1
|
Kim H, Jang H, Song J, Lee SM, Lee S, Kwon HJ, Kim S, Kang T, Park HG. A CRISPR/Cas12 trans-cleavage reporter enabling label-free colorimetric detection of SARS-CoV-2 and its variants. Biosens Bioelectron 2024; 251:116102. [PMID: 38350240 DOI: 10.1016/j.bios.2024.116102] [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: 11/22/2023] [Revised: 01/17/2024] [Accepted: 02/03/2024] [Indexed: 02/15/2024]
Abstract
We present a label-free colorimetric CRISPR/Cas-based method enabling affordable molecular diagnostics for SARS-CoV-2. This technique utilizes 3,3'-diethylthiadicarbocyanine iodide (DISC2(5)) which exhibits a distinct color transition from purple to blue when it forms dimers by inserting into the duplex of the thymidine adenine (TA) repeat sequence. Loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA) was used to amplify target samples, which were subsequently subjected to the CRISPR/Cas12a system. The target amplicons would activate Cas12a to degrade nearby TA repeat sequences, preserving DISC2(5) in its free form to display purple as opposed to blue in the absence of the target. Based on this design approach, SARS-CoV-2 RNA was colorimetrically detected very sensitively down to 2 copies/μL, and delta and omicron variants of SARS-CoV-2 were also successfully identified. The practical diagnostic utility of this method was further validated by reliably identifying 179 clinical samples including 20 variant samples with 100% clinical sensitivity and specificity. This technique has the potential to become a promising CRISPR-based colorimetric platform for molecular diagnostics of a wide range of target pathogens.
Collapse
Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, KRIBB, 181 Ipsin-gil, Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju, Gyeongsangnam-do, 52727, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
2
|
Li D, Sun C, Zhuang P, Mei X. Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods. Talanta 2024; 266:124937. [PMID: 37481886 DOI: 10.1016/j.talanta.2023.124937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.
Collapse
Affiliation(s)
- Dan Li
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co., Ltd., Shenyang, China
| | - Pengfei Zhuang
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Key Laboratory of Medical Tissue Engineering of Liaoning Province, Jinzhou Medical University, Jinzhou, Liaoning, China.
| |
Collapse
|
3
|
Khazir J, Ahmed S, Thakur RK, Hussain M, Gandhi SG, Babbar S, Mir SA, Shafi N, Tonfack LB, Rajpal VR, Maqbool T, Mir BA, Peer LA. Repurposing of Plant-based Antiviral Molecules for the Treatment of COVID-19. Curr Top Med Chem 2024; 24:614-633. [PMID: 38477206 DOI: 10.2174/0115680266276749240206101847] [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: 09/28/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
COVID-19, stemming from SARS-CoV-2, poses a formidable threat to global healthcare, with a staggering 77 million confirmed cases and 690,067 deaths recorded till December 24, 2023. Given the absence of specific drugs for this viral infection, the exploration of novel antiviral compounds becomes imperative. High-throughput technologies are actively engaged in drug discovery, and there is a parallel effort to repurpose plant-based molecules with established antiviral properties. In this context, the review meticulously delves into the potential of plant-based folk remedies and existing molecules. These substances have showcased substantial viral inhibition in diverse in vivo, in silico, and in vitro studies, particularly against critical viral protein targets, including SARS-CoV-2. The findings position these plant-based molecules as promising antiviral drug candidates for the swift advancement of treatments for COVID-19. It is noteworthy that the inherent attributes of these plant-based molecules, such as their natural origin, potency, safety, and cost-effectiveness, contribute to their appeal as lead candidates. The review advocates for further exploration through comprehensive in vivo studies conducted on animal models, emphasizing the potential of plant-based compounds to help in the ongoing quest to develop effective antivirals against COVID-19.
