Rabies is a viral zoonosis that causes an estimated 60,000 human deaths each year, mainly in Africa and Asia. The etiological agent of rabies, the Rabies Lyssavirus or Rabies Virus (RABV) has been characterized in dog populations in Cameroon, in previous studies. However, the dynamics of RABV maintenance and propagation in dogs are still to be documented in Cameroon. This study thus, aimed at investigating the spatial and temporal dynamics of RABV variants in Cameroon. Long genomic sequences of about 4893 nucleotides, encompassing the N, P, M and G genes as well as part of the G-L intergenic region (Ψ), were determined from 56 RABV strains recovered from dog populations in Cameroon from 2010 to 2021. Temporal and spatial dynamics of RABV circulation in Cameroon were investigated by Bayesian analyses with the BEAST 1.10.4 package from extended RABV genomic sequences data combined with their collection dates and the geographical coordinates of their sampling areas. This revealed a genetic evolution rate of 3.14 × 10 substitutions/site/year among Africa-1a and Africa-2 clades of RABV from Cameroon. The most recent common ancestor (MRCA) of the studied strains of the Africa-1a lineage was estimated to have emerged between 1880 and 1906 (95 % HPD; mean 1894), while that of the strains of the Africa-2 clade had a slightly later estimated origin between 1907 and 1928 (95 % HPD, mean 1918). Overall, phylogeographic analyses suggested RABV spread in Cameroon between sub-national regions. Our data provides substantial support to previous findings from similar epidemiological settings, indicating human mediated movements of infected dogs between distant cities may be a key factor in the maintenance of the enzootic cycle of rabies among dogs in Cameroon.

Hepatitis D virus (HDV) is currently classified into 8 genotypes (1 to 8) and several subgenotypes, with distinct distribution worldwide. However, due to the scarcity of complete genome sequences in databases, this classification is constantly being updated and tends to be regularly revisited in upcoming years as more sequence data becomes available. Aiming to increase knowledge about the genetic variability of HDV, this study presents the full-length genomes of 11 HDV samples collected in Brazil in endemic and non-endemic regions, including the first complete genomes of the genotypes 5 and 8 obtained outside Africa. We also determined the co-infecting HBV genotypes to investigate their prevalence among the HDV-infected individuals throughout the country. Whole genome sequencing confirmed our previous findings based on a partial fragment of the HDV genome, in which HDV subgenoypes 3c (9/11; 81.8 %), 5b (1/11; 9.1 %) and one HDV-8 sequence (1/11; 9.1 %) were detected. As previously observed, HDV-8 formed a distinct branch apart from subgenotypes 8a and 8b, a monophyletic clade representing a novel HDV-8 subgenotype, designated as 8c. Among HDV-3 samples, the main co-infecting HBV genotype found was HBV-F (4/8; 50 %), reflecting the higher incidence of this native South American genotype in the endemic Amazon Basin. Both samples infected with HDV-5 and HDV-8 were coinfected with HBV genotype E, also a genotype with African origin. Our findings based on complete genome sequence of HDV corroborated our results based on a partial region of the HDV genome of a novel HDV-8 subgenotype and reinforced the need to use full-length genomes to properly subdivide genotypes with very low intragroup genetic variability, such as HDV-3. The provision of these complete genomes is expected to contribute to the enrichment of sequence databases for future molecular and evolutionary investigations of HDV.

Genetic evolution of resistance due to mutations and transposon insertions is the primary cause of antimicrobial resistance in Streptococcus pneumoniae. Resistance to macrolide, tetracycline, and chloramphenicol is caused by the insertion of specific genes that carried by transposon (Tn). This study aims to analyze transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of S. pneumoniae serotype 19F in Indonesia. S. pneumoniae serotype 19F isolates were collected from nasopharyngeal swab specimens from different regions in Indonesia. Genomic DNA was extracted from sixteen isolates and whole genome sequencing was performed on Illumina platform. Raw sequence data were analyzed using de novo assembly by ASAP and Microscope server. The presence of transposons was identified with detection of int and xis genes and visualized by pyGenomeViz. The genome size of S. pneumoniae ranges from 2,040,117 bp to 2,437,939 bp, with a GC content of around 39 %. ST1464 (4/16) and ST271 (3/16) were found as the predominant sequence type among isolates. Tn2010 was the most common transposon among S. pneumoniae serotype 19F isolates (7/16) followed by Tn2009 (4/16), and Tn5253 (3/16). We identified two deletion sites within the tetM gene (2 bp and 58 bp) that confer tetracycline susceptibility from one isolate. This study suggests that genomic analysis can be employed for the detection and surveillance of antimicrobial resistance genes among S. pneumoniae strains isolated from various regions in Indonesia.

