Infection, Genetics and Evolution

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved since its emergence in the human population in 2019. As of 1st August 2025, more than 1,700 Omicron subvariants have been designated by the Pango nomenclature system. The Pango nomenclature system designates a new lineage based on genetic and epidemiological information of SARS-CoV-2 strains. However, there is a possibility that strains that have similar genetic backgrounds and the same phenotype are given different Pango lineage names. In this paper, we propose a new algorithm, called FindPart-w, which can identify groups of viral lineages that share the same relative effective reproduction numbers. We introduced a new lineage replacement model, called the constrained RelRe model, which constrains groups of lineages to have the same relative effective reproduction numbers. The FindPart-w algorithm searches the equality constraints that minimise the Akaike Information Criterion of constrained RelRe models. Using hypothetical observation count data created by simulation, we found that the FindPart-w algorithm can identify groups of lineages having the same relative effective reproduction number in a practical computational time. Applying FindPart-w to actual real-world data of time-stamped lineage counts from the United States, we found that the Pango lineage nomenclature system may have given different lineage names to SARS-CoV-2 strains even if they have the same relative effective reproduction number and similar genetic backgrounds. In conclusion, this study showed that viruses that had the same relative effective reproduction number were identifiable from temporal count data of viral sequences. These findings will contribute to the future development of lineage designation systems that consider both genetic backgrounds and transmissibilities of lineages.

Understanding the dynamics of HIV epidemics is important to control them effectively. Classical methods that mainly rely on occurrence data are limited by the fact that an unknown part of the epidemic eludes sampling. Since the early 2000s, phylodynamic methods have enabled the estimation of key epidemiological parameters from virus genetic sequence data. These methods have the advantage of being less sensitive to partial sampling and to provide insights about epidemic history that even predates the first samples. In this study, we analysed 2,205 HIV sequences from the French ANRS PRIMO C06 cohort. We identified and were able to reconstruct the temporal dynamics of two large clades that represent the HIV-1 epidemics in the country. Using Bayesian phylodynamic inference models, we found that the first clade, from subtype B, originated in the end of 1970s, grew rapidly during the 80s before decreasing from 2000 to 2015 and stagnating since then. The second clade, from circulating recombinant form CRF02_AG, emerged and spread in the 80s, grew again in the early 2000s, before declining slightly. We also estimated key epidemiological parameters associated with each clade. Finally, using numerical simulations, we investigated prospective scenarios and assessed the possibility to meet the 2030 UNAIDS targets. This is one of the rare studies to analyse the HIV epidemic in France using molecular epidemiology methods. It highlights the value of routine HIV sequence data for studying past epidemic trends or designing public health policies.

Some Anopheles species that act as malaria vectors are members of species complexes, a concept whereby sibling species cannot be differentiated solely on the basis of morphological characters. Therefore, species complexes represent a major problem in malaria vector control, because within an Anopheles complex, vectors cannot be differentiated from non-vector species, unless molecular techniques are used to identify them. The Anopheles tessellatus species complex is an important potential vector in South, East, and Southeast Asia, including certain regions of Indonesia. However, no in-depth studies have been conducted on this species complex in that country. Therefore, this study investigated the taxonomic status of An. tessellatus from diverse populations across five Indonesian islands (Sumatra, Java, West Nusa Tenggara, East Nusa Tenggara, and Sulawesi) and identified interpopulation genetic variation based on molecular data of the ITS2, COI, and COII genes. Phylogenetic relationships were constructed using the Maximum Likelihood method. Haplotype and network analysis were also conducted. The results indicate that An. tessellatus constitutes a monophyletic group comprising three well-defined lineages that exhibit clear intraspecific genetic differentiation. Cluster 1 corresponds to the population of Sumatra, Cluster 2 represents population from Sulawesi, and Cluster 3 encompasses populations from Java, West Nusa Tenggara, and East Nusa Tenggara. These findings demonstrate high haplotype diversity and low nucleotide diversity within the species. Populations from West Sumatra, Manado, Tojo Una - Una, and North Morowali (Sulawesi) have the potential for speciation with a genetic distance of 0.61 - 0.94% for COI, between 0.81 - 0.95% for ITS2, and between 0.62 - 0.71% for COII. These findings underscore the need for further integrative studies to obtain a more comprehensive understanding of the An. tessellatus complex in Indonesia and its role in malaria transmission.

