Infection, Genetics and Evolution

Understanding the immune response against HIV-1 and the natural resistance exhibited by HIV-exposed Seronegative Individuals (HESN) offers the possibility of proposing new control strategies. Several studies suggest an important role of HLA and KIR genes in protecting against HIV-1 infection. Moreover, there is an important gap in the knowledge of these genetic factors in seronegative Latin American men who have sex with men (MSM), a population largely underrepresented in HIV immunogenetic studies. This study aimed to identify HLA and KIR genetic profile associated with potential resistance to HIV-1 acquisition, in a cross-sectional study including a cohort of 60 HIV-1-seronegative Colombian MSM at low and high risk of HIV-1 infection. The high-risk group showed a higher frequency of the HLA-B*18 allele, and a lower frequency of the HLA*B35, which have been previously associated with protection and susceptibility to HIV-1 infection respectively. Likewise, the high-risk group exhibited a low frequency of Bx haplotypes, a higher frequency of one AA haplotype and differences in KIR gene profile, with a low frequency of the inhibitory KIR2DL5 and both activating KIR2DS1, KIR2DS2 and KIR2DS5 genes. These findings suggest that host immunogenetic factors may contribute to resistance to HIV-1 acquisition in highly exposed individuals.

BackgroundHepatitis B virus infection remains a major public health challenge, particularly among people living with human immunodeficiency virus, due to shared transmission routes and the potential for accelerated liver disease progression. Molecular characterization of circulating HBV strains is essential for understanding viral epidemiology, mutation patterns, and implications for diagnostics and vaccination. MethodsThis study investigated the prevalence of hepatitis B infection and molecular characteristics of the hepatitis B virus surface gene among HIV-infected individuals receiving antiretroviral therapy in Nairobi County, Kenya. Plasma samples were screened for hepatitis B surface antigen using enzyme-linked immunosorbent assay. Hepatitis B viral DNA was extracted from HBsAg-positive samples and the surface gene region amplified by polymerase chain reaction. Amplified products were subjected to Sanger sequencing. Sequence assembly, genotype determination, and mutation analysis. ResultsThe prevalence of HIV/HBV co-infection among HIV-positive individuals was determined to be 8.97%. Genotype analysis revealed the circulation of HBV genotype A (sub-genotypes A1 and A4) and genotype D (sub-genotypes D4 and D10) among the studied population. Amino acid sequence analysis of the major hydrophilic region of the surface gene identified several mutations, with R122K and Y134F being the most frequently observed substitutions. ConclusionHepatitis B infection remains prevalent among HIV-infected individuals receiving antiretroviral therapy in Nairobi County. The circulation of multiple hepatitis B virus genotypes and the presence of mutations within the surface gene highlight the importance of continuous molecular surveillance to monitor viral evolution and its potential implications for hepatitis B virus diagnosis, vaccination strategies, and clinical management in HIV-infected populations

IntroductionMalaria is still a pressing global health challenge, especially in sub-Saharan Africa, where behavioral factors such as alcohol consumption may exacerbate its impact. The present study is aimed at investigating the pathogenesis of alcohol-exacerbated malaria in Plasmodium berghei-infected an animal model (mice). MethodsMale mice were separated into four treatment groups: control, alcohol control, P. berghei and P. berghei plus acute alcohol treatment groups. Animals were infected with malaria through intraperitoneal injection of P. berghei and an acute dose of ethanol (20% v/v) was introduced 48 hours post-infection. Parasitaemia was monitored using the Giemsa-stained thin blood smears. Haematological parameters were assessed using automated blood analyser. Liver function was evaluated by measuring serum levels of AST and ALT and cytokine profiles (TNF-, INF-{gamma}, IL-6, IL-1{beta}) were quantified using ELISA kits. ResultsResults show that acute alcohol intake led to a significant increase in parasitaemia in the P. berghei group (p<0.01). Haematological analysis revealed a significant (p<0.001) reduction in RBC count, haemoglobin levels, haematocrit percentage, platelet count and others in the P. berghei plus acute alcohol group. Liver enzyme assays revealed an elevated AST and ALT levels (p<0.001) in the P. berghei group. Cytokine analysis revealed a significant (p<0.01) upregulation of pro-inflammatory cytokines (TNF- INF-{gamma}, IL-1{beta} and IL-6), due to acute alcohol. These results suggest that alcohol exacerbates malaria pathogenesis by increasing parasitaemia, promoting immune dysregulation and liver injury, mediated by a shift toward a pro-inflammatory cytokine profile.

