Sep 2026· Journal of Clinical and Diagnostic Research· 0 citations
TL;DR
Tracking SARS-CoV-2 variants revealed the predominance of the JN.1 sublineage of Omicron with generally mild symptoms, highlighting the need for robust, ongoing genomic surveillance integrated with epidemiological data to enable early detection of emerging variants and strengthen control strategies.
Abstract
Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) shows continuous genetic variation, resulting in the emergence of multiple viral lineages worldwide. These mutations can influence viral transmissibility, pathogenic potential, and immune escape, resulting in changed disease pattern. Genomic surveillance allows systematic tracking of viral evolution and circulating variants; thus, monitoring is essential for informed public health planning and clinical preparedness.
Aim: To detect the emergence of variants of Omicron lineage in the hilly state of Himachal Pradesh, India.
Materials and Methods: This cross-sectional study was conducted at the Shri Lal Bahadur Shastri Medical College, Mandi, Himachal Pradesh, India from January 2024 to June 2024. All the SARS-CoV-2 positive samples with Ct value ≤30 received across the state from the four Virus Research and Diagnostic Laboratories (VRDLs) of the state were included. Ribonucleic acid (RNA) extraction was performed using the Q-Line Molecular Viral RNA Extraction Kit, and Whole Genome Sequencing (WGS) was carried out on the Oxford Nanopore MinION platform. Consensus sequences were generated using Medaka and Nanopolish for variant identification and phylogenetic analysis. All demographic and clinical data, like age, sex, clinical presentation, and vaccination status, were recorded and tabulated in Microsoft Excel 2021. The study focused on genomic sequences generated, and the data were presented as numbers and percentages.
Results: A total of 30 SARS-CoV-2 positive samples were received. Among SARS-CoV-2 positive cases, adult females constituted the highest proportion, 17 (56.7%), with most patients aged 19-60 years, 17 (56.7%), and the majority of samples originating from Shimla, 11 (36.7%). The study identified JN.1 sublineages in 19 (63.3%) as the predominant cause of infection. Most cases, 20 (66.7%) reported to the outpatient department. Mild symptoms such as fever and cough were seen in 7 (35%) cases. Even though 23 (76.7%) of cases were vaccinated with the COVID-19 vaccine, 10 (33.3%) required admissions. However, no mortality was reported.
Conclusion: Tracking SARS-CoV-2 variants revealed the predominance of the JN.1 sublineage of Omicron with generally mild symptoms. Continuous genetic evolution of SARS CoV-2 highlights the need for robust, ongoing genomic surveillance integrated with epidemiological data to enable early detection of emerging variants and strengthen control strategies.
The identification of a novel A2–B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses, and underscores the importance of whole-genome surveillance for accurate viral characterization.
A. Fall, C. Morris, O. Elgazayerly et al.· Microbiology spectrum· 0 citations
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.
B. Borkakoty, N. Bali, Aniruddha Jakharia et al.· Indian Journal of Medical Mi...· 0 citations
Background:
Newcastle disease virus (NDV), is a major avian pathogen with recognized zoonotic potential. Human infections are rare and typically mild and occur mainly in individuals with direct poultry exposure. The implementation of metagenomic sequencing in febrile illness surveillance has increased the detection of unexpected zoonotic agents.
Aim:
To describe the molecular detection and phylogenetic characterization of NDV in a cohort of pediatric patients with undifferentiated acute febrile illness (UAFI) in Colombia.
Methods:
During a 2021 cross-sectional surveillance study at the Colombian–Venezuelan border, serum samples from patients clinically suspected of having dengue were screened by qPCR for dengue, chikungunya, and Zika viruses. Arbovirus-negative samples were pooled and analysed by metagenomic next-generation sequencing using an Illumina MiSeq platform. Viral genome identification was performed with the Genome Detective and CZ ID pipelines. Phylogenetic analyses of the fusion (F) and hemagglutinin-neuraminidase (HN) genes were conducted using maximum likelihood methods.
Results:
NDV sequences were identified in one serum pool sample. Phylogenetic analysis revealed that the virus was within genotype II, clustering closely with the lentogenic LaSota strain. Epidemiological analysis revealed probable exposure to backyard poultry environment among an 8-year-old child residing in a rural area. The clinical presentation was mild and self-limiting. Local veterinary surveillance records confirmed low-virulence NDV outbreaks in the same geographic region.