Taenia multiceps is a neglected parasite having veterinary and public health importance. The predilection sites of the parasite larva (Coenurus cerebralis) are brain (cerebral coenurosis) and subcutaneous (non-cerebral coenurosis). There is a dearth of data regarding molecular characterization of T. multiceps and even fewer population structure-based studies on T. multiceps. The current study was conducted to provide epidemiological information regarding the global population structure of the parasite. The NCBI GenBank database was accessed to download the sequences of cox1 gene, which were further subjected to PopArt software to construct median-joining networks. The DnaSp software was used to compute neutrality and diversity indices. Host and region-wise indices of neutrality and diversity were also computed. There were 166 gene sequences found in the NCBI database. Followed by removal of short gene sequences, 143 were considered to perform bioinformatic analyses. A total of 30 haplotypes with 46 mutations and 23 parsimony informative sites were found. High diversity (Hd = 0.889, π = 0.01186) and negative but statistically insignificant neutrality indices (Tajima's D = -1.57659, Fu's Fs = -10.552) were found. Region-wise results revealed highest haplotype diversities in isolates from KSA (Hd = 1.00) followed by Greece and Italy (Hd = 0.962), and China (Hd = 0.931). Host-wise data analysis showed an overall negative Tajima's D value and there exists highest haplotype diversity in cattle (Hd = 1.00) followed by dogs (Hd = 0.833), sheep (Hd = 0.795) and goats (Hd = 0.788). The findings of the study indicate that the population diversity of T. multiceps will increase worldwide as shown by high diversity and negative neutrality indices. The findings of the study significantly add-in to the existing bank of knowledge about population structure of T. multiceps. We recommend conducting more studies employing different genetic markers to better comprehend the epidemiology of the parasite.

Territories in southern parts of Eastern Europe and in the Caucasus are endemic for tick-borne relapsing fever (TBRF), caused by Borrelia caucasica. This spirochete is transmitted exclusively by the bites of Ornithodoros verrucosus; however, the distribution and genetic diversity of the tick vector have not been explored. To address this, we performed a phylogeographic study of O. verrucosus specimens collected across a large geographic distribution. We sequenced and analyzed complete mitochondrial genomes of 54 individual O. verrucosus ticks representing 23 geographically diverse populations from Ukraine, Georgia, and Azerbaijan. We detected 47 unique haplotypes, with every collection site exhibiting distinct polymorphisms. This, along with other population genetic indices, suggests little evidence of gene flow between populations. The Bayesian coalescent analysis revealed the presence of four lineages that diverged in the Middle Pleistocene (770-126 kya). Two lineages were widespread and present in all study regions, while the other two were restricted to the southern foothills of the Lesser Caucasus mountain range. The sympatry of these ancient lineages suggests that isolation by environment, in addition to geographic distance, may play a role in the intraspecific divergence of tick populations. Using a phylogeographic approach, we provide a snapshot of genetic diversity in O. verrucosus and discuss the evolutionary history of the tick vector.

Feline bocaviruses (FBoVs) have been discovered for a decade and are often detected in feces, possibly associated with diarrhea in cats. Studies on FBoV evolution remain limited and have mainly focused on prevalence and genetic characterization. Although genetic recombination serves as a potential mechanism in bocavirus evolution, research on this process for FBoVs has been scarce. In this study, we characterized 19 complete coding sequences of FBoVs obtained from Thai cats, revealing that FBoV-1, -2, and -3 were endemic in Thailand. Genetic characterizations showed that most Thai FBoVs were closely related to previously detected strains in Thailand and China. Recombination analyses indicated intragenic, intraspecies recombination in all FBoV species, with recombination breakpoints commonly found in the NP1 and VP1/2 genes, highlighting these genes may be hotspots for FBoV recombination. However, no interspecies recombination was detected. Selective pressure analysis of various FBoV genes revealed that these viruses underwent purifying selection. Although the VP1/2 gene of all FBoV species was under the strongest negative selection pressure, positive selection sites were only found in FBoV-1 and FBoV-3. This study is the first to identify natural recombination in FBoV-2 and FBoV-3 and provides evidence that genetic recombination is a potential driver of FBoV evolutions. Additionally, this study offers up-to-date information on the genetic characteristics, evolutionary dynamics, and selective pressure status of FBoVs, which should be continuously monitored.

