Implementation of IFPTML Computational Models in Drug Discovery Against Flaviviridae Family

The Flaviviridae family consists of single-stranded positive-sense RNA viruses, which contains the genera Flavivirus, Hepacivirus, Pegivirus, and Pestivirus. Currently, there is an outbreak of viral diseases caused by this family affecting millions of people worldwide, leading to significant morbidity and mortality rates. Advances in computational chemistry have greatly facilitated the discovery of novel drugs and treatments for diseases associated with this family. Chemoinformatic techniques, such as the perturbation theory machine learning method, have played a crucial role in developing new approaches based on ML models that can effectively aid drug discovery. The IFPTML models have shown its capability to handle, classify, and process large data sets with high specificity. The results obtained from different models indicates that this methodology is proficient in processing the data, resulting in a reduction of the false positive rate by 4.25%, along with an accuracy of 83% and reliability of 92%. These values suggest that the model can serve as a computational tool in assisting drug discovery efforts and the development of new treatments against Flaviviridae family diseases.

Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients

Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.

A copula model for bivariate hybrid censored survival data with application to the MACS study

A copula model for bivariate survival data with hybrid censoring is proposed to study the association between survival time of individuals infected with HIV and persistence time of infection with an additional virus. Survival with HIV is right censored and the persistence time of the additional virus is subject to interval censoring case 1. A pseudo-likelihood method is developed to study the association between the two event times under such hybrid censoring. Asymptotic consistency and normality of the pseudo-likelihood estimator are established based on empirical process theory. Simulation studies indicate good performance of the estimator with moderate sample size. The method is applied to a motivating HIV study which investigates the effect of GB virus type C (GBV-C) co-infection on survival time of HIV infected individuals.

An 85-aa segment of the GB virus type C NS5A phosphoprotein inhibits HIV-1 replication in CD4+ Jurkat T cells

GB virus type C (GBV-C) is an apparently nonpathogenic virus that replicates in T and B lymphocytes and is a common cause of persistent human infection. Among HIV-1-infected individuals, persistent coinfection with GBV-C is associated with prolonged survival, and infection of blood mononuclear cells or CD4+ T cells with GBV-C and HIV in vitro results in significantly reduced HIV-1 replication. To date, the viral protein(s) that lead to HIV inhibition have not been identified. The GBV-C nonstructural phosphoprotein (NS5A) is predicted to have pleotropic effects on cells, including interactions with the IFN-induced dsRNA-activated protein kinase (PKR). We studied GBV-C NS5A to determine whether it is involved in inhibition of HIV replication. GBV-C NS5A protein from an isolate that was cleared by IFN therapy did not inhibit PKR, whereas NS5A from an isolate that was not cleared by IFN-inhibited PKR function in a yeast genetic system. Both of these GBV-C NS5A proteins were expressed in a CD4+ T cell line (Jurkat), and both induced a potent, dose-dependent inhibition of HIV-1 replication, thus the effect was independent of PKR inhibition. NS5A induced the release of the chemokine SDF-1 and decreased surface expression of the HIV coreceptor CXCR4, potentially explaining the HIV inhibition. Deletion mapping of the NS5A protein found that an 85-aa region between amino acids 152 and 237 inhibits HIV-1 replication. Thus, GBV-C NS5A protein alters the cellular milieu necessary for HIV-1 replication and may provide a previously undescribed therapeutic approach for anti-HIV therapy.

[GB virus-C infection in Chinese patients with hepatocellular carcinoma]

Hepatitis B and C viruses (HBV, HCV) are closely related with hepatocellular carcinoma(HCC). The association between the new discovered GB-virus C (GBV-C) and HCC has not yet been known. In this study, 124 HCC patients were detected for the prevalence of GBV-C RNA by the one-step nested reverse transcription polymerase chain reaction (RT-PCR) and followed by hybridization using GBV-C probes located at 3'-untranslated region (3'-UTR) from its reported genomes. The results showed that 33 of 124 (26.6%) HCC cases were GBV-C RNA positive, including 12 cases positive HBsAg and anti-HCV, and 3 for cases negative HBsAg and anti-HCV. The clinical background of the patients with HBsAg and/or anti-HCV who were also positive for GBV-C RNA did not differ from the background of those who were negative for GBV-C RNA except the ratio of blood transfusion history. In conclusion, GBV-C has a high prevalence in Chinese HCC patients. Even though no sufficient data supports the causality of GBV-C on hepatocarcinogenesis, further researches aimed at whether GBV-C infection aggravates the incidence of HCC are warranted.

