Results 1-25 of about 1,000
  1. Abstract Zika virus (ZIKV) garnered global attention over the past decade as outbreaks of the disease were linked to neurological complications. There are currently no antiviral drugs or vaccines with proven efficacy. The identification of human proteins targeted by ZIKV is crucial for deciphering the host pathways hijacked by the virus to replicate, evade innate immunity, and induce neuropathogenesis. In our study, Y2H screening of 8 ZIKV proteins identified 85 interacting host factors. These host factors are primarily involved in immune and inflammatory responses, cell death, centrosome and cell cycle regulation, ubiquitin pathways, central nervous system (CNS) development and neurological disorders. Rho associated coiled-coil containing protein kinase 2 (ROCK2) was selected for further evaluation of its role in ZIKV infection. Immunofluorescence staining showed colocalization between ROCK2 and ZIKV NS5 in the cell nucleus, indicating the interaction likely contributes to viral replication via immune and inflammatory responses. Further siRNA knockdown of ROCK2 resulted in significant inhibition of ZIKV genome copy number. The ZIKV-host interactome was also used as a platform to identify druggable human proteins targeted by existing host-directed antiviral drugs. Taken together, findings of this study aid in improving the understanding of ZIKV pathogenesis and identifying potential therapeutic targets.
    Date: 2024-05-22
    Authors: Komarasamy TV, Adnan NAA, Balasubramaniam VR.
    Ref: Research Square
  2. Background: Paediatric neuroblastoma and brain tumours account for a third of all childhood cancer-related mortality. High-risk neuroblastoma is highly aggressive and survival is poor despite intensive multi-modal therapies with significant toxicity. Novel therapies are desperately needed. The Zika virus (ZIKV) can access the nervous system and there is growing interest in employing ZIKV as a potential therapy against paediatric nervous system tumours, including neuroblastoma. Methods Here, we perform extensive data mining, integration and re-analysis of ZIKV infection datasets to highlight molecular mechanisms that may govern the oncolytic response in neuroblastoma cells. We collate infection data of multiple neuroblastoma cell lines by different ZIKV strains from a body of published literature to inform the susceptibility of neuroblastoma to the ZIKV oncolytic response. Integrating published transcriptomics, interaction proteomics, dependency factor and compound datasets we propose the involvement of multiple host systems during ZIKV infection. Results Through data mining of published literature, we observed most paediatric neuroblastoma cell lines to be highly susceptible to ZIKV infection and propose the PRVABC59 ZIKV strain to be the most promising candidate for neuroblastoma oncolytic virotherapy. ZIKV induces TNF signalling, lipid metabolism, the Unfolded Protein Response (UPR), and downregulates cell cycle and DNA replication processes. ZIKV infection is dependent on sterol regulatory element binding protein (SREBP)-regulated lipid metabolism and three protein complexes; V-ATPase, ER Membrane Protein Complex (EMC) and mammalian translocon. We propose ZIKV non-structural protein 4B (NS4B) as a likely mediator of ZIKVs interaction with IRE1-mediated UPR, lipid metabolism and mammalian translocon. Conclusions Our work provides a significant understanding of ZIKV infection in neuroblastoma cells, which will facilitate the progression of ZIKV-based oncolytic virotherapy through pre-clinical research and clinical trials.
    Date: 2024-05-21
    Authors: Sherwood M, Zhou Y, Sui Y, Wang Y, Skipp P, Kaid C, Gray J, Okamoto K, Ewing RM.
    Ref: F1000Res
  3. ABSTRACT Background Gestational Zika virus (ZIKV) infection is associated with the development of congenital Zika syndrome (CZS), which includes microcephaly and fetal demise. The magnitude and quality of orthoflavivirus-specific humoral immunity have been previously linked to the development of CZS. However, the role of ZIKV NS1-specific humoral immunity in mothers and children with prenatal ZIKV exposure and CZS remains undefined. In addition, considering that most of the at-risk population lives in dengue virus (DENV)-endemic areas, it is not clear what is the association between pre-existing DENV NS1-specific humoral immunity and CZS. Methods Here, we studied 328 mothers and children with a clinical diagnosis and seropositivity for ZIKV infection during pregnancy, included during the 2015-2016 ZIKV epidemic in Colombia. We also performed clinical evaluation and pediatric neurological follow-up. The relative levels of circulating NS1-specific IgM and IgG against ZIKV and DENV were evaluated in mothers and children, and the association with the development of microcephaly was analyzed. Results DENV and ZIKV IgG-NS1 antibodies in pregnant women were placentally transferred, and this passage and its duration in children depended on the maternal levels of the antibodies. We reported that higher concentrations of pre-existing DENV, but not ZIKV IgG-NS1 antibodies, were associated with a reduced risk of CZS-related microcephaly. Also, we observed that the IgM-NS1 response presents as long-term and has a minor association with poor outcomes. Conclusions The development of microcephaly in children prenatally exposed to ZIKV is associated with low plasma levels of placentally transferred, pre-existing DENV IgG-NS1 antibodies. These data are compatible with a protective role of anti-NS1 IgG antibodies against ZIKV infection during pregnancy and highlight the promising role of NS1 as an orthoflavivirus vaccine target in high-risk populations.