Collapse
Affiliation(s)
- Jabeena Khazir
- Department of Chemistry, HKM Govt. Degree College Eidgah, Cluster University Srinagar, J&K, 190001, India
| | - Sajad Ahmed
- Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | - Rakesh Kr Thakur
- Amity Institute of Biotechnology, Amity University, Noida, 201313, India
| | - Manzoor Hussain
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
- Department of Botany, North Campus, University of Kashmir, Delina, Baramulla, J&K, 193103, India
| | - Sumit G Gandhi
- Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | - Sadhana Babbar
- Department of Botany, Swami Shradhanand College, University of Delhi, Delhi, 110036, India
| | - Shabir Ahmad Mir
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah, 11952, Saudi Arabia
| | - Nusrat Shafi
- Department of Chemistry, HKM Govt. Degree College Eidgah, Cluster University Srinagar, J&K, 190001, India
| | - Libert Brice Tonfack
- Laboratory of Biotechnology and Environment, Department of Plant Biology, Faculty of Science, University of Yaounde I, PO Box 812, Yaounde, Cameroon
| | - Vijay Rani Rajpal
- Department of Botany, Hans Raj College, University of Delhi, Delhi, 110007, India
| | - Tariq Maqbool
- Laboratory of Nanotherapeutics and Regenerative Medicine, University of Kashmir, Srinagar, 190006, India
| | - Bilal Ahmad Mir
- Department of Botany, North Campus, University of Kashmir, Delina, Baramulla, J&K, 193103, India
| | - Latif Ahmad Peer
- Department of Botany, University of Kashmir, Srinagar, J&K, 190006, India
| |
Collapse
|
4
|
Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [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: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
Collapse
Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
| |
Collapse
|
5
|
Niveditha D, Khan S, Khilari A, Nadkarni S, Bhalerao U, Kadam P, Yadav R, Kanekar JB, Shah N, Likhitkar B, Sawant R, Thakur S, Tupekar M, Nagar D, Rao AG, Jagtap R, Jogi S, Belekar M, Pathak M, Shah P, Ranade S, Phadke N, Das R, Joshi S, Karyakarte R, Ghose A, Kadoo N, Shashidhara LS, Monteiro JM, Shanmugam D, Raghunathan A, Karmodiya K. A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India. J Infect Public Health 2023; 16:1290-1300. [PMID: 37331277 DOI: 10.1016/j.jiph.2023.06.004] [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: 02/07/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data. METHODS A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a "band of five" outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3-4), and geospatial mapping (Band 5). RESULTS The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. CONCLUSIONS The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.
Collapse
Affiliation(s)
- Divya Niveditha
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Soumen Khan
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ajinkya Khilari
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Sanica Nadkarni
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ritu Yadav
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Jugal B Kanekar
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Nikita Shah
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Bhagyashree Likhitkar
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Rutuja Sawant
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Shikha Thakur
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Dhriti Nagar
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Anjani G Rao
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Rutuja Jagtap
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shraddha Jogi
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Madhuri Belekar
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Maitreyee Pathak
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Priyanki Shah
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, India
| | | | - Nikhil Phadke
- GenePath Diagnostics India Private Limited, Pune 411004, India
| | - Rashmita Das
- Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
| | - Suvarna Joshi
- Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
| | - Rajesh Karyakarte
- Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
| | - Aurnab Ghose
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - L S Shashidhara
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, India
| | - Joy Merwin Monteiro
- Department of Earth and Climate Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; Department of Data Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Dhanasekaran Shanmugam
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Anu Raghunathan
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India.
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
| |
Collapse
|
6
|
Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [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: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
Collapse
Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Mondeali M, Etemadi A, Barkhordari K, Mobini Kesheh M, Shavandi S, Bahavar A, Tabatabaie FH, Mahmoudi Gomari M, Modarressi MH. The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: An in-silico perspective. J Cell Biochem 2023; 124:308-319. [PMID: 36609701 DOI: 10.1002/jcb.30367] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023]
Abstract
The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the recent variants, is located in the RBD. Today's computational approaches in biology, especially during the SARS-CoV-2 pandemic, assist researchers in predicting a protein's behavior in contact with other proteins in more detail. In this study, we investigated the interactions of the S477N-hACE2 in silico to find the impact of this mutation on its binding affinity for ACE2 and immunity responses using dynamics simulation, protein-protein docking, and immunoinformatics methods. Our computational analysis revealed an increased binding affinity of N477 for ACE2. Four new hydrogen and hydrophobic bonds in the mutant RBD-ACE2 were formed (with S19 and Q24 of ACE2), which do not exist in the wild type. Also, the protein spike structure in this mutation was associated with an increase in stabilization and a decrease in its fluctuations at the atomic level. N477 mutation can be considered as the cause of increased escape from the immune system through MHC-II.