Dengue disease remains a significant global health threat, with current vaccines exhibiting variable efficacy and safety concerns. Virus-like particles (VLPs) offer a promising alternative by mimicking native virus structures without infectious genomes. We engineered a mammalian expression plasmid encoding Dengue-1 prM and E proteins, optimized for secretion using Japanese Encephalitis virus signal sequences, and transiently expressed it in HeLa cells. Purified VLPs exhibited spherical morphology ([~]39 nm diameter) consistent with native virions, as confirmed by transmission electron microscopy. Immunization of mice with these VLPs elicited robust Dengue-1 specific IgG antibody responses. Our study demonstrates production of immunogenic Dengue-1 VLPs in HeLa cells, highlighting their potential as a vaccine candidate and a tool for serodiagnosis. Further characterization of VLP epitopes and protective efficacy is warranted to advance vaccine development. ImportanceDengue remains a significant global health challenge, with serotype 1 being one of the dominant strains causing recurrent outbreaks in Nepal. Existing vaccines demonstrate limited efficacy and pose significant safety concerns, particularly in seronegative populations. To address these limitations, this study explores virus-like particles (VLPs) as a safer alternative vaccine platform. VLPs elicit robust immunogenicity by mimicking the structure of native virus while completely lacking genetic components. This study combines DENV1 structural proteins with optimized expression systems to enhance immunogenicity. This work is particularly significant as the first dengue vaccine research conducted in Nepal, directly addressing antigenic mismatches between existing commercial vaccines and locally circulating viral strains. Furthermore, the study provides scalable platform for developing region-specific dengue vaccines for other serotypes and flaviviruses.

Human diversity did not only remain restricted to their socio-cultural and linguistic domains but also have penetrated deep inside their genetic root. Africa harbors more genetic diversity than any other part of the world. Diversification of the African lineages were complex, involving long-distance gene flow. Data from Africansis needed to better understand the origin and evolution of modern humans, the genetic basis local adaptation, and the evolution of complex traits and related diseases. This analysis formed the basis for this study of determining the origin and migration of the Ameru community in Kenya. Blood samples was collected from 132 male adults of 65 year and above. DNA was extracted and analyzed for the Hyper variable region 1and 2. The sequences were sequenced using Sanger sequence alignment and analyzed using Geneious. Phylogenetic analysis was done using Mega-X while haplotype analysis was done using DNASP software. L1 haplogroup (2.9%) was found among Igembe (7%), Tharaka (6%), and Chuka (7%) and is common in West, Central, and parts of East Africa. L2 haplogroup (6.7%) was present in all subgroups except Imenti and Tigania, indicating West and Central African maternal ancestry. L1 and L2 haplotypes indicate that most Ameru subgroups share partial maternal ancestry from West and Central Africa, while Imenti and Tigania have different maternal lineages. L0-L4 haplogroups indicate predominant East, Central, and West African maternal origins, with subgroups showing variation in haplotype frequencies (e.g., L1 and L2 in Igembe, Tharaka, Chuka; L3 in Tharaka, Mwimbi, Chuka; L4 across all subgroups). Subgroup differences suggest that certain communities, particularly Imenti, have distinct maternal lineages, with less contribution from L1, L2, and L3 but potential links to Afro-Asiatic groups via L4 (found in the Middle East). Non-African haplogroups (N and R) point to historical interactions or shared ancestry with populations in Eurasia and the Horn of Africa, primarily in Tigania and Imenti. Overally, the Ameru maternal gene pool is heterogeneous, shaped by multiple migration routes and interactions across East Africa and beyond, with subgroup-specific maternal histories.