[Study on the experimental infection of hepatitis G virus in rhesus monkey]

In order to study the experimental infection of HGV in rhesus monkey, the monkeys were infected using the plasma from a donor with HGV RNA positive. The second generation monkeys were infected with the sera of the first generation monkeys infected after 6 weeks, and also the third generation monkeys were infected with the sera of the second generation monkeys. HGV RNA were detected by RT-nPCR. The results showed that in sera of infected monkeys HGV RNA were positive after 1 week of inoculation, and were consecutively positive for up to 28 weeks at longest. The level of ALT raised a little in monkey No. 1 and higher than 100 U/L in No. 5. The liver biopsy showed viral hepatitis--like histological changes. Comparing the sequence of HGV 5'LTR from sera of the infected monkeys and the blood donor, the homogeneity, to strain HGU44402 was 98.33% and 95.83% to strain HGU36380 was 92.50% and 89.17%, respectively. The results suggested that the rhesus monkey is sensitive to HGV and is suitable for establishment of an animal model.

[Detection of hepatitis C virus and hepatitis G virus RNA by multiplex reverse transcription-polymerase chain reaction and microtiter plate reverse hybridization]

Multiplex reverse transcription-polymerase chain reaction for the simultaneous detection of HCV and HGV RNA has been established, in which primers were deduced from high conservative region of HCV and HGV and PCR amplicons were detected by microtiter plate reverse hybridization with HCV or HGV specific probe. Sequence analyses showed that amplicons of HCV were 93.1%-94.1% and 92.5%-93.7% of nucleotide homology compared with Takamizawa and Choo, and amplicons of HGV were 90.7%-92.5%, 92.0%-92.1% and 94.3%-94.5% of nucleotide homology with Simons, Linnen and Chang. The detective sensitivity was 100 times over that of electrophoretic assay with single amplification. CVs of HCV and HGV were 8.9% and 9.8%, respectively, and the optimal concentration of NaOH for hybridization was 0.1-0.15 mol/L. The optimal time for hybridization was 30-50 minutes. The results of detection with multiplex PCR showed the presence of infection with HCV or HGV alone and coinfection with both % them.

Haemorrhagic fevers and ecological perturbations

Hemorrhagic fever is a clinical and imprecise definition for several different diseases. Their main common point is to be zoonoses. These diseases are due to several viruses which belong to different families. The Flaviviridae have been known for the longest time. They include the Amaril virus that causes yellow fever and is transported by mosquitoes. Viruses that have come to light more recently belong to three other families: Arenaviridae, Bunyaviridae, and Filoviridae. They are transmitted by rodents (hantaviruses and arenaviruses) or from unknown reservoirs (Ebola Marburg). The primary cause of most outbreaks of hemorrhagic fever viruses is ecological disruption resulting from human activities. The expansion of the world population perturbs ecosystems that were stable a few decades ago and facilitates contacts with animals carrying viruses pathogenic to humans. Another dangerous human activity is the development of hospitals with poor medical hygiene. Lassa, Crimean-Congo or Ebola outbreaks are mainly nosocomial. There are also natural environmental changes: the emergence of Sin Nombre in the U.S. resulted from heavier than usual rain and snow during spring 1993 in the Four Corners. Biological industries also present risks. In 1967, collection of organs from monkeys allowed the discovery in Marburg of a new family of viruses, the Filoviridae. Hemorrhagic fever viruses are cause for worry, and the avenues to reduce their toll are still limited.