    Date: 2024-05-07
    Authors: Castro-Trujillo S, Mejía WR, Segura K, Vega R, Salgado D, Fonseca CE, Ortiz ÁM, Perdomo-Celis F, Bosch I, Narváez CF.
    Ref: medRxiv
  4. Abstract After the Zika virus (ZIKV) epidemic in Brazil, ZIKV infections were linked to damage to the central nervous system (CNS) and congenital anomalies. Due to the virus’s ability to cross the placenta and reach brain tissue, its effects become severe, leading to Congenital Zika Syndrome (CZS) and resulting in neuroinflammation, microglial activation, and secretion of neurotoxic factors. The presence of ZIKV triggers an inadequate fetal immune response, as the fetus only has the protection of maternal antibodies of the Immunoglobulin G (IgG) class, which are the only antibodies capable of crossing the placenta. Because of limited understanding regarding the long term consequences of ZIKV infection and the involvement of maternal antibodies, this study sought to assess the impact of the ZIKV+IgG⁺complex on murine microglial cells. The cells were exposed to ZIKV, IgG antibodies, and the ZIKV+IgG⁺complex for 24 and 72 hours. Treatment-induced cytotoxic effects were evaluated using the cell viability assay, oxidative stress, and mitochondrial membrane potential. The findings indicated that IgG antibodies exhibit cytotoxic effects on microglia, whether alone or in the presence of ZIKV, leading to compromised cell viability, disrupted mitochondrial membrane potential, and heightened oxidative damage. Our conclusion is that IgG antibodies exert detrimental effects on microglia, triggering their activation and potentially disrupting the creation of a neurotoxic environment. Moreover, the presence of antibodies may correlate with an elevated risk of ZIKV-induced neuroinflammation, contributing to long-term CNS damage.
    Date: 2024-05-07
    Authors: Siqueira LS, Rodrigues FVF, Zanatta Â, Goncalves JIB, Ghilardi IM, Alcará AM, Becker NB, Pinzetta G, Zanirati G, Becker BMA, Erwig HS, Costa JC, Marinowic DR.
    Ref: Research Square
  5. Abstract Background Arbovirus infection outbreaks are becoming more common in Africa. However, it is still difficult and crucial to better understand arbovirus transmission patterns, disease trends, and burdens. The epidemiology of these infections—dengue virus (DENV), Zika virus (ZIKV), chikungunya virus (CHIKV), West Nile virus (WNV), Rift Valley fever virus (RVFV), and yellow fever virus (YFV)—is unfortunately not well understood. This review provides an epidemiological inventory of DENV, ZIKV, CHIKV, WNV, RVFV, and YFV infections in Africa, with helpful results for risk mapping and upcoming prevention and control initiatives. Methods This systematic review protocol implements the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and an expert-evaluated design and laboratory assay and reporting evaluation (DARE) concept. Two independent reviewers conducted preliminary literature searches in PubMed in May 2023 to improve the search keywords, strategy, and inclusion criteria while considering the context and scientific significance. The final search will be conducted using PubMed, ScienceDirect (SCOPUS), the Web of Science Core Collection, African Journal Online and Google Scholar. Two reviewers will simultaneously and independently conduct searches, screen studies, and extract data. Quality assessment will be performed by two independent epidemiology experts, and discrepancies will be handled by consensus or by consulting a third reviewer. Meta-analysis will be performed to determine the pooled estimates of arbovirus circulation and transmission patterns in Africa. Discussion In this review, we present an epidemiological inventory with information that will be relevant for risk assessment, future arbovirus infection outbreak prevention, and arbovirus infection outbreak control in Africa. This will include estimating the patterns, trends, and burdens of arboviral infection across Africa, as well as identifying the regions with the highest risk of transmission. This approach will be crucial for developing well-informed policies for epidemic prevention. Systematic review registration The review is registered and accessible at Prospero with the registration ID CRD42023434939.
    Date: 2024-05-02
    Authors: Adu EA, John JH, Alani H, Wiredu AP, Boakye AO, Adobasom-Anane AG, Walden FE, Ekekpi RZ, Adusah E, Dadzie WO, Struck NS, Obirikorang C, Awuah AA.
    Ref: Research Square
  6. Abstract The Zika virus (ZIKV) poses a significant threat due to its association with severe neurological complications, particularly during pregnancy. Although viruses exhibit tropism for neural cells, including astrocytes, the role of these cells in controlling ZIKV replication remains unclear. In this study, we demonstrated that ZIKV induces caspase-1 activation in primary astrocytes despite the absence of classical signs of inflammasome activation. Caspase-1/11 −/− astrocytes exhibit heightened permissiveness to viral replication, accompanied by overactivation of glycolytic metabolism. Inhibition of glycolysis reversed the susceptibility of caspase-1/11 −/− astrocytes to ZIKV infection. Protein network analysis revealed mTORC as a link between proteins involved in glycolysis and caspase-1, and mTORC inhibition also suppressed viral replication. Furthermore, we found that the impact of caspase-1/11 on astrocytes is dependent on pyruvate transport to mitochondria for viral replication, emphasizing the role of the mTORC/glycolytic pathway/pyruvate axis in the caspase-1/11-mediated control of ZIKV. Overall, our findings elucidate a caspase-1/11-dependent microbicidal mechanism in astrocytes, providing insights into potential therapeutic targets for ZIKV infection.