Plasmodium falciparum merozoites invade erythrocytes using various ligand-receptor interactions. Important ligands encoded by the eba and Rh gene families have varying expression levels in different parasite isolates, affecting their vaccine candidacy. Analyses of clinical isolates from endemic areas in Africa have indicated that most variation in these expression profiles exists within each local area, and only minor differences are seen between areas, although comparisons with non-African populations have not previously been performed. To enable this, relative transcript levels of three eba genes and five Rh genes have been analysed in new population samples, Malaysian isolates sampled from Sabah State in Borneo prior to endemic malaria elimination, and Gambian isolates, cultured under the same conditions to harvest schizonts for reverse transcription quantitative PCR assays. Significant differences between these populations were seen for three of the ligand genes, levels of eba175 being higher in Malaysia, while levels of eba181 and Rh2b were lower in Malaysia. The gene transcript profiles did not differ between single genotype and or multiple-genotype isolates. The distinctness of the Malaysian population expression profile was also supported by comparing previous data on clinical isolates from Ghana. In tests for correlation with previously determined parasite multiplication rates, eba181 transcript levels correlated positively among Malaysian isolates but not among Gambian isolates. These findings suggest that expression of three P. falciparum merozoite ligands involved in invasion may be regionally differentiated, and further analysis of Asian parasite populations would be important if vaccines based on these candidates are to be considered for future use.

Marine biodiversity documentation from the Mumbai Metropolitan Region (MMR) remains neglected despite the region having diversity of marine coastal habitats. The regions intertidal is one such habitat where species documentation remained heavily deficient due to lack of assessments and general apathy towards the habitat. This study addresses the issue of data deficiency of one of the largest taxa, Gastropoda through a decade long citizen science project, Marine Life of Mumbai. There exist large gaps in taxonomic research that have led to inconsistencies in species identification and inadequate ecosystem representation. This study addresses these issues by focusing on one of the largest taxa, the Molluscan class Gastropoda within the MMR. We present the spatial distribution of gastropod assemblages from 28 rocky, sandy and muddy intertidal sites within the Mumbai Metropolitan Region, on west coast of India. A total of 163 species were recorded from 2164 observations of marine gastropods. Among these, 29 species, 34 genera and one family Limapontiidae are new records for the region. Additionally, this study reports rediscoveries of 7 species from their type locality, with 5 species of Heterobranchs recorded after 78 years: one species from Neogastropoda, Lataxiena bombayana, after 131 years and one from Siphonariida, Siphonaria bassiensis after 31 years, from their type locality. These species are herein illustrated with detailed morphological descriptions and their local distribution on 28 sites in the Mumbai Metropolitan Region. Through this study we elucidate that the citizen science efforts and the subsequent taxonomic analysis provide an effective and low-cost method for filling data gaps from large, understudied geographical areas.

In wildlife forensic practice, species identification and estimation of the Minimum Number of Individuals (MNI) for highly processed specimens have long relied on weight-based conversion methods, which may result in underestimation of the number of individuals involved in a case. Focusing on confiscated casque products of the helmeted hornbill (Rhinoplax vigil), this study combines macroscopic morphological examination with mitochondrial DNA barcoding (16S rRNA, COI, and Cytb) to explore a more robust approach for individual quantification. The results demonstrate that the conventional "weight-based" approach overlooks critical biological information contained in anatomical structures and cannot accurately reflect the actual number of individuals involved. Based on this, we propose an anatomy-based criterion centered on the principle of structural uniqueness: specimens retaining biologically unique beak or casque structures should be directly assigned to a single individual, whereas weight-based estimation should only be applied when original anatomical features are entirely absent. In addition, considering material loss during processing, we propose approximately 85 g as a reference threshold for estimating the number of individuals in heavily processed solid casque products. This approach improves the scientific rigor and accuracy of forensic identification and provides reliable technical support for the conviction, sentencing, and law enforcement of wildlife trafficking cases involving helmeted hornbill and other endangered species.

