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Senthilazhagan K, Sakthimani S, Kallanja D, Venkataraman S. SARS-CoV-2: analysis of the effects of mutations in non-structural proteins. Arch Virol 2023; 168:186. [PMID: 37344726 DOI: 10.1007/s00705-023-05818-2] [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: 03/06/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
A worldwide pandemic that started in China in late 2019 was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus belonging to the family Coronaviridae. Due to its structural variability and mutability, this virus continues to evolve and pose a major health threat around the world. Its characteristics, such as transmissibility, antigenicity, and resistance to drugs and vaccines, are continually altered through mutations. Examining mutational hotspots and their structural repercussions can thus aid in the development of more-effective vaccinations and treatment plans. In this study, we used full genome sequences of SARS-CoV-2 variants to predict structural changes in viral proteins. These sequences were obtained from the Global Initiative on Sharing Avian Influenza Data (GISAID), and a set of significant mutations were identified in each of the non-structural proteins (NSP1-16) and structural proteins, including the envelope, nucleocapsid, membrane, and spike proteins. The mutations were characterized as stabilizing or destabilizing based on their effect on protein dynamics and stability, and their impact on structure and function was evaluated. Among all of the proteins, NSP6 stands out as especially variable. The results of this study augment our understanding of how mutational events influence virus pathogenicity and evolution.
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Affiliation(s)
- Kavya Senthilazhagan
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Seshagiri Sakthimani
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Deepthi Kallanja
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Sangita Venkataraman
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India.
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Bhattacharya M, Alshammari A, Alharbi M, Dhama K, Lee SS, Chakraborty C. A novel mutation-proof, next-generation vaccine to fight against upcoming SARS-CoV-2 variants and subvariants, designed through AI enabled approaches and tools, along with the machine learning based immune simulation: A vaccine breakthrough. Int J Biol Macromol 2023; 242:124893. [PMID: 37207746 DOI: 10.1016/j.ijbiomac.2023.124893] [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: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023]
Abstract
Emerging SARS-CoV-2 variants and subvariants are great concerns for their significant mutations, which are also responsible for vaccine escape. Therefore, the study was undertaken to develop a mutation-proof, next-generation vaccine to protect against all upcoming SARS-CoV-2 variants. We used advanced computational and bioinformatics approaches to develop a multi-epitopic vaccine, especially the AI model for mutation selection and machine learning (ML) strategies for immune simulation. AI-enabled and the top-ranked antigenic selection approaches were used to select nine mutations from 835 RBD mutations. We selected twelve common antigenic B cell and T cell epitopes (CTL and HTL) containing the nine RBD mutations and joined them with the adjuvants, PADRE sequence, and suitable linkers. The constructs' binding affinity was confirmed through docking with TLR4/MD2 complex and showed significant binding free energy (-96.67 kcal mol-1) with positive binding affinity. Similarly, the calculated eigenvalue (2.428517e-05) from the NMA of the complex reveals proper molecular motion and superior residues' flexibility. Immune simulation shows that the candidate can induce a robust immune response. The designed mutation-proof, multi-epitopic vaccine could be a remarkable candidate for upcoming SARS-CoV-2 variants and subvariants. The study method might guide researchers in developing AI-ML and immunoinformatics-based vaccines for infectious disease.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
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A Comparative Study of the Plasma Chemokine Profile in COVID-19 Patients Infected with Different SARS-CoV-2 Variants. Int J Mol Sci 2022; 23:ijms23169058. [PMID: 36012323 PMCID: PMC9409001 DOI: 10.3390/ijms23169058] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Infection caused by SARS-CoV-2 mostly affects the upper and lower respiratory tracts and causes symptoms ranging from the common cold to pneumonia with acute respiratory distress syndrome. Chemokines are deeply involved in the chemoattraction, proliferation, and activation of immune cells within inflammation. It is crucial to consider that mutations within the virion can potentially affect the clinical course of SARS-CoV-2 infection because disease severity and manifestation vary depending on the genetic variant. Our objective was to measure and assess the different concentrations of chemokines involved in COVID-19 caused by different variants of the virus. METHODS We used the blood plasma of patients infected with different variants of SARS-CoV-2, i.e., the ancestral Wuhan strain and the Alpha, Delta, and Omicron variants. We measured the concentrations of 11 chemokines in the samples: CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL7/MCP-3, CCL11/Eotaxin, CCL22/MDC, CXCL1/GROα, CXCL8/IL-8, CXCL9/MIG, CXCL10/IP-10, and CX3CL1/Fractalkine. RESULTS We noted a statistically significant elevation in the concentrations of CCL2/MCP-1, CXCL8/IL-8, and CXCL1/IP-10 independently of the variant, and a drop in the CCL22/MDC concentrations. CONCLUSIONS The chemokine concentrations varied significantly depending on the viral variant, leading us to infer that mutations in viral proteins play a role in the cellular and molecular mechanisms of immune responses.
