:
| |
Collapse
|