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[This corrects the article DOI: 10.3389/fimmu.2023.1130539.].

The highly transmissible Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in late 2021. Initial Omicron waves were primarily made up of sub-lineages BA.1 and/or BA.2, BA.4, and BA.5 subsequently became dominant in mid-2022, and several descendants of these sub-lineages have since emerged. Omicron infections have generally caused less severe disease on average than those caused by earlier variants of concern in healthy adult populations, at least, in part, due to increased population immunity. Nevertheless, healthcare systems in many countries, particularly those with low population immunity, have been overwhelmed by unprecedented surges in disease prevalence during Omicron waves. Pediatric admissions were also higher during Omicron waves compared with waves of previous variants of concern. All Omicron sub-lineages exhibit partial escape from wild-type (Wuhan-Hu 1) spike-based vaccine-elicited neutralizing antibodies, with sub-lineages with more enhanced immuno-evasive properties emerging over time. Evaluating vaccine effectiveness (VE) against Omicron sub-lineages has become challenging against a complex background of varying vaccine coverage, vaccine platforms, prior infection rates, and hybrid immunity. Original messenger RNA vaccine booster doses substantially improved VE against BA.1 or BA.2 symptomatic disease. However, protection against symptomatic disease waned, with reductions detected from 2 months after booster administration. While original vaccine-elicited CD8 + and CD4 + T-cell responses cross-recognize Omicron sub-lineages, thereby retaining protection against severe outcomes, variant-adapted vaccines are required to expand the breadth of B-cell responses and improve durability of protection. Variant-adapted vaccines were rolled out in late 2022 to increase overall protection against symptomatic and severe infections caused by Omicron sub-lineages and antigenically aligned variants with enhanced immune escape mechanisms.

West Nile virus lineage 2 (WNV-2) is a growing public health concern in Europe causing West Nile fever or West Nile neuroinvasive disease (WNND) with substantial morbidity and mortality; however, genomic data from southern Italy are limited despite recent expansion of autochthonous transmission. The aim of the study was to characterize the phylogenetic and molecular features of the WNV-2 strain responsible for the first autochthonous human infection reported in Calabria (2023), and two more additional WNND cases detected in 2024. Full WNV-2 genomes were generated from the three cases. Phylogenetic analysis was performed using all publicly available WNV sequences up to September 2025. Amino acid changes in the polyprotein were compared with known WNV-2 lineage and sub-lineage signatures. The three sequences formed a monophyletic group within sub-lineage WNV-2a, clustering with strains circulating in Central-South-Eastern Europe and showing closest affinity to Hungarian sequences. Non-synonymous substitutions characteristic of the Hungary 578/10 strain (NS2B-119I, NS4B-14G, NS4B-49A, and NS5-298A) were identified and were absent from Central-Northern-Western European and previously reported Italian sequences. Additional substitutions (E-159T, E-399R, and NS3-249P) corresponded to signatures from a fatal WNV-2 infection in a Great Grey Owl in Slovakia. Our study provides the first report of Central-South-Eastern European WNV-2 circulation outside Eastern Europe, supporting its likely spread through the Balkans into Italy by 2022. These findings underscore the rapid spread of WNV-2 in newly affected areas and highlight the critical need for sustained molecular surveillance.

Mycobacterium tuberculosis ( Mtb ) sub-lineage 4.2.2.2 is the most frequently isolated strain of Mtb from Ethiopian treatment-refractory tuberculosis patients. This study investigated the underlying molecular background to Mtb sub-lineage 4.2.2.2 through transcriptomic and genomic analyses. Comparative whole genome sequencing and transcriptomics (RNAseq) was performed with other circulating clinical Ethiopian lineages and sub-lineages: lineage 7, lineage 3, lineage 4 sub-lineage 4.1.2.1, and sub-lineage 4.6.3. We identified seven genes differentially expressed in sub-lineage 4.2.2.2 compared to other Mtb lineages. Of these, six (Rv0331, Rv0720, Rv1993c, Rv2030c, Rv2034 and Rv3129) were upregulated, while Rv0997a was downregulated. These differentially expressed genes are associated with lipid metabolism, stress responses, protein synthesis and metal transport, suggesting that sub-lineage 4.2.2.2 may be better able to adapt to the complex host-pathogen interactions of infection and transmission. Interestingly, this observation is mirrored by mild induction of DosR-regulated genes in sub-lineage 4.2.2.2 compared to other lineages in vitro, suggesting that enhanced expression of the DosR regulon may influence this sub-lineage’s ability to cause disease in Ethiopia. Taken together, our findings reveal genes that might impact the pathogenicity of Mtb clinical isolates in Ethiopia and identifies single nucleotide polymorphisms that could influence their expression.

Background Human metapneumovirus (HMPV) belongs to the family Pneumoviridae. It is one of the emerging respiratory viruses causing both upper and lower respiratory tract illnesses. HMPV has two genotypes: A and B. These genotypes are classified into lineage A1, A2, B1 and B2. Lineage-A2 is further classified as A2a, A2b and A2c. Similarly, B2 is classified as B2a and B2b. Studies have shown the circulation of A2b, B1 and B2 lineages in India. However, a limited amount of data is available on the current circulating genotypes of HMPV in India. Methods Throat swab samples positive for HMPV by real-time RT- PCR, archived at Manipal Institute of Virology as a part of a hospital-based acute febrile illness surveillance study, was used from April 2016 to August 2018 by purposive sampling method. We performed the conventional reverse transcriptase-polymerase chain reaction for twenty samples targeting the G gene and then subjected them to sequencing. Phylogenetic analysis was done using MEGA X software by the Maximum Likelihood method. Results All the twenty sequences belonged to the A2c subgroup. Phylogenetic analysis showed that strains from the study have genetic relation with circulating strains in Japan, China and Croatia. Seven out of the twenty sequences showed 180-nucleotide duplication and eleven sequences showed 111-nucleotide duplication. Two sequences did not show any duplications. Conclusion In the current study, we report that A2c is the sub-lineage in India from April 2016 to August 2018. This study is the first retrospective study reporting the circulation of the A2c sub-lineage among adults in India with 180- and 111-nucleotide duplications in the G gene of human metapneumovirus.