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.

In spite of well-established global immune landscape, SARS-CoV-2 is still able to further spread and continue causing infection waves. The current understanding about the reason behind is limited, and it is still difficult to predict the evolution or spreading tread of SARS-CoV-2. Therefore, it is necessary to investigate whether the establishment of population immunity has changed the virus evolution or spreading pattern. In this investigation, one overall analysis of the SARS-CoV-2 spreading in the past several years have been carried out through one thorough genomic epidemiology study, with Germany being chosen as one representative location in view of the systemic efforts for genomic surveillance. The growth advantage of a few predominant variants in its early spreading period has been evaluated through a logistic regression model. The results have revealed that the major circulating SARS-CoV-2 variants since 2023 are mainly derived from the Omicron BA.2 family. Since middle of 2024, most predominant variants were produced primarily through recombination, indicating that the evolution derived from recombination might be the major driving force for the continuous spread of SARS-CoV-2 despite the existence of population immunity. Furthermore, the lower growth advantage of recently emerged variants might possibly lead to a tread of reduction in the frequency of infection wave. The information revealed from this investigation suggests that although short-term spreading tread can be affected by specific virus feature as well as local immunity landscape, the long-term spreading tread is mainly decided by the genomic diversity of the viruses, and can be predicted through phylogenetic and genomic epidemiology investigation. The results have emphasized the importance of maintaining the efforts for genomic surveillance of SARS-CoV-2, which is essential from both medical and research perspectives.

Since the initial distribution of the SARS-CoV-19 vaccine, its widespread use has been hypothesized to act as a selective pressure that drives the COVID-19 virus to mutate. This study aims to investigate the correlation between global vaccination rates and the mutation rate of the SARS-CoV-2 Beta variant (B.1.351). From January to July 2021, nucleotide diversity increased in tandem with vaccination rates, demonstrating that the virus evolved more rapidly in response to selective pressure from mass vaccination. Statistical analysis revealed statistically significant positive correlations between both vaccination rates and vaccine doses administered with nucleotide diversity. Thus, our findings indicate a positive correlation between rising vaccination rates and nucleotide diversity, suggesting that increased vaccination coverage acted as a selective pressure that accelerated viral evolution of SARS CoV2.

Malaria is one of the deadliest diseases in sub-Saharan Africa and Southeast Asia. The majority of the fatalities occur mostly in children under 5 years and pregnant women and this is due to infection by Plasmodium spp, of which Plasmodium falciparum is the most virulent and is responsible for most of the morbidity and mortality. Despite various public health interventions such as use of insecticide-treated bed nets, spraying of homes with insecticides and use of WHO recommended artemisinin-based combination therapies (ACT), malaria prevention still faces major setback due to drug and insecticide resistance by P. falciparum and mosquitoes respectively. The study uses molecular docking and immunoinformatics to screen various Plasmodium spp antigens and evaluate their antigenicity and suitability as vaccine candidates. The P. falciparum antigens and T-cell receptor (TCR) structures were obtained from Protein Data Bank (PDB) based on a range of factors related to their role in the lifecycle of the parasite and their status as vaccine targets. Protein structures not available in the PDB were predicted using AlphaFold. The 3D structures of selected P. falciparum antigens and TCR structures were downloaded in PDB format then all water molecules, Hetatm, and bound ligands were deleted from the protein structures using BIOVIA Discovery Studio Visualizer. Subsequently, molecular docking was done using ClusPro v2.0 server and docked complexes were compared. The findings of this study gave valuable insights into the interaction of human immune response with P. falciparum antigens. The best three ranked antigen complexes are PfCyRPA, PfMSP10 and PfCSP and this confirm their use as potential candidates for vaccine development. This study highlights the usefulness of computational docking in identifying P. falciparum antigens of excellent immunogenic potential as vaccine candidates.