Background: Spotted fever is caused by spotted fever group rickettsiae (SFGR) belonging to the genus Rickettsia. Transmission to humans is primarily via the bite of infected ticks. Being a vector-borne disease, the occurrence of spotted fever is related to factors that allow the vector to thrive. This spatio-temporal analysis gives an insight into the distribution of cases and correlation with seasonality. Methodology: A suspected AFI patient was considered spotted fever positive if either serology (ELISA/IFA) or molecular assay (Nested PCR/qPCR) was tested positive. Demographic data of confirmed cases were included for the analysis. Results: In the 18-year dataset, a total of 2153 suspected patients were tested for spotted fever, of which 516 (24%) were positive. On spatio-temporal analysis, Vellore district reported 39.9% of cases, Chittoor 38.8%, Tirupattur 12.5%, Ranipet 4.5%, and Tiruvannamalai 4.3%. Maximum spotted fever cases were reported between the months of September to March, with a peak in January. Children below 10 years and housewives were at risk of spotted fever. Conclusion: The findings of this retrospective analysis highlight the importance of considering spotted fever group rickettsioses in patients presenting with acute undifferentiated febrile illness, particularly children aged <10 years, from areas with higher spatial clustering, during or following the monsoon season.

Xenopus is a genus of entirely aquatic frogs found in sub-Saharan Africa. Currently, the complete genomes of two species within the Xenopus genus, Xenopus laevis and Xenopus tropicalis, have been fully sequenced, annotated, and made publicly available. The two species inhabit markedly different environments: X. tropicalis lives in the hot, equatorial regions of Africa, whereas X. laevis resides in the cooler climates of southern Africa. In the present study, mutational profiling, comparative homology modeling, and computational bioinformatics were used to identify the features of adaptive evolution in Xenopus endonuclease G (EndoG) proteins. The multiple characteristics of EndoG isozymes were discovered to vary considerably between the two Xenopus species dwelling in different locations. Most notably, EndoG proteins from the psychrophilic X. laevis exhibit the increased contents of charged and polar residues, elevated pI, higher intramolecular interaction energies, B factors, molecular void volumes, and solvent accessibilities, but the decreased contents of nonpolar and aromatic amino acids, lower hydrophobicity, buried surface area, and molecular packing density compared to those from the thermophilic X. tropicalis. The observed differences strongly suggest that temperature plays a dominant role in EndoG diversification. Evaluation of intramolecular interaction energies appears to be a particularly sensitive and discriminative framework for assessing protein divergence at the structural level. Overall, this study highlights the diversification of homologous proteins in ectothermic vertebrate eukaryotes and provides mechanistic insight into protein adaptation to contrasting environments.

BackgroundTo control leishmaniasis, chemotherapy drugs are currently under development. However, these drugs often exhibit poor efficacy and are associated with toxicity, adverse effects, and drug resistance. At present, no specific drug is available for the treatment of leishmaniasis. Meanwhile, vaccine research is ongoing. Recent studies have analysed some experimental vaccines using mathematical models. AimIn previous work, drug targeting was focused on the entire human body rather than specifically addressing infected macrophages and parasites. In our current approach, we aim to eliminate infected macrophages and parasites through nano-drug design. Specifically, we utilise two types of nanoparticles: iron oxide and citric acid-coated iron oxide. Moving forward, we plan to advance this strategy using mathematical modelling of macrophage-parasite interactions. MethodsWe design PDE-based models of macrophages and parasites, incorporating cytokine dynamics, to support nano-drug development. Drug efficacy is estimated using posterior distributions to analyse phenotypic fluctuations of macrophages and parasites during the design phase. We investigate implicit and semi-implicit treatment schemes, focusing on energy decay properties. To model drug flow during treatment, we introduce a three-phase moving boundary problem. Comparative analyses are conducted to evaluate macrophage and parasite behaviour with and without treatment. Finally, the entire framework is implemented within a virtual lab environment. ResultsThe results show that the nano-drug exhibits better efficacy compared to combined drug doses. We analysed and compared two types of nano-drug particles: iron oxide and citric acid-coated iron oxide. We discuss how the drug effectively targets and eliminates infected macrophages and parasites. ConclusionOur models results and simulations will support researchers conducting further studies in nano-drug design for leishmaniasis. These simulations are performed within a virtual lab environment.

