Biology subjects

Vinetz, J. M.

Publications and source records attributed to Vinetz, J. M..

9 recordsLinked to original sources

bioRxiv2024

Genomic Analysis of Human-infecting Leptospira borgpetersenii isolates in Sri Lanka expanded PF07598 gene family repertoire, less overall genome reduction than bovine isolates

Leptospira borgpetersenii commonly causes human leptospirosis, including severe disease. The first published analysis of L. borgpetersenii, performed on two strains of serovar Hardjo (L550 and JB197), concluded that the L. borgpetersenii genome is in the process of genome decay with functional consequences leading to a more obligately host-dependent life cycle. Yet whole genome analysis has only been carried out on few strains of L. borgpetersenii, with limited closed genomes and comprehensive analysis. Herein we report the complete, circularized genomes of seven non-Hardjo Leptospira borgpetersenii isolates from human leptospirosis patients in Sri Lanka. These isolates (all ST144) were found to be nearly identical by whole genome analysis; serotyping showed they are a novel serovar. We show that the L. borgpetersenii isolated from humans in Sri Lanka are less genomically decayed than previously reported isolates: fewer pseudogenes (N=141) and Insertion Sequence (IS) elements (N=46) compared to N=248, N=270, and N=400 pseudogenes, and N=121 and N=116 IS elements in published L. borgpetersenii Hardjo genomes (L550, JB197 and TC112). Compared to previously published L. borgpetersenii whole genome analyses showing two to three VM proteins in L. borgpetersenii isolates from cattle, rats and humans, we found that all of the human L. borgpetersenii isolates from Sri Lanka, including previously reported serovar Piyasena, have 4 encoded VM proteins, one ortholog of L. interrogans Copenhageni LIC12339 and 3 orthologs of LIC12844. Our findings of fewer pseudogenes, IS elements and expansion of the LIC12844 homologs of the PF07598 family in these human isolates suggests that this newly identified L. borgpetersenii serovar from Sri Lanka has unique pathogenicity. Comparative genome analysis and experimental studies of these L. borgpetersenii isolates will enable deeper insights into the molecular and cellular mechanisms of leptospirosis pathogenesis. Author SummaryLeptospirosis is an emerging bacterial zoonosis worldwide. Leptospira borgpetersenii predominates as the cause of human leptospirosis in some agricultural contexts. We address here the relatively neglected comparative genome analysis of L. borgpetersenii. We show here that L. borgpetersenii isolated from humans in Sri Lanka have less genome reduction compared to available cattle isolates and have novel virulence characteristics compared to isolates from other animals including cattle and rats.

microbiology↗

bioRxiv2024

Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon

Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He) was similar across the subpopulations for both makers: HeMS = 0.68 - 0.78 (p = 0.23) and HeSNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04 - 0.14 and FST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (HeMS = 0 - 0.48 p = 0.03 - 1; HeSNP = 0 - 0.09, p = 0.03 - 1) and pairwise FST comparisons (FST-MS= 0.14 - 0.65, FST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.

genomics↗

bioRxiv2024

Human mobility and malaria risk in peri-urban and rural communities in the Peruvian Amazon

BackgroundWhile the global burden of malaria cases has decreased over the last two decades, the disease remains a major international threat, even on the rise in many regions. More than 85% of Peruvian malaria cases are in the Amazonian region of Loreto. Internal mobility primarily related to occupation is thought to be primarily responsible for maintaining endemicity and introducing and reintroducing malaria parasites into areas of anophelism, a challenge for malaria eradication. MethodsThe assessment of connectivity produced by human mobility was evaluated in three districts of Loreto, through 10 cross-sectional population screening from 2018 to 2020. We use social network analysis (SNA) to obtain weighted and unweighted degrees of connectivity and explore its variability by socio-demographic characteristics. In addition, we integrated travel history and malaria incidence data to estimate parasite connectivity due to internal human mobility between locations. Finally, we used logistic multivariate regressions to explore the factors associated with Plasmodium spp. infection in mobile individuals. ResultsWe found that internal human mobility results in high connectivity between communities from the Mazan, Iquitos, and San Juan Bautista districts. We identified nearby destinations that may act as sinks or sources for malaria transmission, including densely populated towns and rural campsites. In addition, we found that being a male, traveling to rural campsites, and working outdoors are associated with Plasmodium spp. infection in travelers from the Mazan district. ConclusionsWe provide compelling evidence about how human mobility connects rural communities in the Peruvian Amazon. Using SNA, we uncovered district-specific patterns and destinations, providing further evidence of human mobility heterogeneity in the region. To address the challenge of human mobility and malaria in this setting, geographic heterogeneity of malaria transmission must be considered. Author summaryMalaria transmission is complex, involving interactions of parasite, vector biology and ecology, human immune response, and human host behavior. We used social network analysis to understand how the daily lives including occupation-related mobility leads to the maintenance of malaria endemicity and transmission. Rural communities (within the districts of Mazan) and peri-urban communities around the city of Iquitos have different socio-demographic characteristics that determine malaria transmission rates. Networks of fixed rural communities and occupation-related distant camp sites play a key role as reservoirs and sources of parasite movement. Factors including male sex, outdoor occupational activity outdoors, and having rural camp sites as travel destination increase the risk of Plasmodium infection. Factors associated with occupation-related mobility are correlated with incidence and prevalence of malarial disease and parasite infection rates, respectively. This work provides a detailed understanding of the importance of work-related travel to target in malaria elimination programs, key to maintaining malaria transmission both in the Amazon region and more generally.

