Epidemiology and Molecular Characterization of Human Metapneumovirus in Influenza-Like Illness: A Decade of Surveillance in Dibrugarh, Assam (2014-2025).
Aug 2026· Indian Journal of Medical Microbiology· Vol 64, pp.
101241
· 0 citations· 31 references
Medicine
Abstract
Background
Human metapneumovirus (hMPV) is a globally recognized cause of influenza-like illness (ILI), especially among children, but data from Northeast India are limited. This study analyzed epidemiological and molecular features of hMPV detected in Dibrugarh, Assam, over a decade-long surveillance period.
Methods
Between May 2014 and November 2025, 3,597 ILI patients were screened for hMPV at a tertiary hospital in Dibrugarh, Assam. Clinical samples (nasopharyngeal/throat swabs) were tested using multiplex respiratory panels and TaqMan-based real-time RT-PCR. Partial sequencing of the G gene was performed by Sanger sequencing, followed by phylogenetic and glycosylation analyses using MEGA 11, NetNGlyc, and NetOGlyc tools. Statistical analysis was done using SPSS v26.
Results
Overall, hMPV prevalence was 3.1% (112/3597), significantly higher among children aged <5 years than older individuals (3.9% vs. 1.3%; p = 0.003). hMPV activity exhibited marked winter seasonality, with significantly higher positivity during the colder months (5.6% vs. 0.8%; p < 0.001). Phylogenetic analysis demonstrated the circulation of A2.2.1 (A2b1), A2.2.2 (A2b2), and B2 lineages in Assam. The two 2025 A2.2.2 strains harbored the characteristic 111-nucleotide G-gene duplication, while comparative glycosylation analysis revealed lineage-specific variation in predicted N- and O-linked glycosylation profiles.
Conclusion
hMPV remains an important cause of pediatric influenza-like illness in Northeast India, with marked winter seasonality. The detection of A2.2.1, A2.2.2, and B2 lineages, including A2.2.2 strains with the characteristic 111-nucleotide G-gene duplication, underscores the importance of continued molecular surveillance.
Objective: The objectives of this study were to analyze the epidemiological characteristics and whole-genome features of human metapneumovirus (HMPV) among children under 14 years of age in Shijiazhuang during 2022–2025, enrich the whole-genome data of HMPV in China, and provide a basis for further understanding the genetic diversity of the virus and for its prevention, control, and transmission intervention. Methods: A total of 1920 cases of acute respiratory infection were enrolled from three sentinel hospitals in Shijiazhuang. Nucleic acid screening was performed using real-time PCR. Whole-genome sequencing was conducted on 25 positive samples. Phylogenetic trees were constructed using the neighbor-joining method in MEGA, and nucleotide and amino acid sequence identity analyses were performed. Results: The overall detection rate of HMPV from 2022 to 2025 was 4.17%. A prominent peak in winter 2024 was the major distinguishing feature. Temporally, both influenza-like illness (ILI) and severe acute respiratory infection (SARI) cases showed marked seasonality during 2022–2025, with high-incidence periods in December–March and April–June. BLAST alignment and phylogenetic analysis showed that among the 25 sequenced HMPV specimens, genotype B2 was the most frequently identified genotype (13/25, 52%). Conclusions: HMPV epidemics in Shijiazhuang during 2022–2025 mainly occurred in winter–spring and spring–summer, with a notable detection peak in December 2024. The B2 genotype predominated among the sequenced HMPV isolates obtained in this study. The amino acid variation in the G gene was significantly higher than that in other genomic regions.
Human metapneumovirus (hMPV) represents a leading cause of both upper and lower respiratory tract infections among children and adults globally. To investigate the prevalence and evolution of hMPV in the Jiaxing area of China between 2023 and 2025, we screened 3600 pharyngeal swab specimens by real-time PCR, identified 101 positives, and obtained genomic sequences of 48 viral isolates using high-throughput sequencing. Using the sequencing data, we reconstructed a phylogenetic tree and examined amino acid substitutions. The epidemiological analysis revealed an overall hMPV positivity rate of 2.81% (101/3600) in Jiaxing during 2023–2025. Although positive cases were detected across all age groups, they were mainly children, with no significant difference between genders. Regarding seasonal patterns, the peak of hMPV activity occurred predominantly during winter and spring. Over the study period, four genotypes co-circulated, in the order of B2 (41.67%), A2.2.2 (37.50%), A2.2.1 (16.67%), and B1 (4.17%). Further phylogenetic analysis showed that the B1 strains from Jiaxing clustered primarily with those from Beijing, China, while B2, A2.2.1, and A2.2.2 strains were more closely related to strains from the United States and Beijing. Of note, an A2c111nt-dup variant was identified in Jiaxing in 2023. Starting from November 2024, the prevailing genotype transitioned from A2.2.1/A2.2.2 to B2, and B2 emerged as the absolutely dominant strain by 2025. In comparison with earlier circulating strains, several amino acid substitutions have accumulated in current isolates, such as T223N, D280N, I392T, R396Q, S444N, K450R, and T521A in the F protein of B2 strains. Furthermore, the G, L, P, and SH proteins also displayed temporally patterned amino acid replacements. While the biological significance of these mutations is yet to be determined, these results highlight the public health importance of ongoing hMPV surveillance and dynamic monitoring of its genetic evolution.
Ya-Mei Zhou, Yan-Qian Wu, Pei-Yan He et al.· Viruses· 0 citations
BACKGROUND
As part of gastroenteritis surveillance among pediatric patients in Chiang Mai, Thailand, parechovirus A (PeV‑A) was examined in fecal specimens due to its established role as a causative agent of gastroenteritis in children under five years of age.