BackgroundThe World Health Organization (WHO) has raised concerns over increasing Pfhrp2/3 deletions, undermining the sensitivity of Pfhrp2-based rapid diagnostic tests (RDTs). Close monitoring of the population and a change in diagnostic methods are recommended if the prevalence of parasites with Pfhrp2/3 deletions exceeds 5%. In high transmission settings, accurate estimates are hampered by the frequent occurrence of mixed-clone infections (multiplicity of infection; MOI). Objective and MethodsIf parasites with and without deletions are present in an infection, standard molecular assays cannot detect the presence of the former. To accurately estimate frequencies of haplotypes with Pfhrp2/3 deletions in the presence of mixed infections, a novel statistical model that combines genetic/molecular information from Pfhrp2/3 with that from neutral markers is introduced. Maximum-likelihood estimates (MLEs) are obtained for haplotype frequencies characterized by markers at Phrp2/3 loci and loci for neutral markers. The expectation-maximization algorithm is used to derive the MLEs. The adequacy of the method (precision and accuracy) is assessed by numerical simulations. ResultsThe method was applied to an active surveillance study conducted in a tribal community in Jagdalpur, India, which enrolled febrile community members (n = 432) between October and November 2021. Four markers each at Pfhrp2 and Pfhrp3 are combined with one marker each at Pfmsp1 (which encodes P. falciparum merozoite surface protein 1) and Pfmsp2. Data from a total of 117 patients who had both P. falciparum infections and genetic information for the molecular markers underwent further analysis with the novel statistical method. ConclusionResults indicate that this novel method has promising statistical properties (asymptotic and in finite samples) and can be readily applied to real-world situations. A stable implementation of the method in R is provided. This novel approach enables accurate estimation of Pfhrp2/3 deletion frequencies in complex P. falciparum infections, addressing a key limitation of current molecular surveillance methods. Author summaryPlasmodium falciparum (Pf) causes the most severe form of human malaria, accounting for over 90% of cases. Rapid diagnostic tests (RDTs) have become a cornerstone of malaria control. These RDTs detect Pf-specific antigens in a blood drop. HRP2/3 emerged as the best antigen for such tests because it is Pf-specific and expressed in abundance. However, some parasites lack the genes that code for HRP2/3 proteins. If parasites in an infection have such gene deletions, RDT results can be false negative. The WHO considers the containment of such deletions a public health priority and recommends monitoring their prevalence. The detection of HRP deletions is challenging if parasites with and without deletions co-occur in infections because standard molecular assays cannot detect deletions in this situation. To overcome this challenge, we introduce a novel statistical method to estimate the frequency distribution of parasite variants with deletions. The method combines information from neutral molecular markers and from HRP-related markers to correct for unobservable information. Here we provide a derivation of the statistical model, a stable implementation, and test its statistical properties with synthetic and real data, thereby showing that our method is well-suited for the underlying problem.