microbiology↗

bioRxiv2022

Plasmodium exoerythrocytic parasites redirect trafficking of human proteins to the parasitophorous vacuole

Changes in host cell morphology and transcription after apicomplexan parasite infection have long been noted, but there have been few studies of the functional consequences of host cell remodeling. Here we show, using time-dependent immunofluorescence microscopy of multiple human cell lines (HepG2, HC-04, Huh7.5.1 and primary human hepatocytes), infected with multiple Plasmodium species (Plasmodium berghei, P. falciparum and P. vivax (hypnozoites and schizonts)), and antibodies to multiple human proteins (HsNR4A3, HsMUC13, HsGOLGA8A, HsCGA, HsBiP, HsCXCL2), that human protein trafficking is extensively modified in Plasmodium infected cells. Using conventional as well as ultrastructure expansion microscopy we show that newly-synthesized human proteins are trafficked to the parasitophorous vacuole instead of the infected-cell plasma membrane, nucleus or extracellular space. Universal redirection of human signaling proteins cells the parasitophorous vacuole may provide a mechanistic explanation for how apicomplexan parasites can block host cells response to infection.

cell biology↗

bioRxiv2022

Culture-Independent Detection and Identification of Leptospira Serovars

Pathogenic Leptospira, the causative agents of leptospirosis, comprise >200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches--such as multi-locus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test--are tedious and expensive, and require isolation of the organisms in culture media--a protracted and incredibly inefficient process-- precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay--targeting a Leptospira-unique gene encoding a putative polysaccharide flippase--that provides intra-species, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32-based qPCR-based diagnostic tests. The assay, dubbed RAgI ("rage one"), is rapid and affordable, and reliably and specifically detects group I pathogenic Leptospira in culture, serum and urine, with no detectable off-target amplification--even of the genetically related but low virulence group II pathogenic (formerly "intermediate") or non-pathogenic Leptospira. It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine-samples and environmental samples containing varied and complex microbial species-consortia. And holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies.

microbiology↗

bioRxiv2021

SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2 infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named vmiR-5p (for viral miRNA), derived from the SARS-CoV-2 ORF7a transcript. Its abundance ranges from low to moderate as compared to host miRNAs. vmiR-5p functionally associates with Argonaute proteins -- core components of the RNA interference pathway -- leading to downregulation of host transcripts. One such host messenger RNA encodes Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which is linked to interferon signaling. We demonstrate that vmiR-5p production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence. Significance statementWe discovered that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) expresses a small viral non-coding RNA, named vmiR-5p (for viral miRNA), derived from the ORF7a transcript. vmiR-5p associates with the cellular RNA interference machinery to regulate host transcripts likely via target silencing. The production of vmiR-5p relies on cellular machinery and the formation of a strong hairpin within ORF7a sequences. This newly-described vmiR-5p may contribute to SARS-CoV-2 pathogenesis and could become a target for therapeutic intervention.

microbiology↗

bioRxiv2021

Population dynamics of the primary malaria vector Nyssorhynchus darlingi in a high transmission setting dominated by fish farming in western Amazonian Brazil

Vale do Rio Jurua in western Acre, Brazil, has reported highest malaria numbers since 2005, and is considered persistent transmission hotspot. Fish farming development was encouraged to improve standard of living, resulting in productive breeding sites for Amazonian malaria vector species, including Nyssorhynchus darlingi that, combined with the high human density and mobility, adds to the local malaria burden. This study reports entomological profile of immature and adult Ny. darlingi at three sites in Mancio Lima, Acre, during the rainy and dry season (February to September, 2017). From 63 fishponds, 10,859 larvae were collected, including 5,512 first-instar Anophelinae larvae and 4,927 second, third and fourth-instars, of which 8.5% (n = 420) were Ny. darlingi. This species was most abundant in not-abandoned fishponds and in the presence of emerging aquatic vegetation. Seasonal analysis of immatures in urban landscapes found no significant difference in the numbers of Ny. darlingi, corresponding to equivalent population density during the rainy to dry transition period. However, in the rural landscape, significantly higher numbers of Ny. darlingi larvae were collected in August (IRR = 5.80, p = 0.037) and September (IRR = 6.62, p = 0.023) (dry season), compared to February (rainy season), suggesting important role of fishponds for vector population maintenance during the seasonal transition in this landscape type. Adult sampling detected mainly Ny. darlingi (~93%), with similar outdoor feeding behavior, but different abundance according to landscape profile: urban site 1 showed higher peaks of human biting rate in May (46 bites/person/hour), than February (4) and September (15), while rural site 3 shows similar HBR during the same sampling period (22, 24 and 21, respectively). This study contributes to a better understanding of the larvae biology of the main malaria vector in the Vale do Rio Jurua region and, ultimately will support vector control efforts.