Collapse
Affiliation(s)
- Mozhgan Mondeali
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Etemadi
- Medical Biotechnology Department, School of Advanced Technologies in MedicineSchool of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Khabat Barkhordari
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Shavandi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Atefeh Bahavar
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad H Modarressi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
9
|
Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
Collapse
Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
10
|
Xu R, Wang W, Zhang W. As the SARS-CoV-2 virus evolves, should Omicron subvariant BA.2 be subjected to quarantine, or should we learn to live with it? Front Public Health 2022; 10:1039123. [PMID: 36504951 PMCID: PMC9730036 DOI: 10.3389/fpubh.2022.1039123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
It has been nearly 35 months since the COVID-19 outbreak. The pathogen SARS-CoV-2 has evolved into several variants. Among them, Omicron is the fifth variant of concern which have rapidly spread globally during the past 8 months. Omicron variant shows different characteristics from previous variants, which is highly infectious, highly transmissible, minimally pathogenic, vaccine and antibody tolerant; however, it is less likely to cause severe illness, resulting in fewer deaths. Omicron has evolved into five main lineages, including BA.1, BA.2, BA.3, BA.4, and BA.5. Before BA.5, Omicron BA.2 sublineage was the dominant strain all over the world for several months. The experience of prevention and treatment against BA.2 is worth studying and learning for overcoming other Omicron subvariants. Although the Omicron subvariant BA.2 is significantly less severe than that caused by ancestral strains, it is still far more dangerous than influenza, and its long-term sequelae are unknown. Effective treatments are currently limited; therefore, effective defense may be the key to controlling the epidemic today, rather than just "living with" the virus.
Collapse
Affiliation(s)
- Ren Xu
- Pulmonary and Critical Care Medicine Department, First Hospital of Jilin University, Changchun, China
| | - Wanning Wang
- Nephrology Department, First Hospital of Jilin University, Changchun, China
| | - Wenlong Zhang
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, China
| |
Collapse
|
11
|
Halfmann PJ, Minor NR, Haddock III LA, Maddox R, Moreno GK, Braun KM, Baker DA, Riemersa KK, Prasad A, Alman KJ, Lambert MC, Florek K, Bateman A, Westergaard R, Safdar N, Andes DR, Kawaoka Y, Fida M, Yao JD, Friedrich TC, O’Connor DH. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual. Virus Evol 2022; 9:veac104. [PMID: 37692895 PMCID: PMC10491860 DOI: 10.1093/ve/veac104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 09/12/2023] Open
Abstract
Prolonged infections in immunocompromised individuals may be a source for novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population.
