Biology subjects

Pastrana, D. V.

Publications and source records attributed to Pastrana, D. V..

5 recordsLinked to original sources

bioRxiv2024

Heterologous immunization strategy developed broadly reactive human monoclonal antibodies against the BK virus

BK polyomavirus (BKV) causes polyomavirus-associated nephropathy (BKV-nephropathy) and polyomavirus-associated hemorrhagic cystitis (BKV-HC) following kidney transplantation and allogeneic hematopoietic stem cell transplantation (HSCT). BKV strains consist of four distinct genotypes (BKV-I, - II, -III, and -IV) with more than 80% of individuals seropositive for the BKV-I genotype, and lower prevalences of infection or co-infection with the other genotypes. BKV-nephropathy occurs widely in immunosuppressed transplant recipients, with the recommended treatment including reduction of immunosuppressive drugs. High serum titers of BKV-neutralizing antibodies and treatment with BKV-neutralizing intravenous immunoglobulin (IVIG) are associated with reduced levels of BKV-DNAemia in kidney transplant recipients, suggesting anti-BKV antibodies can limit viral load. Thus, we set out to generate broadly neutralizing human monoclonal antibodies (mAbs) against the viral protein 1 (VP1) major capsid protein of BKV genotypes I-IV using VelocImmune(R) transgenic mice that encode for human immunoglobulins. Hybridoma clones from VelocImmune(R) mice immunized with combinations of BKV I-IV VP1 and respective genotypes of BKV pseudoviruses (BK-PsV) were screened using a high-throughput binding assay against BKV-I VP1 expressed in HEK-293 cells. The VP1-binding hybridoma clones were then assessed for neutralization with BK-PsV consisting of respective VP1 proteins from BKV-I, -II, -III, or -IV on the virion surface. Overall, thirty-six broadly cross-neutralizing mAbs against BKV-I, -II, -III, and -IV -were identified. Twenty of the cross-reactive immunoglobulins were subjected to nucleotide sequencing resulting in six clonotype families with fourteen genetically distinct immunoglobulins. Several of the most effective mAbs were fully humanized with the IgG1 Fc domain and broad neutralization of BK-PsV-I, II, III, and IV genotypes with IC50s ranging from [~]7-200 pM. Thus, these cross-neutralizing mAbs represent potential biologics to developed into BKV therapeutics.

microbiology↗

bioRxiv2024

Widespread Horizontal Gene Transfer Among Animal Viruses

The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.

microbiology↗

bioRxiv2022

A Multivalent Polyomavirus Vaccine Elicits Durable Neutralizing Antibody Responses in Macaques

In 2019, there were about 100,000 kidney transplants globally, with more than a quarter of them performed in the United States. Unfortunately, some engrafted organs are lost to polyomavirus-associated nephropathy (PyVAN) caused by BK and JC viruses (BKPyV and JCPyV). Transplant patients are routinely monitored for BKPyV viremia, which is an accepted hallmark of nascent nephropathy. If viremia is detected, a reduction in immunosuppressive therapy is standard care, but the intervention comes with increased risk of immune rejection of the engrafted organ. Recent reports have suggested that transplant recipients with high levels of polyomavirus-neutralizing antibodies are protected against PyVAN. Virus-like particle (VLP) vaccines, similar to approved human papillomaviruses vaccines, have an excellent safety record and are known to induce high levels of neutralizing antibodies associated and long-lasting protection from infection. In this study, we demonstrate that VLPs representing BKPyV genotypes I, II, and IV, as well as JCPyV genotype 2 produced in insect cells elicit robust antibody titers. In rhesus macaques, all monkeys developed neutralizing antibody titers above a previously proposed protective threshold of 10,000. A second inoculation, administered 19 weeks after priming, boosted titers to a plateau of [≥]25,000 that was maintained for almost two years. No vaccine-related adverse events were observed in any macaques. A multivalent BK/JC VLP immunogen did not show inferiority compared to the single-genotype VLP immunogens. Considering these encouraging results, we believe a clinical trial administering the multivalent VLP vaccine in patients waiting to receive a kidney transplant is warranted to evaluate its ability to reduce or eliminate PyVAN. HIGHLIGHTSO_LIRecombinant virus-like particle vaccine was safely administered to rhesus macaques C_LIO_LIVaccination generated high-titer neutralizing antibody responses C_LIO_LIMultivalent BK/JC polyomavirus vaccine was as effective as monovalent vaccines C_LIO_LIHigh neutralizing titers were sustained for 92 weeks without appreciable decline C_LI

immunology↗

bioRxiv2019

Identification of \"Missing Link\" Families of Small DNA Tumor Viruses

Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are viruses that remain capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of animal-specific viruses with two genus-level divisions. We suggest the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.

microbiology↗

bioRxiv2019

Discovery of several thousand highly diverse circular DNA viruses

Although it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBanks RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA viruses and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these "dark matter" sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.

microbiology↗