Dengue is a widespread viral infection transmitted from mosquitoes to humans, mainly in tropical and subtropical climates. In Benin, only dengue virus (DENV) serotype 2 infection has been previously described in humans. This study aimed to investigate DENV infection and serotypes in suspected patients.

Canine babesiosis, a severe haemoparasitic disease caused by Babesia species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of B. vogeli on the basis of the internal transcribed spacer regions (ITS1-5.8S-ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (n = 62) exhibited 92.5-100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5-93.8 % between them. Notably, the newly generated Indian sequences (n = 21) demonstrated a high degree of homology, with 98.3-100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different B. vogeli populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2-25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The B. vogeli populations between Thailand and Tunisia exhibited the highest genetic differentiation (F = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of B. vogeli indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-term molecular surveillance program. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of B. vogeli were observed on the basis of internal transcribed spacer regions (ITS1-5.8S-ITS2).

Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host-virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome b amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus Circovirus, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host-virus interactions.

Bats comprise one of the most diverse and abundant groups of mammals in the world and host a significant viral diversity with zoonotic potential. Bat adenoviruses (bat AdVs), members of the family Adenoviridae, have been detected in several bat species, suggesting that bats are natural reservoirs. Here, faeces and rectal/anal-swabs were collected from 321 bats of an urban Atlantic Forest remnant from Rio de Janeiro, during 2019-2022, and screened for bat AdV nucleic acid with PCR. The positivity of bat AdVs was 3.7 % (12/321). Twelve individuals of four bat species were infected: Artibeus lituratus (66.7 %; 8/12), Desmodus rotundus (8.3 %; 1/12), Platyrrhinus lineatus (16.7 %; 2/12), and Sturnira lilium (8.3 %; 1/12). Phylogenetic analysis based on nucleotide and amino acid sequences showed that the detected bat AdVs clustered into four clades corresponding to the host species, identifying the presence of two potentially new bat adenoviruses. This is the first report of bat AdV detected in Platyrrhinus lineatus.

AIDS remains a significant global health challenge since its emergence in 1981, with millions of deaths and new cases every year. The CCR5 ∆32 genetic deletion confers immunity to HIV infection by altering a cell membrane protein crucial for viral entry. Stem cell transplants from homozygous carriers of this mutation to HIV-infected individuals have resulted in viral load reduction and disease remission, suggesting a potential therapeutic avenue. This study aims to investigate the relationship between genetic ancestry and the frequency of the CCR5 ∆32 mutation in Colombian populations, exploring the feasibility of targeted donor searches based on ancestry composition. Utilizing genomic data from the CÓDIGO-Colombia consortium, comprising 532 individuals, the study assessed the presence of the CCR5 ∆32 mutation and examined if the population was on Hardy-Weinberg equilibrium. Individuals were stratified into clusters based on African, American, and European ancestry percentages, with logistic regression analysis performed to evaluate the association between ancestry and mutation frequency. Additionally, global genomic databases were utilized to visualize the worldwide distribution of the mutation. The findings revealed a significant positive association between European ancestry and the CCR5 ∆32 mutation frequency, underscoring its relevance in donor selection. African and American ancestry showed negative but non-significant associations with CCR5 ∆32 frequency, which may be attributed to the study's limitations. These results emphasize the potential importance of considering ancestry in donor selection strategies, reveal the scarcity of potential donors in Colombia, and underscore the need to consider donors from other populations with mainly European ancestry if the CCR5 ∆32 stem cell transplant becomes a routine treatment for HIV/AIDS in Colombia.

SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.

Opportunist infections caused by nontuberculous mycobacteria (NTM) have emerged as a significant public health problem. Among these, species of the Mycobacterium avium complex (MAC) are the main responsible for the increase in the number of human disease cases. In order to address the current needs in the detection and surveillance of MAC disease cases, we evaluated different species classification methodologies (BLASTn-based marker-gene approach, Kraken v2, rMLST and MLST databases) and their congruence with a core-SNP phylogenetic approach, based on whole genome sequencing (WGS) data. For this purpose, we used a collection of 142 MAC isolates from Portuguese patients diagnosed between 2014 and 2022. The marker-gene approach (based on the rpoB, hsp65 and groEL genes), showed the best results, allowing the identification of the 142 MAC isolates to the species/subspecies level (M. avium subsp. hominissuis, M. intracellulare, M. intracellulare subsp. chimaera, M. intracellulare subsp. yongonense, M. marseillence and M. colombiense). Additionally, we performed drug susceptibility testing that confirmed clarithromycin efficacy as a first-line treatment for MAC disease, as 93 % of the Portuguese isolates were susceptible. Using a core-SNP approach we also performed an in-depth phylogenetic analysis within each identified species group, and despite the high genetic diversity within the MAC species, we were able to clearly distinguish all the species/subspecies and identify genetic clusters with epidemiological potential. We highlight not only the need for the standardization of an appropriate genotyping approach for species identification and management of MAC disease, but also a more robust large-scale WGS data analysis, in a One Health perspective, in order to identify potential routes of transmission.