    Date: 2024-05-02
    Authors: Farias IS, Ribeiro G, Noronha IH, Peron JPS, Vieira PMM, Alves-Filho JC, Bortoluci KR.
    Ref: Research Square
  7. Zika virus (ZIKV) infections cause microcephaly in new-borns and Guillain-Barre syndrome in adults raising a significant global public health concern, yet no vaccines or antiviral drugs have been developed to prevent or treat ZIKV infections. The viral protease NS3 and its co-factor NS2B are essential for the cleavage of the Zika polyprotein precursor into individual structural and non-structural proteins and is therefore an attractive drug target. Generation of a robust crystal system of co-expressed NS2B-NS3 protease has enabled us to perform a crystallographic fragment screening campaign with 1076 fragments. 48 binders with diverse chemical scaffolds were identified in the active site of the protease, with another 6 fragment hits observed in a potential allosteric binding site. Our work provides potential starting points for the development of potent NS2B-NS3 protease inhibitors. Furthermore, we have structurally characterized a potential allosteric binding pocket, identifying opportunities for allosteric inhibitor development.
    Date: 2024-04-29
    Authors: Ni X, Godoy AS, Marples PG, Fairhead M, Balcomb BH, Ferla MP, Tomlinson CW, Wang S, Giroud C, Aschenbrenner JC, Lithgo RM, Winokan M, Chandran AV, Thompson W, Xavier M, Williams EP, Walsh M, Fearon D, Koekemoer L, von Delft F.
    Ref: bioRxiv
  8. ABSTRACT The Zika virus (ZIKV), discovered in Africa in 1947, swiftly spread across continents, causing significant concern due to its recent association with microcephaly in newborns and Guillain-Barré syndrome in adults. Despite a decrease in prevalence, the potential for a resurgence remains, necessitating urgent therapeutic interventions. Like other flaviviruses, ZIKV presents promising drug targets within its replication machinery, notably the NS3 helicase (NS3 Hel ) protein, which plays critical roles in viral replication. However, a lack of structural information impedes the development of specific inhibitors targeting NS3 Hel . Here we applied high-throughput crystallographic fragment screening on ZIKV NS3 Hel , which yielded structures that reveal 3D binding poses of 46 fragments at multiple sites of the protein, including 11 unique fragments in the RNA-cleft site. These fragment structures provide templates for direct design of hit compounds and should thus assist the development of novel direct-acting antivirals against ZIKV and related flaviviruses, thus opening a promising avenue for combating future outbreaks.
    Date: 2024-04-29
    Authors: Godoy AS, Mesquita NCMR, Noske GD, Gawriljuk VO, Lithgo RM, Balcomb BH, Aschenbrenner JC, Tomlinson CW, Winokan M, Scheen J, Marples PG, Chandran AV, Ni X, Thompson W, Fairhead M, Fearon D, Koekemoer L, Xavier ME, Walsh M, Oliva G, von Delft F.
    Ref: bioRxiv
  9. Abstract Background The high frequency of Zika virus (ZIKV) infection prompted the World Health Organization (WHO) to declare it an emerging threat in 2016. Presently, countries in South America continue to report a significant number of Zika virus cases. Zika virus infection has been associated with neurological diseases. This article explores the impact of ZIKV infection on IgG + Zika-reactive conditions using a neurosphere model. Methods Neurospheres derived from Wistar rats were exposed to Zika virus and IgG + Zika-reactive conditions. The study assessed the area, irregularity rate, and relative gene expression of NOTCH-1, HES-1, and HEY-1, as well as the expression of GCSF and IL-10. Results The irregularity rate of ZIKV neurospheres decreased at its lowest concentration; however, our morphology analysis was insufficient to fully elucidate the impact of ZIKV on neurospheres. Interestingly, IgG + serum exhibited neuroprotective effects against subsequent Zika virus exposure, restoring NOTCH-1 and HES-1 expression levels to normal. HEY-1 expression remained unaffected by Zika virus exposure but decreased with IgG + serum. Surprisingly, levels of the anti-inflammatory markers GCSF and IL-10 showed no significant changes. Conclusions These findings highlight the complex interplay between ZIKV infection, immune response, and neurodevelopmental processes. Further research is necessary to elucidate the precise mechanisms underlying these observations and explore potential therapeutic interventions.
    Date: 2024-04-26
    Authors: Plentz I, Pazzin D, Previato T, Wagner F, Boff M, Fernandes L, Gonçalvez J, Marinowic D, Costa J.