The majority of emerging infectious diseases are zoonotic, having their origin in wildlife before spilling over into the human population. While small mammals are recognized as critical reservoirs for these viruses, their viral diversity remains largely uncharacterized across many African countries. We conducted molecular surveillance of synanthropic rodents and shrews in the Kibera informal settlement in Nairobi and the rural Taita Hills region of Kenya to detect and characterize potential zoonotic viruses. Tissue samples from 228 rodents and shrews were screened for six viral families using PCR assays. Rat hepatitis E virus (HEV) (Rocahepevirus ratti), a rodent-associated virus with potential for human spillover, was identified in Mus musculus and Rattus norvegicus from Kibera. NGS was conducted for the HEV positive samples, and we obtained two near-complete HEV genomes from Rattus norvegicus, which clustered within rodent-associated HEV genotypes in the phylogenetic analysis. The two sequences from the Rattus norvegicus cluster together, indicating a close genetic relationship. Paramyxoviruses belonging to the genera Jeilongvirus and Parahenipavirus were detected both from Taita and Kibera in nine different samples from Rattus norvegicus, Mus minutoides, Crocidura sp and Acomys ignitus. One paramyxovirus positive sample (Acomys ignitus) from Taita was selected for further sequencing with NGS, and a complete genome of a new jeilongvirus was assembled. Phylogenetic analysis of the detected viruses confirmed the close relation to previously known rodent-borne jeilongviruses but also revealed potentially novel jeilong- and parahenipavirus species. Our findings highlight the circulation of potentially zoonotic viruses in both urban and rural small mammals in Kenya. It emphasizes the necessity of continued genomic surveillance of zoonotic viruses to mitigate risks of their spillover into human populations. HighlightsO_LISurveillance reveals diverse rodent-borne viruses circulating in Kenya. C_LIO_LIRat-HEV was detected in Rattus norvegicus and Mus musculus from an urban low-income area. C_LIO_LIParamyxoviruses were detected across multiple rodent and shrew species, including novel Acomys ignitus jeilongvirus. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/719784v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@194e81eorg.highwire.dtl.DTLVardef@11342cdorg.highwire.dtl.DTLVardef@186ad97org.highwire.dtl.DTLVardef@eeb516_HPS_FORMAT_FIGEXP M_FIG C_FIG

Mpox virus (MPXV) gained increased attention following the declaration of two Public Health Emergencies of International Concern (PHEICs) in 2022 and 2024. The rapid spread of MPXV and the increase in human-to-human transmission highlighted the need for improved diagnostic tools for characterizing infection patterns and transmission dynamics. While PCR is effective for detecting active infections, serological approaches can help identify previous or asymptomatic infections and support retrospective surveillance. However, many serological assays developed during recent outbreaks have not been evaluated in endemic settings such as the Democratic Republic of the Congo (DRC). This study aims to define antigen-specific serological cutoff values to differentiate MPXV-seroreactive individuals from those with other orthopoxvirus (OPXV) exposure or different vaccination histories, specifically for use in the DRC. Here, we analyzed 134 individuals, divided into six distinct cohorts with different exposures. Serum samples were tested using Mesoscale Discovery (MSD) to screen for five MPXV and vaccinia virus (VACV) orthologous antigens: A29L/A27L, A35R/A33R, B6R/B5R, E8L/D8L, and M1R/L1R. Receiver operating characteristic (ROC) analysis identified the best-performing antigens and established seroreactivity cutoff values. A binary composite rule was also evaluated to improve the classification of these results. We identified three MPXV antigens, E8L (cut-off=12.33 AU/mL), A35R (cut-off=5.22 AU/mL), and B6R (cut-off=9.77 AU/mL), that showed the strongest discriminatory performance in the dataset. Collectively, these three antigens form a significant panel that demonstrated clear separation between our mpox survivor cohort and other OPXV-exposed individuals.

