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Napit R, Ngono AE, Mihindukulasuriya KA, Pradhan A, Khadka B, Shrestha S, Droit L, Paredes A, Karki L, Khatiwada R, Tamang M, Chalise BS, Rawal M, Jha B, Wang D, Handley SA, Shresta S, Manandhar KD. Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597008. [PMID: 38895410 PMCID: PMC11185532 DOI: 10.1101/2024.06.02.597008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. Methods and Results During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1 + participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. Conclusion These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
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Khalid Z, Muhammad J, Ali H, Rana MS, Usman M, Alam MM, Ullah R, Ullah A, Umair M, Ahmad A, Salman M, Ikram A, Khan A, Bari A. Insights into measles virus: Serological surveillance and molecular characterization. J Infect Public Health 2024; 17:994-1000. [PMID: 38636313 DOI: 10.1016/j.jiph.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Measles has been a significant public health concern in Pakistan, especially in the Khyber Pakhtunkhwa (KPK) province, where sporadic and silent epidemics continue to challenge existing control measures. This study aimed to estimate the prevalence and investigate the molecular epidemiology of the measles virus (MeV) in KPK and explore the vaccination status among the suspected individuals. METHODS A cross-sectional study was conducted between February and October 2021. A total of 336 suspected measles cases from the study population were analyzed for IgM antibodies using Enzyme-Linked Immunosorbent Assay (ELISA). Throat swabs were randomly collected from a subset of positive cases for molecular analysis. Phylogenetic analysis of MeV isolates was performed using the neighbor-joining method. The vaccination status of individuals was also recorded. RESULTS Among the suspected participants, 61.0% (205/336) were ELISA positive for IgM antibodies, with a higher prevalence in males (64.17%) compared to females (57.04%). The majority of cases (36.0%) were observed in infants and toddlers, consistent with previous reports. The majority of IgM-positive cases (71.7%) had not received any dose of measles vaccine, highlighting gaps in vaccine coverage and the need for improved immunization programs. Genetic analysis revealed that all MeV isolates belonged to the B3 genotype, with minor genetic variations from previously reported variants in the region. CONCLUSION This study provides valuable insights into the genetic epidemiology of the MeV in KPK, Pakistan. The high incidence of measles infection among unvaccinated individuals highlights the urgency of raising awareness about vaccine importance and strengthening routine immunization programs.
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Affiliation(s)
- Zainab Khalid
- Department of Microbiology, The University of Haripur, Haripur, KP 22610, Pakistan.
| | - Javed Muhammad
- Department of Microbiology, The University of Haripur, Haripur, KP 22610, Pakistan.
| | - Hina Ali
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 200240, China.
| | | | - Muhammad Usman
- National Institute of Health, Islamabad 45500, Pakistan.
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh, Saudi Arabia.
| | - Arif Ullah
- Department of Microbiology, The University of Haripur, Haripur, KP 22610, Pakistan.
| | - Massab Umair
- National Institute of Health, Islamabad 45500, Pakistan.
| | - Ashfaq Ahmad
- National Institute of Health, Islamabad 45500, Pakistan.
| | | | - Aamer Ikram
- National Institute of Health, Islamabad 45500, Pakistan.
| | - Amjad Khan
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, KP, Pakistan; The University of Kentucky, KY 40506, United States.
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King Saud University, Riyadh, Saudi Arabia.
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Anguinze RS, Touré A, Cissé F, Grayo S, Troupin C, Tordo N, Kouamou E, Roques P. Viral etiology of measles-like rash in Guinean children during the COVID epidemic in 2022. J Med Virol 2024; 96:e29437. [PMID: 38305059 DOI: 10.1002/jmv.29437] [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: 09/06/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024]
Abstract
Covid-19 in West Africa masked outbreaks of vaccine-preventable diseases such as the measles epidemic in children in Guinea in 2021-2022 characterized by a lack of confirmation of suspected clinical cases. During weeks 13-22 of 2022, saliva samples were collected from 213 children (3-60 months old) with measles-like symptoms within the St Gabriel dispensary in Conakry. Samples were processed in Virus Transport Medium (VTM) and tested on the same day by triplex reverse transcriptase -real-time polymerase chain reaction for Measles, Rubella and RNaseP. Samples were also tested for HHV6 and Parvovirus B19, viruses causing clinical signs similar to measles. We confirmed 146 (68.5%) measles cases, 27 (12.7%) rubella, 5 (2.3%) double-positive measles-rubella, 35 (16.4%) HHV-6 and 8 (3.75%) Parvovirus B19. To test the assay's robustness, 27 samples were kept at 26-30°C. Measles and rubella were still detected after 7 days at 26-30°C, and after 21 days measles and rubella were still detectable in all samples but one. Sequencing indicated the circulation of the B3 measles genotype, as expected in West Africa. This study highlights the robustness of the measles/rubella diagnostic test on saliva samples stored in VTM. The high level of rubella detection questioned the single valence measles vaccination strategy.
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Affiliation(s)
| | | | | | | | - Cécile Troupin
- Medical Virology and Rabies group, Institut Pasteur du Laos, Vientiane, Laos
| | - Noël Tordo
- Institut Pasteur de Guinée, Conakry, Guinea
| | | | - Pierre Roques
- Institut Pasteur de Guinée, Conakry, Guinea
- CEA, Institut François Jacob, Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Le Kremlin Bicêtre, France
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Zubach V, Schulz H, Kim K, Hole D, Severini A, Hiebert J. Genome sequence of a measles virus strain with a novel loss of stop codon mutation in the phosphoprotein gene. Microbiol Resour Announc 2024; 13:e0083323. [PMID: 38038439 DOI: 10.1128/mra.00833-23] [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: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 12/02/2023] Open
Abstract
Measles virus genotype B3 coding-complete genome sequence from a 2019 case showed a novel mutation in the phosphoprotein (P) gene that abrogates the established stop codon. A downstream stop codon has been identified, resulting in a putative P that would be 19 amino acids longer than wild type.
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Affiliation(s)
- Vanessa Zubach
- Viral Exanthemata and STD Section, National Microbiology Laboratory, Public Health Agency of Canada, JC Wilt infectious Diseases Research Center , Winnipeg, Manitoba, Canada
| | - Helene Schulz
- Viral Exanthemata and STD Section, National Microbiology Laboratory, Public Health Agency of Canada, JC Wilt infectious Diseases Research Center , Winnipeg, Manitoba, Canada
| | - Kihun Kim
- Department of Microbiology, University of Manitoba , Winnipeg, Manitoba, Canada
| | - Darian Hole
- Computational and Operational Genomics Section, National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg, Manitoba, Canada
| | - Alberto Severini
- Viral Exanthemata and STD Section, National Microbiology Laboratory, Public Health Agency of Canada, JC Wilt infectious Diseases Research Center , Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba , Winnipeg, Manitoba, Canada
| | - Joanne Hiebert
- Viral Exanthemata and STD Section, National Microbiology Laboratory, Public Health Agency of Canada, JC Wilt infectious Diseases Research Center , Winnipeg, Manitoba, Canada
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