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Beta human papillomaviruses (β-HPVs) are ubiquitous double-stranded DNA (dsDNA) viruses that may promote skin cancers by destabilizing the host genome. Supporting this, expression of the E6 gene from a β-HPV (β-HPV 8 E6) results in increased micronuclei that should induce an innate immune response that eliminates these cells. However, β-HPV 8 E6 promotes rather than restricts proliferation. We hypothesize that β-HPV 8 E6 accomplishes this by attenuating the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway, an innate immune pathway that becomes activated in response to cytosolic dsDNA. Here, we show that in response to dsDNA transfection, β-HPV 8 E6 reduced the intensity of cGAS-STING pathway activation via a reduction in STING phosphorylation. Additionally, our unbiased assessment found that β-HPV 8 E6 broadly downregulates innate immunity. This impairment of the cGAS-STING innate immune response could contribute to the prevalence of β-HPV infections.IMPORTANCEBeta human papillomaviruses (β-HPVs) may promote non-melanoma skin cancers in certain immunocompromised populations by destabilizing the host genome. Our group has previously documented the ability of a specific β-HPV, type 8, to promote proliferation despite antiproliferative stimuli, including mitotic errors such as anaphase bridges, micronuclei, and chromothripsis. The mechanisms β-HPV uses to overcome these challenges are not yet fully elucidated. This paper addresses one possible mechanism by proposing that β-HPVs suppress cGAS-STING signaling to promote proliferation under conditions that would typically initiate an innate immune response, resulting in apoptosis or senescence. We found that β-HPVs can impair cGAS-STING signaling at a post-translational modification level and play a role in broadly downregulating innate immune-associated genes. Similarly, alpha human papillomaviruses (α-HPVs) display the ability to downregulate many of the same interferon-inducible genes. This suggests that there is a shared need between β-HPV and α-HPVs to target innate immune responses.

Pneumococcal vaccination is essential to prevent invasive Streptococcus pneumoniae infections in immunocompromised individuals, including kidney transplant recipients. Current recommendations favor single-dose immunization with higher-valent conjugate vaccines, including PCV20 or PCV21. Five years ago, sequential administration of the 13-valent conjugate vaccine (PCV13) followed by the 23-valent polysaccharide vaccine (PPSV23) represented standard of care. Long-term data on antibody persistence after this regimen remain limited. In this prospective 5-year follow-up study, 46 kidney transplant recipients previously vaccinated sequentially with PCV13 and PPSV23 were re-evaluated. Nine patients were lost to follow-up, and 11 had died during the observation period. The remaining 26 participants were re-enrolled and completed the 5-year assessment. Global and serotype-specific IgG anti-pneumococcal antibody concentrations were quantified and compared with baseline and 12-month post-vaccination levels. Clinical outcomes, including pneumococcal infections and allograft status, were recorded. Five years after vaccination, antibody concentrations remained above baseline levels in most participants. Mean IgG levels were still approximately threefold higher than pre-vaccination values. Even for serotype-specific responses, mean antibody levels showed minimal changes compared with those measured 12 months after the first vaccination, although absolute titers remained considerably lower than those observed in healthy individuals. No cases of pneumococcal pneumonia or vaccine-associated allograft rejection occurred during follow-up. Sequential vaccination elicits durable immune responses in kidney transplant recipients, persisting up to 5 years post-immunization. With the availability of new vaccines covering additional serotypes, and given the generally lower antibody responses in this high-risk population, a booster with PCV20 or PCV21 appears advisable to enhance and broaden protection.IMPORTANCEKidney transplant recipients are at high risk for invasive pneumococcal disease, yet long-term vaccine-induced immunity in this population remains poorly defined. This study provides one of the longest longitudinal assessments of humoral responses following sequential PCV13 and PPSV23 vaccination, extending to 5 years post-immunization. We demonstrate sustained but heterogeneous antibody persistence and serotype-dependent responses to PCV20 booster vaccination. These results are directly relevant to transplant clinicians, vaccinologists, and public health policy, offering critical insight into long-term pneumococcal immunity in immunocompromised hosts and guiding future vaccine scheduling in solid organ transplantation.