Chikungunya virus is an Alphavirus belonging to the family Togaviridae that is transmitted to humans by an infected Aedes mosquito. Patients develop fever, inflammatory arthritis, and rash during the acute stage of infection. Although the illness is self-limiting, atypical and severe cases are not uncommon, and 60% may develop chronic symptoms that persist for months or even for longer durations. Having a distinct periodical epidemiologic outbreak pattern, chikungunya virus reappeared in Thailand in December 2018. Here, we describe a cohort of acute chikungunya patients who had presented to the Bangkok Hospital for Tropical Diseases during October 2019. Infection was detected by a novel antigen kit and subsequently confirmed by real-time RT-PCR using serum collected at presentation to the Fever Clinic. Other possible acute febrile illnesses such as influenza, dengue, and malaria were excluded. We explored the sequence of clinical manifestations at presentation during the acute phase and associated the viral load with the clinical findings. Most of the patients were healthy individuals in their forties. Fever and arthralgia were the predominant clinical manifestations found in this patient cohort, with a small proportion of patients with systemic symptoms. Higher viral loads were associated with arthralgia, and arthralgia with the involvement of the large joints was more common in female patients.

ABSTRACT Avian influenza A virus subtype h9N2 has been in circulation since last two decades in poultry industry of Pakistan. This virus is causing huge economic loss every year due to poor weight gain, drop in egg production and mortality of birds since first reported in 1998. Influenza viral surface protein neuraminidase enhances both virus replication and its release from host cells. In this study we isolated nineteen h9N2 viruses from infected birds of various farms from Punjab, Pakistan. Neuraminidase gene of these viruses was amplified using RT-PCR and sequenced to perform mutational analysis. Phylogenetic analysis revealed that B2 sub-lineage is endemic in the country as all isolated h9N2 strains belongs to this clade of G-1 lineage. Two isolated h9N2 strains A/Chick/Pak/303/2018 and A/Chick/Pak/436/2019 contain six glycosylation sites instead of seven as found in their ancestral strains. A comparative analysis of neuraminidase amino-acids sequences of B2 sub-lineage with Y-280 lineage and B1 sub-lineage demonstrated that there were no human related substitutions, insertion or deletions in hem-absorbing site and loop of h9N2 isolates. Two unique substitutions, Gln39Arg and Lys47Glu have been noted in NA stalk domain of all isolates of this study which might be indirectly enhancing the virulence of virus. These findings demonstrated that new mutations are emerging in B2 sub-lineage and there is need for constant surveillance of evolving genome of h9N2 virus prevailing in the country to combat the future challenges of avian influenza out breaks in Pakistan.

BACKGROUND: The variation of human papillomavirus (HPV) genes or HPV variants demonstrates different risks of cervical cancer. Mutation in the long control region (LCR) at YY1-motifs is one of the mechanisms for enhancing viral oncogene expression during the course of cancer cell progression. In Thai women, cervical cancers are almost always associated with HPV16 variant sub-lineage Asian (HPV16As); however, the mechanism involved remains elusive. The aim of this study was to understand further the oncogenic potential of HPV16As. METHODS: A total of 82 HPV16-positive specimens from Thai women were selected from formalin-fixed paraffin-embedded cervical tissues, and the full length E6 gene of each specimen was amplified and sequenced. LCRs of the HPV16As-positive cases were amplified and sequenced to analyze their polymorphisms. Transcriptional activities of the HPV16As LCRs were then compared with sub-lineage European (EUR), sub-lineage Asian-American 1 (AA1) and HPV16 prototype by insertion of the LCRs into the pGL3-Basic vector. RESULTS: The HPV16 DNA sequences were classified as HPV16 prototype (18.3%), Asian (As, 61%), Asian American-1 (AA1, 8.5%), European (EUR, 7.3%), Asian African-2 (AFR2, 3.7%) and Java-135C (J135C, 1.2%). The prevalence of HPV16As was 30% in low-grade squamous intraepithelial lesion (LSIL), while that in high-grade squamous intraepithelial lesion (HSIL) and squamous cell cervical carcinoma (SCC) were 63.9% and 66.7%, respectively, which demonstrates a significant association of HPV16As with the disease severity. LCR polymorphisms from 43 HPV16As positive cases were analyzed by PCR-sequencing. Thirty-eight nucleotide variation positions spanned nucleotide positions 7157–82. Ten new mutations found in the HPV16As LCRs were located predominantly at the enhancer and proximal to the 3’-end of the early promoter. The LCRs of the common HPV16As, EUR and AA1 showed 5, 13 and 23-fold higher activity than the HPV16 prototype LCR, while those of the new nucleotide variations of As showed 19 (As-sv1) and 30 (As-sv14) -fold higher activity than the HPV16 prototype. CONCLUSIONS: HPV16As DNA sequence variation, especially at the proximal to early promoter in the LCR, enhances transcriptional activity. This could be one of the possible mechanisms for HPV16As-associated cervical cancer development.