We sequenced the nearly complete mitochondrial genome of the hammerhead flatworm Bipalium nobile Kawakatsu and Makino, 1982 using short-read sequencing technology, yielding a 16,018 bp genome comprising 12 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The composition and order of genes were consistent with those observed in the closely related species Bipalium kewense and Diversibipalium multilineatum, except for the position of tRNA-Glu. Phylogenetic analysis based on all mitochondrial proteins from species within the family Geoplanidae supports the monophyly of a clade comprising B. nobile, B. kewense, and D. multilineatum. The mitochondrial genome sequence obtained in this study provides a valuable resource for investigating the genetic diversity and population structure of B. nobile, a soil-dwelling predator with the potential for global spread as an invasive organism.

Burkholderia mallei, a facultative intracellular Gram-negative pathogen, is the causative agent of glanders that primarily affects solipeds and sporadically transmitted to humans. Current interventions mainly rely on antibiotics; however, increasing resistance and the lack of a licensed vaccine further complicate disease management. In the present study, a consensus-based computational framework was employed on the B. mallei turkey2 proteome. Total 59 proteins - including porins, TonB receptors, autotransporters, and efflux components - were identified as surface exposed outer membrane {beta}-barrel (OMBB) proteins that were used to design a multi-epitope vaccine (MEV) construct. B- and T-cell epitopes were predicted from 59 proteins, and ten epitopes each of cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell were chosen based on their antigenicity, non-allergenicity, non-toxicity, surface accessibility, and conservation across 32 B. mallei strains. The MEV was included with suitable adjuvants at the N-terminus to enhance its immunogenicity. The 780 amino acid MEV construct was predicted to be antigenic, and soluble upon overexpression with 62.69% random coils, while the rest formed -helices and {beta}-strands. The tertiary structure of the MEV was generated and subsequently validated, indicating good structural quality. Molecular docking of the MEV with toll-like receptor 4 (TLR4) demonstrated strong affinity, and molecular dynamics simulation confirmed the structural stability of the MEV-TLR4 complex. In-silico immune simulation showed the capability of MEV to induce a strong immune response. The study proposes an MEV construct by utilizing surface exposed OMBB proteins which directly interact with the host and serve as effective immunogenic targets against B. mallei infection. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/727591v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@10cd6d8org.highwire.dtl.DTLVardef@1ed3f0borg.highwire.dtl.DTLVardef@c6173forg.highwire.dtl.DTLVardef@1204f73_HPS_FORMAT_FIGEXP M_FIG C_FIG