    Ref: Research Square
  10. The Advisory Committee on Immunization Practices (ACIP) recommended that dengue pre-vaccination screening tests for Dengvaxia administration have at least 98% specificity and 75% sensitivity. This study evaluates the performance of commercial anti-DENV IgG tests to identify tests that could be used for pre-vaccination screening. First, for 7 tests, we evaluated sensitivity and specificity in early convalescent dengue virus (DENV) infection, using 44 samples collected 7-30 days after symptom onset and confirmed by RT-PCR. Next, for the 5 best performing tests and two additional tests (with and without an external test reader) that became available later, we evaluated performance to detect past dengue infection among a panel of 44 specimens collected in 2018-2019 from healthy 9-16-year-old children from Puerto Rico. Finally, a full-scale evaluation was done with the 4 best performing tests using 400 specimens from the same population. We used virus focus reduction neutralization test and an in-house DENV IgG ELISA as reference standards. Of seven tests, five showed ≥75% sensitivity detecting anti-DENV IgG in early convalescent specimens with low cross-reactivity to Zika virus. For the detection of previous DENV infections the tests with the highest performance were the Euroimmun NS1 IgG ELISA (sensitivity 84.5%, specificity 97.1%) and CTK Dengue IgG rapid test R0065C with the test reader (sensitivity 76.2% specificity 98.1%). There are IgG tests available that can be used to accurately classify individuals with previous DENV infection as eligible for dengue vaccination to support safe vaccine implementation.
    Date: 2024-04-21
    Authors: Medina FA, Vila F, Adams LE, Cardona J, Carrion J, Lamirande E, Acosta LN, De León-Rodríguez CM, Beltran M, Grau D, Rivera-Amill V, Balmaseda A, Harris E, Madewell ZJ, Waterman SH, Paz-Bailey G, Whitehead S, Muñoz-Jordán JL.
    Ref: medRxiv
  11. ABSTRACT Mosquito-borne Zika virus (ZIKV; orthoflavivirus, Flaviviridae ) has become a global health problem due to expansion of the geographic distribution of Asian Lineage virus. Contemporary ZIKV strains of African lineage have recently gained increased attention due to their epidemic potential and their capacity to be highly teratogenic in humans. The ZIKV non-structural NS1 protein from recent West African strains Africa was been studied where with view of its importance in the pathogenicity. NS1 protein from contemporary West African ZIKV (NS1 CWA ) and historical African ZIKV strain MR766 (NS1 MR766 ) differ by seven amino-acid substitutions. Expression of recombinant NS1 proteins showed differences in the subcellular distribution between NS1 CWA and NS1 MR766 in HEK-293T cells. There was an increased secretion efficiency of soluble NS1 CWA compared to NS1 MR766 . The replication of a chimeric MR766/NS1 CWA virus was studied in Vero and A549 cells. Insertion of NS1 CWA into MR766 enhances virus replication in both cell lines leading to more pronounced cell death. This correlated with lower up-regulation of IFN-β and interferon-stimulated gene mRNA in A549 cells infected by MR766/NS1 CWA virus. Our data raise the question on the importance of NS1 protein in the pathogenicity of contemporary ZIKV from West Africa, and point to differences within viral strains belonging to the same African lineage. AUTHOR SUMMARY Mosquito-borne Zika virus (ZIKV) of African lineage has the potential to cause epidemic along with a high risk of fetal pathogenicity. Too little is still known on the features of contemporary ZIKV from West Africa. We find there is a remarkable conservation of NS1 amino-acid residues between ZIKV strains recently isolated in Senegal and Guinea. Analysis of recombinant ZIKV NS1 protein revealed efficient secretion of contemporary African NS1 protein from human cells. Using infectious molecular clone of African ZIKV, we showed that contemporary West Africa NS1 protein influences virus replication and innate immune activation. The NS1 protein has been proposed as playing a major role in the pathogenicity of contemporary ZIKV from West Africa.
    Date: 2024-04-11
    Authors: Dana M, Marie-Pierre C, Eva O, Alain K, Desprès P, Marjolaine R.
    Ref: bioRxiv
  12. Previous studies about vector-borne diseases have emphasized the feedback between human psychology and diseases but neglected the changes in psychological processes. Here I first studied whether and how the two types of psychological dynamics in people’s Terror-To-Death (TTD) — periodical terror reinforcement and memory decay of terror — can influence the host-vector-pathogen interactions. Through developing a generic Ross-MacDonald model with TTD dynamics tailored for Zika virus transmitted by Aedes aegypti mosquito, I found that in general, the increase in initial terror increases control effort, while memory decay of terror decreases disease control. Memory decay also exhibits a threshold effect: when initial terror is below certain level, TTD decay would not influence the system much; once initial terror reaches a threshold, memory decay of TTD can largely reduce the public’s control effort, increase mosquito population and disease level in the system under a larger mosquitoes’ carrying capacity. Adding periodical terror reinforcement could introduce dynamical oscillation to the system, dampen the peak of human infection, and shorten the time of disease outbreak. If the reinforcement frequency is large enough, system dynamics could approach the scenario with constant TTD in the absence of memory decay. This work significantly advances the theory in disease epidemiology and biopsychology and can provide guidance for disease control by considering the joint effects of initial terror, the public’s memory decay, and the frequency of terror reinforcement simultaneously.
    Date: 2024-04-05
    Authors: Jiao J.
