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Paião HGO, da Costa AC, Ferreira NE, Honorato L, dos Santos BM, de Matos MLM, Domingues RB, Senne CA, Lopes ADO, de Paula VS, Witkin SS, Tozetto-Mendoza TR, Mendes-Correa MC. Phylogenetic Analysis of Varicella-Zoster Virus in Cerebrospinal Fluid from Individuals with Acute Central Nervous System Infection: An Exploratory Study. Viruses 2025; 17:286. [PMID: 40007041 PMCID: PMC11860453 DOI: 10.3390/v17020286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 02/15/2025] [Accepted: 02/16/2025] [Indexed: 02/27/2025] Open
Abstract
BACKGROUND There is scarce information on Varicella-Zoster virus genetic variability in individuals with acute central nervous system infection in Brazil. The objective of this study was the molecular characterization of Varicella-Zoster virus isolates in cerebrospinal fluid from individuals with acute central nervous system infection. METHODS Cerebrospinal fluid samples were collected from individuals evaluated in emergency and community healthcare services in São Paulo, Brazil. Varicella-Zoster virus identification was performed using commercial platforms Biofire-FilmArray Meningitis/Encephalitis (BioMérieux, Craponne, France) and XGEN-UMLTI-N9® (Mobius Life, Pinhais, Brazil). Positive samples were further characterized as wild-type or vaccine-strain by a real-time polymerase chain reaction assay that targeted a single nucleotide polymorphism in open reading frame 62. We also estimated the mean genetic distance and phylogenetic reconstruction based on open reading frames 22, 38, 54, and 62 in relation to sequences of intercontinentally circulating Varicella-Zoster virus isolates. RESULTS Among the 600 cerebrospinal fluid samples, we identified Varicella-Zoster virus in 30 (5%) samples. None were positive for the vaccine-strain. Twelve samples were sequenced and phylogenetically classified into Clades 1 (41.7%), 2 (25%), 3 (8.3%), 5 (16.7%), or 6 (8%). CONCLUSION Enhanced characterization of circulating Varicella-Zoster virus Clades in Brazil identified previously unreported Clades 2 and 6 as well as three other Clades disseminated intercontinentally. These findings reinforce the importance of Varicella-Zoster virus molecular surveillance in cerebrospinal fluid.
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Affiliation(s)
- Heuder G. O. Paião
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
- Departamento de Infectologia e Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Arnaldo, 455, São Paulo 01246-903, Brazil
| | - Antônio C. da Costa
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
| | - Noely E. Ferreira
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
- Departamento de Infectologia e Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Arnaldo, 455, São Paulo 01246-903, Brazil
| | - Layla Honorato
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
- Departamento de Infectologia e Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Arnaldo, 455, São Paulo 01246-903, Brazil
| | - Bianca M. dos Santos
- Serviço de Cuidados Paliativos do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, R. Cotoxó, 1142, São Paulo 05021-001, Brazil;
| | - Maria L. M. de Matos
- Faculdade de Medicina, Universidade de São Caetano do Sul, R. Santo Antônio, 50, São Caetano do Sul 09521-160, Brazil;
| | - Renan B. Domingues
- Laboratório Senne Liquor, Av. Angélica, 2071, São Paulo 01239-030, Brazil; (R.B.D.); (C.A.S.)
| | - Carlos A. Senne
- Laboratório Senne Liquor, Av. Angélica, 2071, São Paulo 01239-030, Brazil; (R.B.D.); (C.A.S.)
| | - Amanda de O. Lopes
- Laboratório de Virologia Molecular do Instituto Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Brazil; (A.d.O.L.); (V.S.d.P.)
| | - Vanessa S. de Paula
- Laboratório de Virologia Molecular do Instituto Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Brazil; (A.d.O.L.); (V.S.d.P.)
| | - Steven S. Witkin
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
- Departamento de Infectologia e Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Arnaldo, 455, São Paulo 01246-903, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10001, USA
| | - Tânia R. Tozetto-Mendoza
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
- Departamento de Infectologia e Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Arnaldo, 455, São Paulo 01246-903, Brazil
| | - Maria Cássia Mendes-Correa
- Laboratório de Virologia (LIM52), Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (S.S.W.); (T.R.T.-M.); (M.C.M.-C.)