Collapse
Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Nicholas R Minor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Luis A Haddock III
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Robert Maddox
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kasen K Riemersa
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Ankur Prasad
- Division of Allergy, Pulmonary and Critical Care Medicine, School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705-2281, USA
| | - Kirsten J Alman
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Matthew C Lambert
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Allen Bateman
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Ryan Westergaard
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Nasia Safdar
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - David R Andes
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Madiha Fida
- Division of Infectious Diseases, Mayo Clinic, 200 First St. SW, Rochester, Rochester, Minnesota 55905, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| |
Collapse
|
12
|
Bobrin V, Chen SPR, Grandes Reyes CF, Smith T, Purcell DFJ, Armstrong J, McAuley JL, Monteiro MJ. Surface Inactivation of Highly Mutated SARS-CoV-2 Variants of Concern: Alpha, Delta, and Omicron. Biomacromolecules 2022; 23:3960-3967. [PMID: 35994316 PMCID: PMC9454278 DOI: 10.1021/acs.biomac.2c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/04/2022] [Indexed: 11/28/2022]
Abstract
Continued SARS-CoV-2 transmission among the human population has meant the evolution of the virus to produce variants of increased infectiousness and virulence, coined variants of concern (VOCs). The last wave of pandemic infections was driven predominantly by the delta VOC, but because of continued transmission and adaptive mutations, the more highly transmissible omicron variant emerged and is now dominant. However, due to waning immunity and emergence of new variants, vaccines alone cannot control the pandemic. The application of an antiviral coating to high-touch surfaces and physical barriers such as masks are an effective means to inactivate the virus and their spread. Here, we demonstrate an environmentally friendly water-borne polymer coating that can completely inactivate SARS-CoV-2 independent of the infectious variant. The polymer was designed to target the highly glycosylated spike protein on the virion surface and inactivate the virion by disruption of the viral membrane through a nano-mechanical process. Our findings show that, even with low amounts of coating on the surface (1 g/m2), inactivation of alpha, delta, and omicron VOCs and degradation of their viral genome were complete. Furthermore, our data shows that the polymer induces little to no skin sensitization in mice and is non-toxic upon oral ingestion in rats. We anticipate that our transparent polymer coating can be applied to face masks and many other surfaces to capture and inactivate the virus, aiding in the reduction of SARS-CoV-2 transmission and evolution of new variants of concern.
Collapse
Affiliation(s)
- Valentin
A. Bobrin
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sung-Po R. Chen
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Smith
- Department
of Microbiology and Immunology, The University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Damian F. J. Purcell
- Department
of Microbiology and Immunology, The University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jason Armstrong
- Boeing
Research and Technology Australia, Level 2, Hawken building (50), Staff House Rd, Brisbane, QLD 4072, Australia
| | - Julie L. McAuley
- Department
of Microbiology and Immunology, The University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Michael J. Monteiro
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
13
|
Caputo E, Mandrich L. Structural and Phylogenetic Analysis of SARS-CoV-2 Spike Glycoprotein from the Most Widespread Variants. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081245. [PMID: 36013424 PMCID: PMC9410480 DOI: 10.3390/life12081245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The SARS-CoV-2 pandemic, reported for the first time at the end of 2019 in the city of Wuhan (China), has spread worldwide in three years; it lead to the infection of more than 500 million people and about six million dead. SARS-CoV-2 has proved to be very dangerous for human health. Therefore, several efforts have been made in studying this virus. In a short time, about one year, the mechanisms of SARS-CoV-2 infection and duplication and its physiological effect on human have been pointed out. Moreover, different vaccines against it have been developed and commercialized. To date, more than 11 billion doses have been inoculated all over the world. Since the beginning of the pandemic, SARS-CoV-2 has evolved; it has done so by accumulating mutations in the genome, generating new virus versions showing different characteristics, and which have replaced the pre-existing variants. In general, it has been observed that the new variants show an increased infectivity and cause milder symptoms. The latest isolated Omicron variants contain more than 50 mutations in the whole genome and show an infectivity 10-folds higher compared to the wild-type strain. Here, we analyse the SARS-CoV-2 variants from a phylogenetic point of view and hypothesize a future scenario for SARS-CoV-2, by following its evolution to date.