    Ref: Research Square
  13. Mosquito-borne viruses cause more than 400 million annual infections and place over half of the world’s population at risk. Despite this importance, the mechanisms by which arboviruses infect the mosquito host and disseminate to tissues required for transmission are not well understood. Here, we provide evidence that mosquito immune cells, known as hemocytes, play an integral role in the dissemination of dengue virus (DENV) and Zika virus (ZIKV) in the mosquito Aedes aegypti . We establish that phagocytic hemocytes are a focal point for virus infection and demonstrate that these immune cell populations facilitate virus dissemination to the ovaries and salivary glands. Additional transfer experiments confirm that virus-infected hemocytes confer a virus infection to non-infected mosquitoes more efficiently than free virus in acellular hemolymph, revealing that hemocytes are an important tropism to enhance virus dissemination in the mosquito host. These data support a “trojan horse” model of virus dissemination where infected hemocytes transport virus through the hemolymph to deliver virus to mosquito tissues required for transmission and parallels vertebrate systems where immune cell populations promote virus dissemination to secondary sites of infection. In summary, this study significantly advances our understanding of virus infection dynamics in mosquitoes and highlights conserved roles of immune cells in virus dissemination across vertebrate and invertebrate systems.
    Date: 2024-04-04
    Authors: Hall DR, Johnson RM, Kwon H, Ferdous Z, Laredo-Tiscareño SV, Blitvich BJ, Brackney DE, Smith RC.
    Ref: bioRxiv
  14. Usutu (USUV), West Nile (WNV), and Zika virus (ZIKV) are neurotropic arthropod-borne viruses (arboviruses) that cause severe neurological disease in humans. However, USUV-associated neurological disease is rare, suggesting a block in entry to or infection of the brain. To investigate whether USUV is able to infect the brain similarly to WNV and ZIKV, we determined the replication, cell tropism and neurovirulence of these arboviruses in human brain tissue using a well-characterized human fetal organotypic brain slice culture model. Furthermore, we assessed the efficacy of interferon-β and 2’C-methyl-cytidine, a synthetic nucleoside analogue, in restricting viral replication. All three arboviruses replicated within the brain slices, with WNV reaching the highest titers. USUV and ZIKV reached comparable titers and all three viruses primarily infected neuronal cells. USUV- and WNV-infected cells exhibited a shrunken morphology, not associated with detectable cell death. Pre-treatment with interferon-β inhibited replication of the arboviruses, while 2’C-methyl-cytidine reduced titers of USUV and ZIKV, but not WNV. Collectively, USUV can infect human brain tissue, showing similarities in replication, tropism and neurovirulence as WNV and ZIKV. Further, this model system can be applied as a preclinical model to determine the efficacy and safety of drugs to treat viral infections of the brain.
    Date: 2024-04-04
    Authors: Marshall EM, Rashidi AS, Gent M, Rockx B, Verjans GMGM.
    Ref: Research Square
  15. Zika virus (ZIKV) is a notable arbovirus with maternal, sexual, and TORCH-related transmission capabilities. After 2015, Brazil had the highest number of ZIVK-infected pregnant women who lost their babies or delivered them with Congenital ZIKV Syndrome (CZS). ZIKV infection has been linked to variations in endogenous retroviruses (ERVs) and interleukins within the placenta. ERVs, remnants of ancient viral infections integrated into the genome, include syncytin receptors crucial for placental development. Interleukins, immune response regulators, aid immune tolerance and support syncytial structure development in the placenta, where syncytin receptors facilitate vital cell-to-cell fusion events. Since ZIKV can infect trophoblast cells, we investigated the relationship between ZIKV infections and ERV and interleukin modulations. Investigating the impact of ZIKV on trophoblast cells, we examined two cell types (BeWo and HTR8) infected with ZIKV-MR766 (African) and ZIKV-IEC-Paraíba (Asia-Brazilian) using Taqman and RT2 Profiler PCR Array assays. While early ZIKV infection (24-48 hours) did not induce differential ERV and interleukin expression, future studies involving additional trophoblastic cell lineages and extended infection timelines will illuminate the dynamic interplay between ZIKV, HERVs, interleukins, and cytokines essential for placental formation and function.
    Date: 2024-04-02
    Authors: Costa ALd, Prieto-Oliveira P, Duarte-Barbosa M, Andreata-Santos R, Peter CM, Prolo T, Antoneli F, Carvalho MIVGd, Durães-Carvalho R, Briones MRdS, Maricato JT, Zanotto PMA, Jacob Machado D, Janini LMR.
    Ref: Preprints.org
  16. Background Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, barriers to broader take-up include the need for high sequencing depths, long turnaround times, and limited sensitivity. Newer metagenomics protocols based on Oxford Nanopore Technologies (ONT) sequencing allow acquisition and analysis of data in real time, potentially reducing the need for high-volume sequencing and enabling point-of-care testing. Furthermore, targeted approaches that selectively amplify known pathogens could improve sensitivity. Methods We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Biosciences Comprehensive Viral Research Panel (VRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. Results Capture with the Twist VRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6,000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the VRP and ONT. Conclusions Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist VRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
    Date: 2024-03-29
    Authors: Buddle S, Forrest L, Akinsuyi N, Bernal LMM, Brooks T, Venturini C, Miller C, Brown JR, Storey N, Atkinson L, Best T, Roy S, Goldsworthy S, Castellano S, Simmonds P, Harvala H, Golubchik T, Williams R, Breuer J, Morfopoulou S, Montaguth OET.