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Mendiola-Pastrana IR, López-Ortiz E, Río de la Loza-Zamora JG, González J, Gómez-García A, López-Ortiz G. SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review. Life (Basel) 2022; 12:life12020170. [PMID: 35207458 PMCID: PMC8879159 DOI: 10.3390/life12020170] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. Two databases (PubMed and ScienceDirect) were searched for original articles published from 1 January 2020 to 23 November 2021. The articles that met the selection criteria were appraised according to the Newcastle–Ottawa Quality Assessment Scale. Results: Thirty-three articles were included, involving a total of 253,209 patients and 188,944 partial or complete SARS-CoV-2 sequences. The most reported SARS-CoV-2 variants showed changes in the spike protein, N protein, RdRp and NSP3. In 28 scenarios, SARS-CoV-2 variants were found to be associated with a mild to severe or even fatal clinical outcome, 15 articles reported such association to be statistically significant. Adjustments in eight of them were made for age, sex and other covariates. Conclusions: SARS-CoV-2 variants can potentially have an impact on clinical outcomes; future studies focused on this topic should consider several covariates that influence the clinical course of the disease.
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Affiliation(s)
- Indira R. Mendiola-Pastrana
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - Eduardo López-Ortiz
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - José G. Río de la Loza-Zamora
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - James González
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico;
| | - Anel Gómez-García
- Centro de Investigación Biomédica de Michoacán, Instituto Mexicano del Seguro Social, Morelia 58351, Mexico;
| | - Geovani López-Ortiz
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
- Correspondence:
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Rahkmawati NA, Akbar A, Adhilaksono B, Baharuddin F, Hidayat R. Indonesia COVID-19 cases report using Linked Open Data. PROCEDIA COMPUTER SCIENCE 2022; 197:362-369. [PMID: 35043070 PMCID: PMC8756766 DOI: 10.1016/j.procs.2021.12.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Coronavirus disease is a worldwide pandemic. The need for accurate data and information become an important thing in this pandemic situation. In Indonesia, the government provides an official website for displaying COVID-19 spread statistics. However, the data provided does not follow the 5-star open data. As a result, the data is not reusable and integrated easily into another dataset and application. In this paper, we proposed an RDF vocabulary for presenting COVID-19 data in Indonesia. In addition, two queries are presented as an example for using our vocabulary and dataset as part of Linked Open data movement.
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Li G, Zhang L, Xue P. Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105175. [PMID: 34871776 PMCID: PMC8641433 DOI: 10.1016/j.meegid.2021.105175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.
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Affiliation(s)
- Gun Li
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China.
| | - Liang Zhang
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China
| | - Pei Xue
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China
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Rashid F, Suleman M, Shah A, Dzakah EE, Chen S, Wang H, Tang S. Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Front Microbiol 2021; 12:789062. [PMID: 34925297 PMCID: PMC8671833 DOI: 10.3389/fmicb.2021.789062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/29/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made this virus more infectious. Previous studies have confirmed that non-structural protein 13 (NSP13) plays an important role in immune evasion by physically interacting with TANK binding kinase 1 (TBK1) to inhibit IFNβ production. Mutations have been reported in NSP13; hence, in the current study, biophysical and structural modeling methodologies were adapted to dissect the influence of major mutations in NSP13, i.e., P77L, Q88H, D260Y, E341D, and M429I, on its binding to the TBK1 and to escape the human immune system. The results revealed that these mutations significantly affected the binding of NSP13 and TBK1 by altering the hydrogen bonding network and dynamic structural features. The stability, flexibility, and compactness of these mutants displayed different dynamic features, which are the basis for immune evasion. Moreover, the binding was further validated using the MM/GBSA approach, revealing that these mutations have higher binding energies than the wild-type (WT) NSP13 protein. These findings thus justify the basis of stronger interactions and evasion for these NSP13 mutants. In conclusion, the current findings explored the key features of the NSP13 WT and its mutant complexes, which can be used to design structure-based inhibitors against the SARS-CoV-2 new variants to rescue the host immune system.