Here we evaluated the performance of a previously published tiling PCR primer scheme by Ringlander et al. (2022) for whole-genome amplification of Hepatitis B virus (HBV) in combination with Oxford Nanopore sequencing. The primer set originally developed for Ion Torrent sequencing was adapted by removing platform-specific adapters and tested using clinical serum or plasma samples submitted for routine HBV genotyping and resistance testing. Two multiplexing strategies were compared: a single PCR pool containing all primers and a two-pool strategy with non-overlapping amplicons. Sequencing reads were processed using a Nanopore analysis pipeline, and genome coverage and amplicon performance were compared across samples spanning a wide Ct range and representing HBV genotypes A-E. Across all samples, the median genome coverage was approximately 50%, although recovery varied widely, ranging from complete failure to nearly full genomes. Combining all primers into a single PCR reaction, or separating overlapping amplicons into different reactions, had little overall impact on genome recovery, and no consistent differences between the two pooling strategies were observed. In contrast, amplification efficiency differed markedly between individual amplicons. Amplicons 1-5 generally produced higher sequencing depth, whereas amplicons 6-10 frequently showed low coverage and contributed to incomplete genome recovery. Genome coverage was strongly associated with Ct values, with higher coverage observed in samples with lower Ct values, while coverage was broadly similar across genotypes. These results demonstrate that the Ringlander et al. primer scheme can be adapted for multiplex PCR and Nanopore sequencing of HBV, but uneven amplicon performance limits consistent full-genome recovery and highlights the need for further optimization of HBV tiling PCR designs.

There is an ongoing Oropouche Fever (OF) outbreak in Brazil since 2024. There are dengue and chikungunya prediction models available, but none to help discriminate dengue, chikungunya, and OF. Objective: This study aims to develop and validate clinical prediction models for dengue, chikungunya, OF. Methods: This study uses surveillance data from Espirito Santo state / Brazil, from 2023-2025. Epidemiological investigations and biological samples were used to conclude cases as either (a) clinical-epidemiologically confirmed, (b) laboratory confirmed, or (c) discarded. The predictors were all data related to signs, symptoms, and comorbidities available in the notification forms. The analysis was performed using random forest regression models, one for each outcome, in development and validation datasets. Results: A total of 465,280 observations were analyzed, 261,691 dengue cases (56.6%), 18,676 chikungunya cases (4.0%), 12,174 OF cases (2.6%), and 179,115 discarded cases (38.6%). All three models had good discrimination and moderate to good calibration after scaling prediction. The models retained from 26 to 16 predictors each. Leukopenia and vomiting were the most discriminatory predictors for dengue, arthritis, arthralgia, and rash were the most discriminatory for chikungunya, and epidemiological features were the most relevant for OF. The dengue, chikungunya, and OF models had ROC AUC of 0.726, 0.851, and 0.896 in the validation set, respectively. Conclusion: This research identified predictors most discriminative between dengue, chikungunya, and OF. We developed and validated predictive models, one for each condition, with moderate to very good performance available at https://pedrobrasil.shinyapps.io/INDWELL/. One may use them in diagnostic work-up and arbovirus surveillance.

Morgellons disease is a poorly understood and controversial condition characterized by cutaneous, often fibrous lesions, as well as variable systemic symptoms, such as fatigue, muscle and joint pain, and cognitive dysfunction. While there have been links suggested between Morgellons and known pathogens, most frequently Borrelia burgdorferi, the current medical consensus is that Morgellons disease is a form of delusional parasitosis, where patients falsely believe they are infected with parasites. Despite this controversy, there has not been a deep metagenomic exploration of Morgellons disease. Here, we use deep metagenomic sequencing and metagenomic analysis to characterize Morgellons lesions and unaffected skin from five individuals in a family cohort. We find that Morgellons lesions contain sequences poorly represented in existing databases, and demonstrate that lesions may harbor sequences with novel function. We further demonstrate that MAGs assembled from lesion samples vary taxonomically from MAGs assembled from unaffected skin, and that there is a phylogenetically informed microbial signature associated with Morgellons lesions. These findings motivate further investigation into a possible microbial etiology in Morgellons disease.