    Ref: medRxiv
  17. The 2016 outbreak of Zika virus (ZIKV) infected millions and resulted in thousands of infants born with malformations. Though the clusters of severe birth defects resulting from this outbreak have subsided, ZIKV continues to be a concern throughout much of Latin America and the Caribbean. Travel and sexual intercourse remain the dominant transmission risk factors for women of reproductive age and their partners. This is particularly true for communities in Brooklyn, New York, that comprise large immigrant and foreign-born populations. Practitioners of public health understand little about how women at risk for ZIKV are most likely to receive information about the virus or who they trust most to provide that information. In the context of five focus group discussions, this study explored the knowledge and communication preferences of 20 women of reproductive age in Central Brooklyn. Results derived from a thematic analysis suggest that while most women are familiar with mosquitos as ZIKV vectors, knowledge of sexual transmission is considerably lower. Many respondents believe that only women who are pregnant or trying to become pregnant are at risk, and public health agencies, such as the U.S. Centers for Disease Control and Prevention, remain the most trusted sources of information. These findings can support more effective communication about the risks of ZIKV infection and other vector-borne diseases to women in New York City and similar urban communities.
    Date: 2024-03-29
    Authors: Dowling R, Kolokotronis S, Thompson AB.
    Ref: medRxiv
  18. SUMMARY Subgenomic flavivirus RNAs (sfRNAs) are structured RNA elements encoded in the 3’-UTR of flaviviruses that promote viral infection by inhibiting cellular RNA decay machinery. Herein, we analyze the production of sfRNAs using single-molecule RNA fluorescence in situ hybridization (smRNA-FISH) and super-resolution microscopy during West Nile virus, Zika virus, or Dengue virus serotype 2 infection. We show that sfRNAs are initially localized diffusely in the cytosol or in processing bodies (P-bodies). However, upon activation of the host antiviral endoribonuclease, Ribonuclease L (RNase L), nearly all sfRNAs re-localize to antiviral biological condensates known as RNase L-induced bodies (RLBs). RLB-mediated sequestration of sfRNAs reduces sfRNA association with RNA decay machinery in P-bodies, which coincides with increased viral RNA decay. These findings establish a role of RLBs in promoting viral RNA decay, demonstrating the complex host-pathogen interactions at the level of RNA decay and biological condensation. Highlights Single-molecule imaging of sfRNA production and localization sfRNAs localize to RNase L-induced bodies RNase L-induced bodies sequester sfRNAs away from P-bodies Sequestration of sfRNAs by RNase L-induced bodies enhances decay of viral genomes
    Date: 2024-03-27
    Authors: Watkins JM, Burke JM.
    Ref: bioRxiv
  19. Unbiased long read sequencing holds enormous potential for the detection of pathogen sequences in clinical samples. However, the untargeted nature of these methods precludes conventional PCR approaches, and the metagenomic content of each sample increases the challenge of bioinformatic analysis. Here, we evaluate a previously described novel workflow for unbiased RNA virus sequence identification in a series of contrived and real-world samples. The novel multiplex library preparation workflow was developed for the Oxford Nanopore Technologies (ONT) MinION TM sequencer using reverse transcription, whole genome amplification, and ONT’s Ligation Sequencing Kit with Native Barcode Expansion. The workflow includes spiked MS2 Phage as an internal positive control and generates an 8-plex library with 6 samples, a negative control and a gfp transcript positive control. Targeted and untargeted data analysis was performed using the EPI2ME Labs framework and open access tools that are readily accessible to most clinical laboratories. Contrived samples composed of common respiratory pathogens (Influenza A, Respiratory Syncytial Virus and Human Coronavirus 229E) in viral transport media (VTM) and bloodborne pathogens (Zika Virus, Hepatitis A Virus, Yellow Fever Virus and Chikungunya Virus) in human plasma were used to establish the limits of detection for this assay. We also evaluated the diagnostic accuracy of the assay using remnant clinical samples and found that it showed 100% specificity and 62.9% clinical sensitivity. More studies are needed to further evaluate pathogen detection and better position thresholds for detection and non-detection in various clinical sample metagenomic mixtures.
    Date: 2024-03-27
    Authors: Kappell AD, Schulte KQ, Scheuermann EA, Scholz MB, Keplinger NC, Scholes AN, Wolt TA, June VM, Schulte CJ, Allen LW, Ternus KL, Hewitt FC.