Conclusion:
In this report, we showed the detection of NDV sequences in a febrile paediatric patient in the Colombian–Venezuelan border. These findings underscore 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
Introduction several studies have shown the evolution of SARS-CoV-2 between 2020 and 2023 in Guinea. This study provides updated information on the circulation dynamics of SARS-CoV-2 from 2024 to 2025 and the variants circulating in Guinea. Methods as part of the integrated influenza/COVID-19 sentinel surveillance program, 2423 nasopharyngeal samples were analysed using RT-PCR, and those positive for SARS-CoV-2 were sequenced using the Illumina COVIDSeq Assay protocol. Results all age groups, ranging from <2 years to > 64 years, were affected by COVID-19, with an average SARS-CoV-2 positivity rate of 2.3%. The virus showed sporadic activity throughout the 2024-2025 period, with a higher level of activity during epidemiological week 42 (October) of 2024. Genomic analysis showed that only the Omicron variant circulated, along with its subvariants JN.1 and LF.7, in 2024. Subvariant LF.7 and recombinant XFJ also circulated in 2025. Conclusion SARS-CoV-2 subvariants continue to circulate sporadically in Guinea, with the XFJ recombinant having been detected in humans. Therefore, it is imperative to strengthen sentinel, genomic, and environmental surveillance for the early detection of any new COVID-19 outbreak and the potential emergence of new variants.
M. Keita, Bassala Traoré, Houssainatou Bah et al.· The Pan African Medical Jour...· 0 citations
BACKGROUND
Seasonal human coronaviruses (HCoVs) can cause acute respiratory infections in children; however, their epidemiology and clinical features in the post-coronavirus disease 2019 era remain incompletely characterized.
METHODS
We retrospectively analyzed children under 16 years old with respiratory symptoms who underwent multiplex polymerase chain reaction testing at a hospital in Hokkaido, Japan, between April 2021 and September 2025. Demographic and clinical data were extracted from medical records.
RESULTS
Among 15,197 specimens, 1212 (8.0%) tested positive for HCoVs, including 361 (29.8%) single infections. OC43 was the most frequently detected species (530/1212; 43.7%), followed by NL63 (382/1212; 31.5%), HKU1 (277/1212; 22.9%) and 229E (56/1212; 4.6%). HCoVs circulated year-round, with seasonal peaks shifting from autumn to winter in 2021 and summer in 2022 to winter-spring from 2023 onward. Among single HCoV infections, the median age was 2.0 (interquartile range, 1.0-4.0) years, and 64.8% were male children. Upper respiratory infection was the most common diagnosis, and 14.7% of patients required hospitalization. Species-specific differences were observed: OC43 was associated with younger age, NL63 with croup and HKU1 with headache. Compared with severe acute respiratory syndrome coronavirus 2, seasonal HCoV infections occurred at younger ages and were more frequently associated with lower respiratory tract involvement, despite similar hospitalization rates.
CONCLUSIONS
Seasonal patterns of HCoVs were temporarily altered during the coronavirus disease 2019 pandemic but returned to their pre-pandemic winter-spring predominance from 2023. Species-specific clinical differences were observed; compared with severe acute respiratory syndrome coronavirus 2, HCoV infections occurred at younger ages and were more often associated with lower respiratory tract involvement.
Mayu Hachiya, Kenji Kondo, Hikaru Takahashi et al.· The Pediatric Infectious Dis...· 0 citations
BACKGROUND
Respiratory viruses are major contributors to severe acute respiratory infections (SARI) in children. Data on their molecular epidemiology in northern India remains limited, particularly in the post-COVID-19 period. This study aimed to determine the prevalence and distribution of respiratory viral pathogens among hospitalized pediatric SARI patients in Kashmir.
METHODS
A prospective study was conducted from October 2023 to April 2025 at Sher-i-Kashmir Institute of Medical Sciences, Srinagar. Children aged ≤15 years meeting the World Health Organization SARI case definition were enrolled. Nasopharyngeal and/or oropharyngeal samples were collected and tested using real-time polymerase chain reaction assays for SARS-CoV-2, Influenza A and B, Respiratory Syncytial virus (RSV) A and B, Adenovirus, Human metapneumovirus, Rhinovirus, and Para-influenza viruses.
RESULTS
A total of 326 pediatric SARI cases were included. At least one respiratory virus was detected in 200 patients (61.3%). RSV was the most frequently detected virus, with RSV-B identified in 111 cases (34.0%) and RSV-A in 26 cases (7.9%). Influenza viruses accounted for a smaller proportion, including influenza A(H1N1) in 12 cases (3.6%), influenza A(H3N2) in 6 cases (1.8%), and influenza B (Victoria lineage) in 21 cases (6.4%). Other viruses detected included Adenovirus, Para-influenza virus, Rhinovirus, and Human metapneumovirus. Most infections occurred during winter months and predominantly affected infants.
CONCLUSION
Respiratory viruses account for a substantial proportion of pediatric SARI cases in Kashmir, with RSV emerging as the predominant pathogen in the post-pandemic period. Strengthening molecular surveillance may improve diagnostic stewardship and guide targeted prevention strategies.
S. Wani, B. Fomda, M. Bhat et al.· Indian Journal of Medical Mi...· 1 citation