Arthropod microbiota plays an important role in host physiology, and there is growing interest in using vector symbionts to modify vector competence and control parasite transmission. This study aims to characterise the blackfly Simulium damnosum s.l. gut microbiota and to explore possible associations with various bio-ecological determinants of the Onchocerca volvulus establishment and the transmission in blackfly. Adult female blackflies were caught in three Cameroonian health districts belonging to different bioecological zones endemic for onchocerciasis. Flies were dissected and qPCR screened for Onchocerca volvulus infection. The diversity of the blackflies gut microbiota was assessed by high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA. Subsequent metataxo-genomic, multivariate, and association analysis were used to investigate the variables that influence the microbiota diversity. Transmission index rates ranging from 20.7 to 6.0 % and 6.2to 2.0 % for infection and infectivity rates, respectively, indicate ongoing transmission of onchocerciasis across all surveyed health districts. The identified bacterial taxa were clustered into four phyla, five classes, and 23 genera. The S. damnosum s.l. gut microbiota was dominated by Wolbachia and by Rosenbergiella in Wolbachia-free Simulium. Significant differences were observed in the diversity of S. damnosum s.l. microbiota concerning parity status (P = 0.007), health district of origin (P = 0.001), and the presence of the Onchocerca volvulus. Simulium from the Bafia health district also showed increased bacterial diversity between two consecutive years (P = 0.001). Four bacterial taxa, including Serratia, were associated with the absence of the O. volvulus infection. These results indicate that S. damnosum s.l. from different onchocerciasis foci in Cameroon, exhibit distinguishable gut microbial compositions which are dynamic over time. Some bacterial species are associated with the O. volvulus infection and could be further investigated as biological target/tool for vector modified-based onchocerciasis control.

Considering the significant role of commensal Neisseria carried in the pharynx on the variation of N.meningitidis and the acquisition of its resistance genes, understanding the true Neisseria population colonizing the human pharynx is of great significance. In this study, we carried out a five-month continuous survey of oropharyngeal carriage in a certain healthy population to reveal the long-term carriage status of different Neisseria species. Totally, 419 Neisseria strains were isolated from 203 out of 205 pharyngeal swabs of 49 participants. Using combined methods (MALDI-TOF-MS, rplF sequencing and genome sequencing), the isolates were identified as N.subflava (n = 290), N.mucosa (n = 52), N.oralis (n = 8), N.elongata group (n = 6) and non-species-confirmed (n = 63). N.subflava was isolated from all individuals and 168 swabs (81.95 %). N.mucosa, N.oralis, N.elongata and non-species-confirmed were isolated from 25 (45), 6 (7), 4 (5) and 20 (53) individuals (swabs) respectively. It was common that multiple Neisseria spp. or multiple clones of one species were isolated from a single sample. An identical strain could be isolated frequently from a single person within five months. These results indicate that Neisseria spp. and N.subflava are ubiquitous in human pharynx and both have diverse population; we should pay more attention to them when studying N.meningitidis or other respiratory pathogens; robust and handy method for identifying Neisseria species remains to be developed.

G9P[8] has been the predominant rotavirus A (RVA) genotype in Malaysia since the 2000s. However, the overall genetic makeup and evolution of Malaysian G9P[8] strains are still unknown. Therefore, this study aimed to evaluate and characterize the complete genomes of three G9P[8] RVA strains isolated from diarrheic children under five years old in Sabah. Contrary to the classical Wa-like constellation, these strains contained a DS-1-like genotype. Two strains, namely L202 and L234, were genotype G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, while one (KN102) was genotype G9-P[8]-I1-R1-C1-M1-A2-N1-T1-E1-H1. Phylogenetic analysis revealed that the NSP4 genes of L202 and L234 strains were closer to that of G9P[8]-E2 strains from Japan, suggesting they might share a common ancestor. The findings from this study provide new insights into the genetic characteristics of circulating G9P[8] strains in Sabah, which are important for rotavirus surveillance and potential vaccine development in the region.