METHODS
Stool samples were collected from pediatric patients with acute gastroenteritis who admitted to the hospitals in Chiang Mai, Thailand during January 2017 to December 2022. The viral RNA genome was extracted and reverse-transcribed into cDNA, followed by amplification of PeV-A genome by using primers specific for the 5' untranslated region (5'UTR). All positive specimens were further characterized by amplification of VP1 gene, sequencing and comprehensive bioinformatic analysis. The VP1 sequences of PeV-A1 detected in this study (2017-2022) were analyzed alongside those of 2011-2016 reported previously from the same geographical area.
RESULTS
Of 2415 samples, 2.86% (69/2415) were positive for PeV-A. Genotyping showed that PeV-A1 was the predominant genotype, followed by PeV-A4, PeV-A14, PeV-A3, PeV-A6, PeV-A5, PeV-A8, and PeV-A2. The prevalence of PeV-A infection before the COVID-19 pandemic (2017-2019) was significantly higher than during the pandemic (2020-2022) (OR, 2.96; 95% CI: 1.54-5.69). Phylogenetic analysis revealed the presence of clades PeV-A1a and PeV-A1b. Several amino acid substitutions were identified relative to the prototype Harris strain, but these changes were conserved within clades. Selection pressure analysis detected one positively selected site at amino acid position 627 and 162 negatively selected sites (p < 0.05). The overall evolutionary rate of PeV-A1 was estimated at 1.49 × 10⁻⁴ substitutions/site/year with PeV-A1b evolving faster than PeV-A1a.
CONCLUSION
Despite genetic diversity, PeV-A1 strains remained locally established in Chiang Mai, Thailand for more than a decade. The conserved characteristics and evolutionary patterns of PeV-A1 may contribute to its sustainable predominance.
Rungnapa Malasao, P. Khamrin, K. Kumthip et al.· Journal of Infection and Pub...· 0 citations
The detection of NDV sequences in a febrile paediatric patient in the Colombian–Venezuelan border showed the importance of integrating metagenomic diagnostics and One Health surveillance strategies for the early detection of potential emerging zoonotic viruses.
M. Carrillo-Hernández, Lucy Jaimes, K. Ciuoderis et al.· Open Veterinary Journal· 0 citations
Influenza D virus (IDV) is an emerging Orthomyxovirus primarily associated with cattle and increasingly recognized as a pathogen of veterinary and zoonotic relevance. Despite growing evidence of its circulation across Asia, Europe, and North America, no data have previously been available from Kazakhstan or Central Asia. This study investigated the presence of IDV in domestic livestock samples collected during active surveillance between 2023 and 2026. A total of 867 biological samples were obtained from cattle (n = 611), camels (n = 175), Maral Deer (n = 51), and pigs (n = 30) across multiple regions of Kazakhstan. Viral RNA was screened by reverse transcription polymerase chain reaction (RT-PCR) targeting the HEF, PB1, PB2, and P3 genes using a newly designed primer panel. Positive amplicons were subjected to Sanger sequencing and phylogenetic analysis. IDV RNA was detected in 11 animals, corresponding to an overall prevalence of 1.27%. Positive samples were identified in several geographically distinct regions, indicating wider circulation than previously recognized. Complete HEF gene sequences were successfully obtained from two representative cattle strains, designated D/bovine/Zhetysu/KAZ/678/2025 and D/bovine/Zhetysu/KAZ/680/2025. Phylogenetic analysis demonstrated that both strains clustered within the D/Yama2019 lineage and shared >98.83% nucleotide identity with contemporary Asian strains. To our knowledge, this is the first report of IDV detection in Kazakhstan. These findings expand the known geographic range of IDV and suggest possible transboundary transmission routes across Central Asia. Continued molecular surveillance is warranted to clarify epidemiology, host range, and potential economic impact.
Yermukhammet Kassymbekov, T. Sabyrzhan, S.Sh. Nuralibekov et al.· Frontiers in Veterinary Scie...· 0 citations
BACKGROUND
Diphtheria remains endemic in Pakistan with cases increasing following the COVID-19 pandemic despite on-going vaccination programs. This study analyzes the genomic diversity, virulence and antimicrobial resistance patterns of pharyngeal diphtheria strains collected during the Karachi outbreak.
METHODS
C. diphtheriae isolates from a tertiary care hospital laboratory in Karachi (August 2023- October 2024) were included. Antimicrobial susceptibility testing and whole-genome sequencing of phenotypically confirmed isolates was performed. Phylogenetic and bioinformatics analysis was done using diphtOscan and AMRfinderPlus tools.
RESULTS
A total of 47 pharyngeal C. diphtheriae isolates were included. Median age of patients was 7 years and male to female ratio was 1.6:1. The tox gene was present in 89.4% of isolates, while only 29% (n=13/45) demonstrated toxin production. Genomic analysis identified ten sequence types; ST384 and ST698 were most prevalent. Phenotypically, 34% (n=16) were resistant to both erythromycin and penicillin and 49% (n=23) were multi-drug resistant. The most prevalent resistance genes were sul1 (100%), ermX (76.6%) and pbp2m (51.1%).
CONCLUSION
Circulation of diverse C. diphtheriae strains with alarming antimicrobial resistance underscores the need for genomic surveillance to evaluate transmission trends. We further highlight Elek test limitations in detecting toxin production and the need for improved diagnostics in low- and middle-income countries.
Sobia Khan, S. Irfan, J. Ashraf et al.· International Journal of Inf...· 0 citations
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