Mass drug administration (MDA) of azithromycin (AZ) and case finding and treatment of children with cutaneous ulcers (CUs) have been trialed as strategies to eliminate yaws. Metagenomic sequencing of CU swabs obtained from children 3 to 4 years after the initiation of a yaws elimination campaign on Lihir Island showed enrichment for Treponema pallidum subsp. pertenue (TPE), Haemophilus ducreyi (HD), Streptococcus pyogenes (SP), and several anaerobic bacteria. Whether these results were influenced by AZ pressure or are generalizable to other populations is unknown. Here, we performed quantitative PCR (qPCR) for TPE, HD, and SP DNAs and metagenomic sequencing on 260 CU specimens collected from children on New Britain Island, whose inhabitants had not received MDA of AZ. Based on qPCR results, specimens were classified as containing no pathogens, a single pathogen, or multiple pathogens. 31.9% of the specimens contained SP, 28.1% HD, and 25.4% TPE DNAs; mixed infections with two or three pathogen DNAs occurred in 16.5% of cases. No pathogen DNA was detected in 31.5% of the specimens, which were defined as idiopathic ulcers (IUs). In most categories, the same pathogen(s) used to classify the ulcers by qPCR were the most abundant taxa present in the specimens. In IU, the most abundant taxon was Arcanobacterium haemolyticum; however, its relative abundance was similar across all groups, suggesting that this organism may adapt to the CU environment rather than represent a cause of IU. These data indicate that TPE, HD, and SP are the primary causes of CU in this untreated population.IMPORTANCECutaneous ulcers (CUs) affect ~100,000 children annually in tropical regions. After mass drug administration (MDA) of azithromycin (AZ) failed to eradicate yaws, the World Health Organization proposed an integrated disease management strategy to control CU, which emphasizes identifying the causative pathogens in each population. This is critical because organisms associated with CU vary geographically, with Treponema pallidum subsp. pertenue (TPE), Haemophilus ducreyi (HD), Streptococcus pyogenes (SP), and Leishmania spp. predominating in different countries. We previously found that TPE, HD, and SP DNAs were enriched in CU specimens from children on Lihir Island in Papua New Guinea (PNG), a population heavily exposed to AZ. Here, we show that these three organisms were also the major pathogens in CU specimens from children on New Britain Island in PNG, whose population had not received MDA of AZ, suggesting that our previous findings are generalizable within PNG and not a consequence of AZ exposure.

Human papillomavirus-associated head and neck squamous cell carcinomas (HPV+ HNSCCs) lack early diagnostics and continue to rise in incidence. HPV16 has been detected in ~90% of HPV+ oropharyngeal cancers (HPV+ OPCs), an anatomical subset of HNSCC, with the majority retaining episomal viral genomes. Despite this, existing episomal HPV16+ OPC cell lines are especially scarce. UMSCC104s were initially reported as episomal; however, the literature contains conflicting reports regarding the genome status of these cells. We now show that UMSCC104s rapidly undergo integration and E2 loss under standard monoculture, and later lots are fully integrated. These findings resolve prior discrepancies and underscore the instability of episomes in monoculture. Accurate models of HPV-driven cancers are critically needed. We propose fibroblast co-culture methods, traditionally utilized for HPV+ keratinocyte models, as a strategy to preserve episomal status in cancer models by supporting viral and host genome stability.

Recent studies reveal that a suboptimal vaginal microbiome (VMB), including the enrichment of anaerobic bacteria associated with multiple female genital disorders, is linked to adverse pregnancy and birth outcomes in pregnant people. Problematically, however, the majority of the available data, to date, is biased toward highly developed, Global North countries, leaving underrepresented populations like the Democratic Republic of the Congo (DRC) poorly characterized. Here, we investigate the VMB from a cohort of 82 pregnant people living with human immunodeficiency virus (PLWH) on antiretroviral therapy (ART) from the DRC. Specifically, we explore the associations between the VMB via 16S rRNA gene sequencing and maternal peripheral immune factors. Additionally, we compare the VMB of pregnant PLWH-ART from DRC with publicly available VMB data (5 studies, 1861 samples) in a meta-analysis to elucidate the impact of HIV on the VMB. Combined, these analyses revealed the differences in community structure and predicted function of the microbiota between pregnant PLWH-ART and pregnant people without HIV (PWoH). Taxonomically, the VMB of DRC PLWH-ART were enriched for Lactobacillus iners-dominated VMBs (53%) or a diverse, polymicrobial VMB, that is, bacterial vaginosis (BV) (43%). Functional predictions made from these taxa suggested that protein-coupled receptors, amino sugar and nucleotide sugar metabolism, fatty acid metabolism, and polycyclic aromatic hydrocarbon degradation pathways were differentially abundant between the communities. Correlation with host plasma immune factors revealed putative links between some VMB metrics (e.g., alpha diversity and species abundance) that have been linked to adverse pregnancy and birth outcomes.