Bovine tuberculosis (TB), caused by Mycobacterium bovis, has become a global concern over the last two decades. Bovine TB primarily affects cattle, but other domestic livestock are also affected and it is more common in less developed and developing countries. The significant loss of livestock leads to trade restrictions and economic crises. Zoonotic potential of bovine TB raises health concerns for the public. Currently, no effective treatment is available and animal slaughtering is usually undertaken to reduce the burden of it in the environment. Antibiotic therapy can be used on animals living in captivity, but it is not reliable for herd or free-grazing animals. The BCG vaccine is another option available for treating the disease, but it shows limited efficacy in cattle. The prevention of bovine TB is a long-term goal that can only be accomplished by developing a more effective vaccine than BCG and designing new drugs. In this research, we propose therapeutic drug targets and vaccine for treating bovine TB. The conceptual framework for vaccine developed in this study uses a number of bioinformatics approaches to identify potential vaccine candidates and construct an in-silico epitope-based vaccine. Our holistic framework identified potential therapeutic candidates by directly analysing the proteome of TB bacterial strains. Specifically, we performed a comparative proteomic analysis of 11 Mycobacterium bovis strains to cover the diversity and identify conserved proteins among those strains for developing the bovine TB vaccine. An extensive reverse vaccinology and immunoinformatics analysis provided 26 highly immunogenic, non-toxic and non-allergenic epitopes (CTL epitopes-8, HTL epitopes-2 and B-cell epitopes-16) for Mycobacterium bovis required for three-dimensional structure construction of TB vaccine. The constructed epitope-based vaccine showed a potent interaction inside the host, thus generating efficient cell-mediated and humoral immune responses. Next, a framework based on a novel subtractive proteomic approach was developed for identifying bovine TB drug targets. We performed this approach on the 11 Mycobacterium bovis strains and identified nine drug targets that are conserved, essential, antigenic and have unique metabolic pathways in Mycobacterium bovis. These drug targets could further help investigate therapeutic drugs for the treatment of bovine TB. Several bioinformatics prediction tools were used together to ensure checks and balances, aiming to reduce the chance of errors and provide accurate results. The vaccine and drug targets developed in this study can be tested experimentally with confidence for further validation as therapeutics with the potential to eradicate bovine TB globally. The strategies implemented in the study are generic and can be used for other zoonotic infectious diseases. This study would be a game changer in the field of bovine tuberculosis treatment.

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants caused by the peste des petits ruminants virus (PPRV), which is classified into four distinct genetic lineages (I-IV). A critical concern in the recent epidemiological history of PPRV is the rapid and widespread expansion of lineage IV (LIV) across West Africa over the past decade. This dominance suggests a potential adaptive advantage of circulating LIV strains in the regions current epidemiological context. In this study, we obtain the genome sequence of 26 new PPRV samples, including historical (pre-2000) and many recent African LIV isolates, offering the first opportunity to investigate the evolutionary history of LIV in Africa and identify genetic events potentially associated with its recent spread. Phylogenomic analyses implemented on a dataset of 167 curated PPRV genome sequences reveal that the most ancestral LIV group comprises strains circulating in Sub-Saharan Africa (designated clade LIVssa), providing robust evidence for an African origin of lineage IV. Our results further indicate that PPRV strains linked to the recent West African expansion of LIV belong to a specific LIVssa subgroup, termed NigB. We identified multiple signatures of selection pressure within the LIVssa sublineage, particularly in the NigB cluster. Several amino acid substitutions unique to LIVssa or NigB were detected, some of which may impact protein function and warrant prioritised investigation. Additional genomic data are required to confirm the association between the NigB group and the ongoing spread of LIV in West Africa. The evolutionary adaptations observed in LIVssa - potentially enhancing transmission efficiency, host range or pathogenicity - could undermine current disease control strategies in regions where PPR poses significant threats to food security and local economies. Author SummaryPeste des petits ruminants virus (PPRV) infects sheep and goats across Africa, Middle East, Asia and Europe, causing disease with major impact on global economy and food security. One genetic lineage of PPRV, called lineage IV (LIV), is at the origin of most recent expansion of the distribution of the disease, including replacement of other lineages in areas of African where PPRV is historically present. Here, we generated genome sequences from PPRV LIV isolates from different dates and places to study the evolution of this genetic lineage and explore whether its recent spread can be associated with the appearance of new mutations in the virus genome. Our results provide evidence that the PPRV LIV originated in Sub-Saharan Africa and identify mutations present only virus isolates currently spready in new regions of Africa. Further research should investigate the impact of these mutations on protein functions and capacity of transmission of PPRV.

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.