The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter aerogenes, Corynebacterium sp., Acinetobacter sp., Aeromonas punctata, Ralstonia picketti, Staphylococcus aureus, Stenotrophomonas maltophillia, and Citrobacter freundii. The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging blaOXA-58blaOXA-22qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA, aadB, blaVIM, blaOXA-48 and blaNDM. Pseudomonas aeruginosa (1: TN/I/2020) showed presence of 3 resistance genes. qnrB (489 bp) gene was present in maximum of 7 isolates while blaVIM (196 bp) gene was present in 6 isolates. The resistance genes blaNDM (621 bp) was present in three different isolates; aac (X):6)-lb-cr (482 bp), qepA (495 bp), aadB (500 bp), blaOXA-58 (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in Pseudomonas aeruginosa. There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.

Data on HIV drug resistance in Madagascar are rare and outdated. In this study, we assessed the prevalence of HIV drug resistance mutations to antiretrovirals (ARVs) and genetic diversity of circulating strains in treatment-naive people living with HIV (PLHIV) in Madagascar.

To investigate host genetic susceptibility to tuberculosis (TB), we conducted a replication study focussed on candidate SNPs, previously reported to be associated with TB. We examined nine candidate SNPs and genotyped them in an independent cohort of TB cases and household contacts from West Bengal, India. The association with TB was replicated for rs2919643 (Chr 18), rs2057178 (Chr 11) and rs1009170 (Chr 14). rs2919643-C (p = 8.81E-5) was a risk allele and rs2057178-A (p = 0.04188) was protective against TB in our population. Association of rs1009170; previously reported by us with TB was also replicated in the new set of samples (p = 0.0359). rs2919643 is a missense variant present in linkage disequilibrium with a TB associated synonymous SNP rs61104666. The risk genotype rs2919643-CC was associated with higher levels of plasma RANTES and IL5 in household contacts. rs2919643 is an eQTL for an immunosuppressive gene SIGLEC15 and autophagy related gene EPG5. rs2057178 is an eQTL for a pseudogene and present within weak enhancer marks in the lungs. The genomic locus around this SNP rs1009170 encompasses an active transcription factor peak in CD14 monocytes and also serves as an eQTL for NDUFB1, ATXN3 and SLC24A4. TB cases with rs1009170-TT genotype showed lower expression of plasma RANTES compared to the heterozygote. All three associated SNPs have putative regulatory role in lungs and immune associated cells and organs which may be relevant to TB pathogenesis.

Effective management of emerging diseases relies on timely pathogen identification and monitoring. The emergence of COVID-19 in December 2019, rapidly evolved into a global pandemic, with millions of cases and deaths reported worldwide. The accumulation of SARS-CoV-2 genomes provided unprecedented opportunities for studying the virus's evolutionary dynamics, understanding the impact of mutations, and identifying emerging Variants of Interest (VOIs) and Variants of Concern (VOCs). During the COVID-19 pandemic, health systems faced challenges in promptly detecting such variants and timely notifying. To facilitate the continuous monitoring of mutations, various initiatives and open-source pipelines have been established. However, these platforms often lack integration for conducting user sequence analysis and comparing it with publicly reported data on platforms like GISAID. Here, we present CoVEx, an easy-to-use tool for analyzing and visualizing SARS-CoV-2 variant sequences obtained using Illumina sequencing technology. CoVEx integrates quality control, alignment, genome annotation, lineage designation, and mutation analysis tools. Implemented in Python, CoVEx also has a mutation explorer feature that generates interactive graphs summarising identified mutations in an intuitive manner. Similarly, it leverages the Outbreak.info package to create heatmaps highlighting the mutations associated with designated Pangolin lineages. Furthermore, by comparing mutation profiles against GISAID data, CoVEx offers valuable insights into the prevalence and distribution of mutations worldwide. We validated CoVEx using raw sequence data (n = 108) and demonstrated its accuracy in assembling sequences and predicting Pangolin and Nextclade Pango lineages. Notably, the tool revealed the emergence of a previously unreported mutation, ORF1a:I2501T, within the Costa Rica GN.1 lineage. This finding highlights CoVEx's capability to identify novel mutations in the different lineages, providing valuable information to researchers and public health decision makers. CoVEx and documentation are freely available on GitLab: https://gitlab.com/CNCA_CeNAT/covex.