Purpose/ObjectiveThis study aimed to design and computationally evaluate a synthetic GluN1-mimetic peptide as a decoy to bind and neutralize pathogenic autoantibodies in anti-NMDA receptor (NMDAR) encephalitis, a severe autoimmune neurological disorder affecting approximately 1.5 per million individuals annually. MethodsKey GluN1 epitope residues (351-390 of the amino-terminal domain) were identified from crystallographic evidence and patient-derived antibody binding studies. Multiple peptide variants were rationally designed to mimic the antibody-binding interface. AlphaFold2 was used to predict peptide structures. Rigid-body docking simulations were conducted with HADDOCK 2.4 to model peptide-antibody complexes, and binding affinities were quantified using PRODIGY. A scrambled peptide control was included to establish docking specificity. ResultsThe top-performing peptide demonstrated favorable predicted binding ({Delta}G = -21.5 kcal/mol, Kd = 1.7 x 10-{superscript 1} M) with an average pLDDT score of 90%, a buried surface area of 3,255.5 [A]{superscript 2}, and 18 intermolecular hydrogen bonds. Relative to the scrambled control ({Delta}G = -8.3 kcal/mol), the designed peptide showed substantially stronger predicted binding. Conclusion/ImplicationsThese results support the validity of an epitope-mimicry design strategy and establish a scalable computational framework for prioritizing peptide decoy candidates applicable to other antibody-mediated autoimmune disorders. Experimental validation remains necessary to confirm real-world efficacy.

Toxoplasma gondii is a widespread human pathogen that has multiple, clinically relevant stages in its complex life cycle, including fast-replicating tachyzoites and latent bradyzoites. Bradyzoite differentiation is triggered by stress responses that lead to changes in transcription, translation, and metabolism. Two aspects of this process are addressed in this report: first, whether proteins that play roles in bradyzoite differentiation are specific to T. gondii and other bradyzoite-forming parasites of the Sarcocystidae family, and second, whether new bradyzoite differentiation proteins can be identified in T. gondii. To answer these questions, a phylogenetic approach was used, comparing proteomes of select members of the Sarcocystidae family that form morphologically different bradyzoite cysts and members of the Eimeriidae family that do not form cysts. This approach resulted in 8 distinct clusters of T. gondii proteins that reflected different conservation patterns; for example, one cluster showed conservation among all organisms, while another showed conservation in bradyzoite cyst-forming organisms. Known T. gondii proteins involved in bradyzoite differentiation were found in all clusters, indicating that this process uses both highly conserved pathways as well as bradyzoite-specific pathways. Importantly, the cluster containing proteins that are conserved in bradyzoite-forming organisms contained several known regulators of bradyzoites, and will be a source for identifying novel T. gondii proteins that are involved in bradyzoite differentiation.

Foodborne illness is a significant public health concern worldwide. Shiga toxin-producing Escherichia coli and Campylobacter species are recognized as important zoonotic bacterial pathogens contributing to human infections through the food chain, particularly via foods of animal origin. Although goat meat is in high demand in the southern region of Thailand, studies on foodborne pathogens in this livestock species remain limited. The current study aimed to (i) determine the antimicrobial susceptibility of Campylobacter spp. and STEC isolated from goats, and (ii) analyze the genetic relationships among Campylobacter spp. And E. coli O157 isolates obtained from different sources. Campylobacter jejuni and C. coli isolates were characterized based on sequences of seven housekeeping genes using the Achtman multilocus sequence typing scheme. For E. coli O157:H7, core genome multilocus sequence typing analysis was performed using whole-genome sequencing data. Genetic diversity was observed among C. jejuni, whereas a clonal population structure was detected in C. coli and E. coli O157:H7. Overlapping genetic characteristics were observed between C. jejuni isolates from goats and those previously reported in livestock and humans in Thailand. Among Campylobacter species, resistance to fluoroquinolones, including ciprofloxacin and nalidixic acid, was observed, whereas resistance to fosfomycin was most frequently detected in Shiga toxin-producing E. coli. Tetracycline-resistant isolates were identified in both Campylobacter species and Shiga toxin-producing E. coli at moderate levels. A multidrug-resistant pattern was observed only in C. coli, whereas no multidrug-resistant C. jejuni or Shiga toxin-producing E. coli isolates were detected. These findings indicate that healthy goats may serve as potential reservoirs of zoonotic pathogens and antimicrobial resistance in southern Thailand, where goat meat is frequently consumed.