BackgroundDengue virus infection remains a significant public health concern in India, with changing serotype dynamics influencing disease epidemiology. Understanding local serotype distribution and clinical characteristics is crucial for effective disease management and surveillance. ObjectivesTo determine the prevalence of dengue virus serotypes and analyze their clinical characteristics among NS1-positive patients at a tertiary-care hospital in Gujarat, India. MethodsA cross-sectional study was conducted on NS1-positive dengue patients admitted to AIIMS Rajkot from September 2023 to November 2024. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed for serotype identification. Clinical and demographic data were collected and analyzed. ResultsNS1-positive patients (70) were confirmed by RT-PCR. DENV-2 was the predominant serotype (53 cases, 75.7%), followed by DENV-1 and DENV-3 (7 cases each, 10.0%), and DENV-4 (2 cases, 2.9%). One co-infection case (DENV-2 + DENV-3) (1.4%) was identified. The mean age was 27.7 {+/-} 14.4 years, with male predominance (58.6%). Young adults (19-35 years) were most affected (45.7%), followed by pediatric patients [&le;]18 years (32.9%). Severe dengue occurred in only one case (1.4%), while hospitalization was required in 25 cases (35.7%). All patients presented with fever, chills, headache (50%), rashes (56%), and malaise (56%), being the most common associated symptoms. ConclusionsDENV-2 showed clear predominance in the Rajkot region during the study period, with low rates of severe disease. The significant pediatric and young adult involvement highlights the need for targeted prevention strategies. These findings contribute to the understanding of regional dengue epidemiology and support evidence-based surveillance and control measures.

Cryptosporidium parvum is a protozoan parasite responsible for cryptosporidiosis, significantly threatening immunocompromised individuals, particularly HIV/AIDS patients, by causing severe diarrhea and potential mortality. Current treatments are largely ineffective, prompting investigations into new therapeutic options. This study evaluated two antiparasitic drugs: Mebendazole, used for helminth infections, and Artemisinin, used for malaria. The SKSR gene family encodes virulence factors in C. parvum, and Calcium-dependent protein kinase1 (CpCDPK1) regulates the life cycle of C. parvum; targeting these proteins may reduce growth and infection in hosts. In the current study, molecular docking was conducted taking Mebendazole and Artemisinin drugs as ligands, SKSR gene family and CpCDPK1 proteins as drug targets. Results with SKSR showed binding energy of -4.9 kcal/mol, -6.72 kcal/mol for Mebendazole and Artemisinin, respectively. Whereas, with CpCDPK1, the binding energies were -6.44 kcal/mol, -9.18 kcal/mol for Mebendazole and Artemisinin, respectively. Docking of Nitazoxanide (an in-use drug for C. parvum) with SKSR and CpCDPK1 revealed binding energies -4.2 kcal/mol, -4.81 kcal/mol, respectively. The stability of the proteins (targets) upon binding to the ligands was assessed by performing all-atom MD simulations for 100ns using the GROMACS package. No major variations were observed upon binding of Artemisinin and Mebendazole to SKSR and CpCDPK1. The findings of MD simulations imply that both proteins maintain their stability upon binding of Artemisinin and Mebendazole. Molecular Docking and MD simulation studies suggest that Artemisinin and Mebendazole are potential candidates for repurposing in the treatment of C. parvum infections, with recommendations for in vitro studies to validate these findings.