- Departamento de Infectologia e Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Arnaldo, 455, São Paulo 01246-903, Brazil
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Hanif S, Johnson S, Siddique M, Salman M, Rana MS, Sharif S, Faryal R. A hidden dilemma; post COVID-19 first detection of Varicella zoster M4 genotype from Pakistan. Acta Trop 2024; 253:107162. [PMID: 38428628 DOI: 10.1016/j.actatropica.2024.107162] [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: 10/20/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVES During the COVID-19 pandemic, the risk of childhood infectious diseases was increased. Post-COVID-19 escalation of chickenpox cases, becoming an emerging public health concern. Thus, the study was designed to compare chickenpox prevalence and Varicella zoster virus (VZV) genotypes circulating before, during, and post-COVID-19 in Pakistan. METHODS A total of 267 lesion specimens collected from tertiary care hospitals, and chickenpox outbreaks from Pakistan were analysed by a two-amplicon approach with phylogenetic analysis. RESULTS Among suspected cases, overall 178/267 were VZV positive. Majority (84.2 %; 150/178) cases were of post-COVID-19 pandemic time. Small outbreaks occurred soon after COVID-19 in Rawalpindi and Islamabad (Pakistan), 40 positive cases out of 178 cases were outbreak cases. There was first time detection of the M4 genotype, which was significantly associated with disease severity (p = 0.0006) and post-COVID-19 chickenpox outbreaks in 2021 (77.9 %; 46/59; p < 0.00001). However, in pre-COVID-19 only M2 genotype was detected. The M2 prevalence varied from 2019 (100 %; 19/19) to 2022 (3.2 %; 3/91). However, the most prevalent strain of 2022 belonged to the M1 genotype (64.8 %; 59/91). CONCLUSION A significant rise in chickenpox cases detected soon after COVID-19 in Pakistan, and oscillation of different VZV genotypes with first time detection of M4 genotype is an alarming situation. This demands further detailed genotypic studies on transmission dynamics of a rare M4 with other genotypes to protect the local population and restrict spread in other regions.
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Affiliation(s)
- Saba Hanif
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Sarah Johnson
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Maryam Siddique
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Public Health, National Institute of Health, Chak Shahzad, Pakistan
| | | | - Shawana Sharif
- Department of Dermatology, Benazir Bhutto Hospital Rawalpindi/Rawalpindi Medical University, Pakistan
| | - Rani Faryal
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.
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Kumar A, Rajan LS, Sabarinath PS K, Shete AM, Sahay RR, Patil DY, Ingole N, K K, Padinakarai AC, GB S, Shastri J, Padukone S, Joshi Y, Patil S, Majumdar T, Verma A, Yemul J, Shende N, Kumari V, Vedpathak P, Sathe S, Gawande P, Yadav PD. First detection of Varicella Zoster Virus clade 9 cases in India during mpox surveillance. Ann Med 2023; 55:2253733. [PMID: 37672487 PMCID: PMC10484040 DOI: 10.1080/07853890.2023.2253733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The multi-country mpox outbreak across the globe has led to the systematic surveillance of mpox cases in India. During the surveillance of mpox, we encountered cases of Varicella Zoster Virus (VZV) in suspected mpox cases amongst children & adults. This study focused on the genomic characterization of VZV in India. METHODS A total of 331 mpox suspected cases were tested for VZV through real-time PCR, and the positive samples were subjected to next-generation sequencing to retrieve the whole genome of VZV using CLC genomics software. Phylogenetic analysis has been done in MEGA 11.0 software to identify circulating clades. RESULT Of the 331 suspected cases, 28 cases with vesicular rashes were found to be positive for VZV. The maximum genome could be retrieved from the clinical specimens of 16 cases with coverage greater than 98% when mapped with reference strain Dumas (NC 001348). The phylogenetic analyses of these sequences determined the circulation of clades 1, 5, and 9 in India. Further, the sequence analysis demonstrated non-synonymous single nucleotide polymorphism (SNPs) among specific ORF of VZV including ORF 14, ORF 22, ORF 36, ORF 37 and ORF 51. Although clade 1 and 5 has been reported earlier, the circulation of clade 9 of VZV has been determined for the first time in India. CONCLUSION Although the circulation of different clades of VZV was reported from India, the presence of clade 9 was detected for the first time during the mpox surveillance.
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Affiliation(s)
- Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Lekshmi S. Rajan
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Deepak Y. Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nayana Ingole
- Virus Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Kaveri K
- King Institute of Preventive Medicine and Research, Chennai, India
| | | | - Shantala GB
- Bangalore Medical College and Research Institute, Bengaluru, India
| | - Jayanthi Shastri
- Virus Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | | | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Ajay Verma
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jyoti Yemul
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nandini Shende
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Vaishnavi Kumari
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pratiksha Vedpathak
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Shubhangi Sathe
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pranita Gawande
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
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