Collapse
Affiliation(s)
- Emilia Caputo
- Institute of Genetics and Biophysics-IGB-CNR, “A. Buzzati-Traverso”, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems-IRET-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
- Correspondence:
| |
Collapse
|
14
|
Tiecco G, Storti S, Arsuffi S, Degli Antoni M, Focà E, Castelli F, Quiros-Roldan E. Omicron BA.2 Lineage, the "Stealth" Variant: Is It Truly a Silent Epidemic? A Literature Review. Int J Mol Sci 2022; 23:7315. [PMID: 35806320 PMCID: PMC9266794 DOI: 10.3390/ijms23137315] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 12/29/2022] Open
Abstract
The epidemic curve of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is silently rising again. Worldwide, the dominant SARS-CoV-2 variant of concern (VOC) is Omicron, and its virological characteristics, such as transmissibility, pathogenicity, and resistance to both vaccine- and infection-induced immunity as well as antiviral drugs, are an urgent public health concern. The Omicron variant has five major sub-lineages; as of February 2022, the BA.2 lineage has been detected in several European and Asian countries, becoming the predominant variant and the real antagonist of the ongoing surge. Hence, although global attention is currently focused on dramatic, historically significant events and the multi-country monkeypox outbreak, this new epidemic is unlikely to fade away in silence. Many aspects of this lineage are still unclear and controversial, but its apparent replication advantage and higher transmissibility, as well as its ability to escape neutralizing antibodies induced by vaccination and previous infection, are rising global concerns. Herein, we review the latest publications and the most recent available literature on the BA.2 lineage of the Omicron variant.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Eugenia Quiros-Roldan
- Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, ASST Spedali Civili di Brescia, University of Brescia, 25123 Brescia, Italy; (G.T.); (S.S.); (S.A.); (M.D.A.); (E.F.); (F.C.)
| |
Collapse
|
15
|
Fan X, Lu S, Bai L, Liu H, Fu J, Jin X, He Y, Lu J, Dong X. Preliminary Study of the Protectiveness of Vaccination Against the COVID-19 in the Outbreak of VOC Omicron BA.2 - Jilin City, Jilin Province, China, March 3-April 12, 2022. China CDC Wkly 2022; 4:377-380. [PMID: 35686205 PMCID: PMC9167613 DOI: 10.46234/ccdcw2022.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 04/21/2022] [Indexed: 11/14/2022] Open
Abstract
What is already known about this topic? An outbreak of coronavirus disease 2019 (COVID-19) of Omicron BA.2 emerged in Jilin City since March 3, 2022, which involved in 27,036 cases by April 12. The vaccination program with inactivated COVID-19 vaccines has been implemented since the beginning of 2021. What is added by this report? The incidences of moderate, severe, and critical cases in the whole population of the group of 0+1 dose were 1.82-, 9.49-, and 3.85-fold higher than those in the group of 2 doses, and 5.03-, 44.47-, and ∞-fold higher than those received 3 doses vaccination. For the population ≥60 years, the incidences of moderate, severe, and critical cases in the group of 0+1 dose were 29.92, 9.62, and 4.27 per 100,000, showing 4.13-, 43.72-, and 4.85-fold higher than 2 doses, as well as 13.28-, 22.37-, and ∞-fold higher than 3 doses. What are the implications for public health practice? The incidences of each type of COVID-19 in the population who were fully vaccinated or booster vaccinated in Jilin City were significantly lower than those who were unvaccinated and/or partially vaccinated. Booster vaccination with homologous inactivated vaccines induces stronger protectiveness for COVID-19 caused by variant of concern (VOC) Omicron.
Collapse
Affiliation(s)
- Xuebin Fan
- Jilin Municipal Center for Disease Control and Prevention, Jilin City, Jilin Province, China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lu Bai
- Jilin Municipal Center for Disease Control and Prevention, Jilin City, Jilin Province, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junshao Fu
- Jilin Municipal Center for Disease Control and Prevention, Jilin City, Jilin Province, China
| | - Xiaoxun Jin
- Jilin Municipal Center for Disease Control and Prevention, Jilin City, Jilin Province, China
| | - Yulong He
- Tongliao Municipal Center for Disease Control and Prevention, Tongliao City, Inner Mongolia Autonomous Region, China
| | - Jinxing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoping Dong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan City, Hubei Province, China.,China Academy of Chinese Medical Sciences, Beijing, China.,Shanghai Institute of Infectious Disease and Biosafety, Shanghai, China
| |
Collapse
|