Pasteurella multocida is a facultative anaerobic, Gram-negative coccobacillus that causes pasteurellosis in companion animals (cats and dogs), livestock, and poultry. Close contact with infected animals poses a significant zoonotic risk to humans through bite wounds, scratches, licking and transfer of bodily fluids. Current treatment relies mainly on antibiotics, and the lack of a licensed human vaccine further exacerbates the challenge. In the present study, a consensus-based computational approach was employed on the P. multocida Past 9 proteome. A total of 29 outer membrane {beta}-barrel (OMBB) proteins, including TonB-dependent receptors, porins, autotransporters, adhesins and efflux pumps, were identified and used to design a multi-epitope vaccine (MEV) construct. B-cell and T-cell epitopes were predicted from the identified proteins. Ten epitopes each of cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL), and three B-cell epitopes were selected based on their antigenicity, non-allergenicity, non-toxicity, surface accessibility, and conservation across eight P. multocida human-infecting strains. The MEV was supplemented with suitable adjuvants at the N-terminus to enhance its immunogenicity. The MEV construct, with a length of 459 amino acids, was predicted to be antigenic, non-allergenic, non-toxic and soluble upon expression. The MEV structural model was generated and subsequently validated, which indicated good structural quality. Molecular docking between MEV and human toll-like receptor 4 (TLR4) demonstrated strong binding affinity, and molecular dynamics simulation confirmed the structural stability of the MEV-TLR4 complex. Immune simulation of the MEV construct elicited a strong immune response. This study proposes a designed MEV candidate against human pasteurellosis and highlights OMBB proteins as potential immunogenic targets for vaccine development. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/728361v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@320d63org.highwire.dtl.DTLVardef@d0ddeorg.highwire.dtl.DTLVardef@1099802org.highwire.dtl.DTLVardef@dab304_HPS_FORMAT_FIGEXP M_FIG C_FIG

Treponema pallidum ssp. pallidum, the causative agent of syphilis, has a small proteome and encompasses numerous strains. Knowledge gaps remain in understanding the molecular mechanisms of pathogenesis of this bacterium, as well as the structure and function of the full complement of proteins encoded by T. pallidum. Here, an AI-based structure-to-function modeling workflow was used to investigate the complement of proteins encoded by T. pallidum. High-confidence structure models were generated for 976 T. pallidum proteins, covering 99% of the proteome. Analysis of the generated models using the protein structure comparison server DALI enabled high-confidence, structure-based functional annotation of 877 T. pallidum proteins, including 240 of the 323 proteins of unknown function encoded by this pathogen. Additionally, 63 putative pathogenesis related proteins (PPRPs) and seven treponemal proteins with previously uncharacterized similarity to outer membrane proteins (OMPs) from Gram-negative bacteria were identified. A workflow for B cell epitope (BCE) prediction identified 1133 surface-exposed, host-facing potential epitopes in known and predicted T. pallidum OMPs, of which 92 were prioritized based on bioinformatic analyses, biophysical properties, amino acid sequence conservation, and previous protein expression data. This work provides insight into T. pallidum pathogenesis through structure modeling-based functional annotation, including characterization of proteins of unknown function. This study also informs syphilis vaccine design by identifying new potential T. pallidum OMPs, as well as host-facing regions of T. pallidum OMPs that have conserved amino acid sequences in globally circulating strains. Statement of importance/impactThis study presents the first AI-based global structure modeling-to-function analysis of the proteome of Treponema pallidum, the bacterium that causes syphilis. Structure-based functional predictions of previously uncharacterized proteins, including proteins potentially involved in virulence, provide novel insight into mechanisms of pathogenesis. The work also informs syphilis vaccine development by the identification and structural characterization of new candidate vaccine proteins in globally circulating strains of T. pallidum.

The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome, PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and non-model based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data, and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time [~]140,000 generations ago from an ancestral population of [~]65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of [~]220,000 individuals in the Chinese population and [~]14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.

Tomato brown rugose fruit virus (Tobamovirus fructirugosum) is an emerging virus that affects tomatoes, capsicum, and chili. Since its first detection in Jordan in 2015, the virus was reported in more than 40 countries across all the continents. In Morocco, the virus was reported for the first time in October 2021. However, its genetic diversity remains unexplored. In this work, we used a collection of tomato fruits from local markets to investigate the variability of the virus in the country. We explored the different pressures acting on the N-terminus of the RNA-dependent RNA polymerase, the movement protein, and the coat protein genes. Then, we used haplotype network analyses to reveal the population structure within the Moroccan isolates and studied their relationships with the ones from the world. We found that genetic diversity is low, which is consistent with the global situation. No signatures of diversifying selection were detected across the analyzed genes. However, the virus sequences from Morocco showed a clear geographic structure, suggesting that geographic factors probably combined with agricultural practices may contribute to shaping the population structure of ToBRFV in Morocco.

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.