    Ref: medRxiv
  20. ABSTRACT Zika virus (ZIKV) have become a global health problem over the past decade due to the extension of the geographic distribution of ZIKV of Asian genotype. Epidemics of Asian ZIKV have been associated with developmental disorders in humans. ZIKV of African lineage would have an epidemic potential associated to fetal pathogenicity requiring a greater attention towards the most recently isolated viral strains from West Africa. In the present study, an infectious molecular clone GUINEA-18 has been obtained from viral strain ZIKV-15555 that had been sequenced from an individual infected by ZIKV in Guinea in 2018. A molecular clone-based comparative study between GUINEA-18 and viral clone MR766 MC from historical African ZIKV strain MR766 revealed a lower replication rate for GUINEA-18 associated to a weaker cytotoxicity and reduced innate immune system activation in Vero E6, A549 and HCM3 cell lines. Analysis of chimeric viruses between MR766 MC and GUINEA-18 stressed the importance NS1/NS4B proteins with a particular focus for NS4B on GUINEA-18 replication properties. ZIKV has developed strategies to prevent cytoplasmic stress granule formation which occurs in response to virus infection. Study of G3BP protein showed that GUINEA-18 but not MR766 MC was efficient to inhibit stress granule assembly in A549 cells subjected to a physiological stressor. GUINEA-18 depends on NS1/NS4B proteins for suppressing stress granule response to environmental stress. The involvement of GUINEA-18 NS1/NS4B proteins on virus replication capability and host-cell responses to ZIKV infection raises the question of the importance of nonstructural proteins in the pathogenicity of contemporary viral strains from West Africa. AUTHOR SUMMARY Most of studies having for objectives to understand the biology of Zika virus (ZIKV) were carried out using epidemic viral strains of Asian lineage. It is now admitted that ZIKV of African genotype would have also a great epidemic potential associated a high risk of fetal pathogenicity. Today, it is urgent to improve our knowledge on recently isolated ZIKV strains in West Africa. In our study, we used the sequence of viral strain from an individual infected by ZIKV in Guinea in 2018 to generate an infectious molecular clone. Analysis of viral clone highlighted the preponderant role of NS1/NS4B proteins in virus replication strategy and cell interactions with a particular focus on ZIKV-specific stress granule formation blockade. We believe that our data will improve our knowledge on the biology of contemporary West Africa ZIKV opening perspectives towards a better understanding on the pathogenicity of African viral strains.
    Date: 2024-03-14
    Authors: Machmouchi D, Courageot M, El-Kalamouni C, Kohl A, Desprès P.
    Ref: bioRxiv
  21. RNA viruses play diverse functional roles in engineered ecosystems, influencing biotechnological process and serving as indicators of human health. Comprehending the ecological and health significance of RNA viruses in wastewater treatment plants (WWTPs) can derive their valuable implications on microbial community control and wastewater-based epidemiology. This study delved into an extensive analysis of RNA sequencing data, totally over 3.8 Tb, sourced from 557 metatranscriptomes across global WWTPs, to scrutinize the diversity, host associations, and auxiliary metabolic functions of RNA viruses. We identified 11414 RNA virus operational taxonomic units from the WWTPs, doubling the current known diversity of the RNA viruses in global engineered systems. Phylogenetic analysis of RNA-dependent RNA polymerases supported the establishment of the five established RNA virus phyla while also advocating for taxonomy revisions due to our discovery of novel clades. Notably, the RNA viral community within the WWTPs was predominated by prokaryotic viruses, encompassing both previously identified RNA phage lineages ( Leviviricetes and Cystoviridae ) and potential prokaryotic viruses from newly-identified clades. Detections of prevalent human RNA viruses such as Astrovirus , Respirovirus , Rotavirus , and Norovirus , alongside high-risk human RNA viruses like SARS-Cov-2 and Zika virus, highlighted the potential of leveraging wastewater-based surveillance for human health protection. Moreover, the presence of auxiliary metabolic genes encoded by RNA viruses suggested their involvement in diverse host metabolic processes, including enhancing translation efficiency, cellular respiration, nitrogen metabolism, and even antibiotic resistance. Collectively, our findings unveil the previously hidden diversity, health implications, and biochemical impacts of RNA viruses within WWTPs, underscoring their multifaceted roles in engineered environmental systems.
    Date: 2024-03-12
    Authors: Yuan L, Ju F.
    Ref: bioRxiv
  22. The influenza virus has been the primary cause of the pandemic, posing a constant threat to human society. Due to its genetic evolution and continuous outbreak, antiviral research currently focuses on exploring a novel lead agent. A comprehensive antiviral screening discovered a marine bacterium whose extract exerted excellent efficacy against influenza viruses. Parerythrobacter sp. M20A3S10, a novel strain under the family Erythrobacteraceae, could produce carotenoids exhibiting antiviral and anticancer activity by enhancing the cellular immune system. Post-treatment of M20A3S10 extract showed outstanding therapeutic indexes: against influenza virus A/PR8 (H1N1) [selectivity index (SI) = 24.0], A/Wisconsin/15/2009 (H3N2) (SI = 30.1) and B/Florida/78/2015 (SI = 38.2). Comparably, the effectiveness was demonstrated against Zika virus (ZIKV) and dengue virus type 2 (DENV2) with an SI of 22.5 and 24.1, respectively, namely broad-spectrum activity. Of note, the antiviral responses resulted from the common replication mechanism between IAV, ZIKV, and DENV2. The stimulation of apoptosis-mediated cellular immunity prevented the viral release and protected the host, suggesting that switching from necroptosis to apoptosis is a novel antiviral target. Although the specific compound affecting the antiviral activity was not identified, its promising efficacy with broad activity will contribute to developing a strategy for preventing future pandemics.