Importance: Human immunodeficiency virus (HIV) remains prevalent in sub-Saharan Africa, where it has been linked to adverse birth outcomes. Suboptimal vaginal microbiomes (VMBs) have shown similar links. This pilot study fills critical gaps in understanding how HIV interacts with the pregnant VMB in populations underrepresented in microbiome research, like the Democratic Republic of the Congo (DRC). We identified maternal systemic immune factors associated with suboptimal VMBs that have been linked to poor birth outcomes. In a global meta-analysis, we found significant taxonomic and functional differences in the VMBs between pregnant people living with and without HIV, revealing potential biomarkers that increase the risk of adverse birth outcomes. These findings provide crucial insights into VMB features that may influence pregnancy health in PLWH-ART, guiding future research and tailored interventions to support safer pregnancies in the DRC and similar populations.This study is registered with NCT03048669.

Emerging viruses remain a threat to human health; however, many aspects of their infection cycle are still poorly understood. Host lipid structures and abundances are observed to be significantly altered during infection, and the mechanisms regulating lipid synthesis and modification remain largely unknown. In this work, we analyzed a large multi-omic data set from three Middle East respiratory syndrome coronavirus (MERS-CoV)-infected primary human lung cell types, all derived from three distinct donors to investigate the changes in lipid species during infection. Analysis of lipidomics data identified perturbations of various lipid classes, and we hypothesized and confirmed that MERS-CoV infection orchestrates an increase in ceramide via sphingomyelinase pathways required for infection. We also identified a minor subset of proteins with lipid-related functions with increased differential expression among a striking majority of lipid-related proteins with decreased differential expression. The most prominent of these is ACSL3, a long-chain acyl-CoA synthetase that is key for the synthesis of triacylglycerides and is associated with lipid droplet formation, an established feature of coronavirus-infected cells. Accordingly, the inhibition of acyl-CoA synthetase activity reduced MERS-CoV replication. These results suggest a model wherein coronaviruses perturb overall cellular metabolism to shift resources to the production of ceramides and triacylglycerides, particularly through acyl-CoA synthetase activity. Our findings suggest a strategy for targeting CoV replication through the inhibition of specific subsets of lipid metabolism.

Importance: Combating emerging viral threats requires an in-depth understanding of how the virus commandeers host resources to facilitate replication. Viral particles are comprised of protein and lipids; hence, the synthesis of both is critical for virus spread. Our studies have demonstrated that the synthesis of two lipid species, ceramides and triacylglycerides, is essential for Middle East respiratory syndrome coronavirus replication and that virus replication is impaired if these synthetic pathways are blocked. These results suggest a model wherein coronaviruses perturb overall cellular metabolism to shift resources to the production of ceramides and triacylglycerides. Our findings suggest a strategy for targeting coronavirus replication through the inhibition of specific subsets of lipid metabolism.

Zoonotic Onchocerca lupi (Spirurida, Onchocercidae) has attracted the interest of the scientific community worldwide, by causing severe ocular infections in domestic animals (dogs, cats) and can infect wild carnivores (wolves, coyotes), as well as humans. Though recent advancements in scientific knowledge have been gained, gaps still remain about the biology of this filarioid, as well as its genetic structure. Based on mitochondrial genes, two highly divergent genotypes were identified, in the Iberian Peninsula (genotype 2) and Europe, Asia, and the United States (genotype 1), meanwhile only a draft nuclear genome of O. lupi from the United States is available. This study aimed to fill knowledge gaps about the genomic characterization of this filarioid and its Wolbachia endosymbiont. This study described the shotgun sequencing of an adult specimen of O. lupi isolated from a dog living in Portugal using the PacBio long-read sequencing technology. Three distinct genomes, such as the nuclear, mitochondrial, and Wolbachia endosymbiont, were assembled and analyzed. The assembled nuclear genome, Olupi_PT2024, exhibited high contiguity, accuracy, and completeness. Pairwise mitogenome comparative analyses among several Onchocerca species corroborated the high divergence between the two genotypes from Portugal and the USA, although the observed differences remained within the range of intra-species variation. The complete genome of the Wolbachia endosymbiont of O. lupi confirmed its classification within supergroup C and its close phylogenetic relationship with Wolbachia endosymbionts associated with the genus Onchocerca. The data on these three genomes may provide valuable resources for understanding the biology, population genetics, and phylogeography of this parasite.IMPORTANCEOnchocerca lupi, a zoonotic parasite, causes ocular onchocerciasis in both domestic and wild carnivores, as well as humans. Despite recent scientific advances, gaps remain in both the biology and genetic structure of this parasite. To date, two genotypes have been described (genotype 1 distributed in Europe, Asia, and the United States, and genotype 2 circulating in the Iberian Peninsula) based on mitochondrial gene analysis. This study provided three distinct genomes (nuclear, mitochondrial, and Wolbachia endosymbiont) of O. lupi isolated from a dog living in Portugal. Overall, the data presented here corroborate the divergence between the two genotypes and provide new insights into the identification of genes that could serve as novel therapeutic targets for this filarial disease.