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Affiliation(s)
- Farooq Rashid
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Mingora, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Dir, Pakistan
| | - Emmanuel Enoch Dzakah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Shuyi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shixing Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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Pattnaik B, Suresh KP, Sridevi R, Yadav MP, Shivamallu C, Kollur SP, Dharmashekar C, Patil SS. QUASISPECIES FEATURE IN SARS-CoV-2. JOURNAL OF EXPERIMENTAL BIOLOGY AND AGRICULTURAL SCIENCES 2021; 9:591-597. [DOI: 10.18006/2021.9(5).591.597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Since the identification of the SARS-CoV-2, genus Beta- Coronavirus, in January 2020, the virus quickly spread in less than 3 months to all continents with a susceptible human population of about a 7.9billion, and still in active circulation. In the process, it has accumulated mutations leading to genetic diversity. Regular emergence of variants of concern/significance in different ecology shows genetic heterogeneity in the base population of SARS-CoV-2 that is continuously expanding with the passage of the virus in the vast susceptible human population. Natural selection of mutant occurs frequently in a positive sense (+) single-stranded (ss) RNA virus upon replication in the host. The Pressure of sub-optimal levels of virus-neutralizing antibodies and also innate immunity influence the process of genetic/ antigenic selection. The fittest of the mutants, that could be more than one, propagate and emerge as variants. The existence of different lineages, clades, and strains, as well as genetic heterogeneity of plaque purified virus population, justifies SARS-CoV-2 as ‘Quasispecies’ that refers to swarms of mutant sequences generated during replication of the viral genome, and all mutant sequences may not lead to virion. Viruses having a quasispecies nature may end up with progressive antigenic changes leading to antigenic plurality that is driven by ecology, and this phenomenon challenges vaccination-based control programs.
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Dao TL, Hoang VT, Colson P, Lagier JC, Million M, Raoult D, Levasseur A, Gautret P. SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. J Clin Med 2021; 10:2635. [PMID: 34203844 PMCID: PMC8232800 DOI: 10.3390/jcm10122635] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND We conducted this review to summarize the relation between viral mutation and infectivity of SARS-CoV-2 and also the severity of COVID-19 in vivo and in vitro. METHOD Articles were identified through a literature search until 31 May 2021, in PubMed, Web of Science and Google Scholar. RESULTS Sixty-three studies were included. To date, most studies showed that the viral mutations, especially the D614G variant, correlate with a higher infectivity than the wild-type virus. However, the evidence of the association between viral mutation and severity of the disease is scant. A SARS-CoV-2 variant with a 382-nucleotide deletion was associated with less severe infection in patients. The 11,083G > U mutation was significantly associated with asymptomatic patients. By contrast, ORF1ab 4715L and S protein 614G variants were significantly more frequent in patients from countries where high fatality rates were also reported. The current evidence showed that variants of concern have led to increased infectivity and deteriorating epidemiological situations. However, the relation between this variant and severity of COVID-19 infection was contradictory. CONCLUSION The COVID-19 pandemic continues to spread worldwide. It is necessary to anticipate large clinical cohorts to evaluate the virulence and transmissibility of SARS-CoV-2 mutants.
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Affiliation(s)
- Thi Loi Dao
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France; (T.L.D.); (V.T.H.)
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- Thai Binh University of Medicine and Pharmacy, Thai Binh 410000, Vietnam
| | - Van Thuan Hoang
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France; (T.L.D.); (V.T.H.)
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- Thai Binh University of Medicine and Pharmacy, Thai Binh 410000, Vietnam
| | - Philippe Colson
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Jean Christophe Lagier
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Matthieu Million
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Didier Raoult
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Anthony Levasseur
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Philippe Gautret
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France; (T.L.D.); (V.T.H.)
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
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