    Date: 2024-03-11
    Authors: Moon K, Choi G, Jung S, Kim H, Park J, Kwon YM, Cho E, Shin MY, Yu J, Choi JA, Baek Y, Park S.
    Ref: Preprints.org
  23. Host factors that regulate cellular vesicular trafficking also contribute to progeny virions’ destination, thus representing as potential antiviral drug targets. Here we demonstrate that genetic deletion of ARF4, a regulator in vesicle transport, repressed multiple pathogenic RNA viral infections including Zika virus (ZIKV), influenza A virus (IAV), SARS-CoV-2 and Vesicular Stomatitis virus (VSV). ARF4 activation was stimulated upon viral infection, and viral production was rescued when reconstituted with the activated ARF4, but not the inactivated mutants. Mechanically, ARF4 deletion obstructed viral normal translocation into Golgi complex, but led to mis-sorting for lysosomal degradation, consequently caused the blockage of final release. More importantly, ARF4 targeting peptides achieved significant therapeutic efficacy against ZIKV and IAV challenge in mice by blocking ARF4 activation. Hence, we clarify the critical role of ARF4 during viral infection, providing a broad-spectrum antiviral target and the basis for further pharmaceutical development.
    Date: 2024-03-11
    Authors: Qin C, Li M, Deng K, Cheng X, Siu LY, Naik TS, Stancheva VG, Cheung P, Gao Z, Teo QW, Leur SWv, Wong H, Lan Y, Zhang N, Zhang Y, Cao T, Yang F, Deng Y, Sanyal S.
    Ref: Research Square
  24. Although rare neurodevelopmental conditions have a large Mendelian component, common genetic variants also contribute to risk. However, little is known about how this polygenic risk is distributed among patients with these conditions and their parents, its interplay with rare variants, and whether parents’ polygenic background contributes to their children’s risk beyond the direct effect of variants transmitted to the child (i.e. via indirect genetic effects potentially mediated through the prenatal environment or ‘genetic nurture’). Here, we addressed these questions using genetic data from 11,573 patients with rare neurodevelopmental conditions, 9,128 of their parents and 26,869 controls. Common variants explained ∼10% of variance in overall risk. Patients with a monogenic diagnosis had significantly less polygenic risk than those without, supporting a liability threshold model, while both genetically undiagnosed patients and diagnosed patients with affected parents had significantly more risk than controls. In a trio-based model, using a polygenic score for neurodevelopmental conditions, the transmitted but not the non-transmitted parental alleles were associated with risk, indicating a direct genetic effect. In contrast, we observed no direct genetic effect of polygenic scores for educational attainment and cognitive performance, but saw a significant correlation between the child’s risk and non-transmitted alleles in the parents, potentially due to indirect genetic effects and/or parental assortment for these traits. Indeed, as expected under parental assortment, we show that common variant predisposition for neurodevelopmental conditions is correlated with the rare variant component of risk. Our findings thus suggest that future studies should investigate the possible role and nature of indirect genetic effects on rare neurodevelopmental conditions, and consider the contribution of common and rare variants simultaneously when studying cognition-related phenotypes.
    Date: 2024-03-06
    Authors: Huang QQ, Wigdor EM, Campbell P, Malawsky DS, Samocha KE, Chundru VK, Danecek P, Lindsay S, Marchant T, Musa MK, Amanat S, Bonifanti D, Sheridan E, Radford EJ, Barrett JC, Wright CF, Firth HV, Warrier V, Young AS, Hurles ME, Martin HC.
    Ref: medRxiv
  25. At the start of the Zika virus (ZIKV) epidemic in 2015, ZIKV spread across South and Central America, and reached parts of the southern United States placing pregnant women at risk for fetal microcephaly, fetal loss, and other adverse pregnancy outcomes associated with congenital ZIKA syndrome (CZS). For this reason, testing of a safe and efficacious ZIKV vaccine remains a global health priority. Here we report that a single immunization with Ad26.M.Env ZIKV vaccine, when administered prior to conception, fully protects pregnant rhesus macaques from ZIKV viremia in blood and tissues with no adverse effects in dams and fetuses. Furthermore, vaccination prevents ZIKV distribution in fetal tissues including brain. ZIKV associated neuropathology was absent in offspring of Ad26.M.Env vaccinated dams, although pathology was limited in sham vaccinated controls. Vaccine efficacy is associated with induction of ZIKV neutralizing antibodies in pregnant rhesus macaques. A Phase I trial showed that Ad26.M.Env (Ad26.ZIKV.001) was safe and immunogenic in people. These data suggest the feasibility of vaccine prevention of ZCS in humans.
    Date: 2024-03-05
    Authors: Martinot A, Cox F, Abbink P, Hecht J, Bronson R, Borducchi E, Rinaldi W, Ferguson M, Barrera RDL, Fits Lvd, Barouch D.
    Ref: Research Square
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