ecology↗

bioRxiv2020

Novel R-type Lectin Domain-Containing Cytotoxins Comprise a Family of Virulence-Modifying Proteins in Pathogenic Leptospira

Leptospirosis is a globally important neglected zoonotic disease subject to both small scale outbreaks and weather-driven, large-scale epidemics. Due to gaps in our understanding of Leptospira biology, pathogenetic mechanisms of leptospirosis remain largely unknown. Previous data suggest that a gene family, PF07598, unique amongst most known bacterial pathogens and encoding so-called "Virulence-Modifying (VM)" proteins, are important virulence determinants. Here, we show that VM proteins are potent cytotoxins, sharing a distinct domain organization while exhibiting varied mechanisms of cellular toxicity. Structural homology searches using Phyre2 suggest that VM proteins are novel R-type lectins containing an N-terminal ricin B chain-like domain. As is known for native ricin B-chain, recombinant full-length rLA3490 (most highly up-regulated in vivo) and an N-terminal fragment, t3490, containing a partial ricin B-domain, bound to asialofetuin and directly competed for asialofetuin binding with recombinant ricin B chain. While t3490 bound to the HeLa cell surface but was neither internalized nor cytotoxic, rLA3490 bound to the HeLa cell surface, was rapidly internalized, translocated to the nucleus inducing chromosomal fragmentation, and was rapidly cytolethal, providing strong evidence that Leptospira VM proteins are bona fide cytotoxins. Because monoclonal antibodies impeding cell entry or intracellular trafficking of ricin holotoxin clearly mitigate its toxicity, that VM proteins share binding and intracellular trafficking mechanisms suggests that anti-VM-protein antibody-based (anti-toxin) therapeutics could ameliorate severe complications of leptospirosis thereby improving prognosis. As most VM proteins are restricted to high-virulence Leptospira species with some, e.g., LA3490, being exceptionally potent, their level in serum might be a potentially useful indicator of a poor prognosis, thus identifying high risk patients. Author SummaryThe PF07598 gene family encoding Virulence-Modifying (VM) proteins in pathogenic Leptospira species is associated with severe manifestations of leptospirosis. Structural homology searches indicate that VM proteins contain an N-terminal ricin B chain-like domain, biochemically confirmed in asialofetuin binding and competitive-binding assays suggesting that VM proteins bind to terminal galactosyl residues of this model ricin B domain binding protein. The leptospiral N-terminal ricin B chain-like domain mediated VM protein binding to HeLa cells. Full-length recombinant protein rapidly led to cell death. Amino acid conservation among PF07598 family members at the N-terminal ricin B chain-like domain suggests that VM protein levels in serum might be a useful biomarker for quickly identifying at-risk patients, and that novel "anti-toxin"-based therapeutics could ameliorate severe complications of leptospirosis, both of which remain to be explored.

microbiology↗

bioRxiv2016

Complete avian malaria parasite genomes reveal host-specific parasite evolution in birds and mammals

Avian malaria parasites are prevalent around the world, and infect a wide diversity of bird species. Here we report the sequencing and analysis of high quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum. We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species and using amino acid divergence between species, we estimate the avian and mammalian-infective lineages diverged in the order of 10 million years ago. Consistent with their phylogenetic position, we identify orthologs of genes that had previously appeared to be restricted to the clades of parasites containing P. falciparum and P. vivax - the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show that the avian lineage is remarkable in the extent to which invasion related genes are evolving. The subtelomeres of the P. relictum and P. gallinaceum genomes contain several novel gene families, including an expanded surf multigene family. We also identify an expansion of reticulocyte binding protein homologs in P. relictum and within these proteins, we detect distinct regions that are specific to non-human primate, humans, rodent and avian hosts. For the first time in the Plasmodium lineage we find evidence of transposable elements, including several hundred fragments of LTR-retrotransposons in both species and an apparently complete LTR-retrotransposon in the genome of P. gallinaceum.

genomics↗