Biology subjects

Montoya, V.

Publications and source records attributed to Montoya, V..

3 recordsLinked to original sources

bioRxiv2026

Functional genomic analysis reveals mechanisms of epigenetic interference in SARS-CoV-1 and SARS-CoV-2

Small viral RNAs (svRNA) are key factors in host adaptation and virulence and are previously identified in SARS-CoV-2 and SARS-CoV-1. Little is known about svRNA conservation among high-risk coronaviruses (subgenus Sarbecovirus) or how svRNAs might contribute to COVID-19. Here, using functional genomics we identify six novel svRNA-triplex-forming oligonucleotides (svRNA-TFOs) in SARS-CoV-2, and through comparative analyses with SARS-CoV-1, delineate evolutionary pathways for svRNA-TFOs in Sarbecovirus. In addition to significant enrichment of the svRNA-TFO enhancer-associated gene targets among differentially expressed gene sets collected during SARS-CoV-2 infection, we find statistical support for non-random associations with >25 % of recombination breakpoints and hotspots in the Wuhan-Hu-1 genome. Small RNA-sequencing reveals highly abundant svRNA-TFO-N derived from the nucleocapsid of SARS-CoV-2. Using synonymous site conservation analysis, we find svRNA-TFO-N, and other svRNA-TFOs are conserved among both SARS-CoV-2- and SARS-CoV-1-related lineages. Furthermore, BLASTn reveals svRNA-TFO-N, svRNA-TFO-S.1 and svRNA-TFO-E share sequence homology against various mammalian genomes supporting a potential mechanism of host adaptation. Finally, we identify potential links between the putative svRNA-TFO-S.1 and svRNA-TFO-N RNA progenitor structures with variant of concern-associated S:D614G and N:D377Y mutations, respectively. Collectively these findings support a role for epigenetic interference with potential to reveal critical insights into the evolution of SARS-CoV-2 and SARS-CoV-1.

genetics↗

bioRxiv2019

Systematic determination of in vitro phenotypic resistance to HIV-1 integrase strand transfer inhibitors from clinical samples

Phenotypic resistance data is relatively sparse for the newest HIV-1 integrase strand transfer inhibitors (INSTIs), dolutegravir (DTG), bictegravir (BIC), and cabotegravir (CAB). In this study, we report the phenotypic susceptibility of a large panel of oligo-clonal patient-derived HIV-1 integrase viruses. Representative clinical samples (N=141) were selected from a large database (N=17,197) of clinically-derived HIV integrase sequences, based on the presence of permutations of substitutions at 27 pre-defined positions in integrase (N=288). HIV-1 RNA was extracted from patient samples and diluted to approximately 500 HIV RNA copies/mL. Using an \"oligo-clonal\" amplification approach to achieve single-copy amplification, these dilutions were subjected to 12 parallel RT-PCR reactions to amplify integrase. Confirmed clonal amplicons were co-transfected with linearized pNL4.3{triangleup}int into CEM-GXR cells. In total, 162 HIV-1 viruses that carried no mixtures and had a unique sequence were harvested, and phenotyped in MT4-LTR-EGFP cells subsequently. Variants with the highest fold change (FC) had G140S and Q148R/H and resistant to all five drugs; R263K was the only single variant conferring >3-FC to DTG, BIC and CAB. There was extensive cross-resistance between DTG, BIC, and CAB and phenotypic resistance values for all the three INSTIs were almost collinear. The greatest exceptions were variants with N155H/G163E or L74I/T97M/F121C/V151I/E157Q/G163K, where both had >70-FC for CAB, while <3-FC for DTG and BIC. While site-directed mutagenesis is invaluable; the systematic selection of representative mutational patterns observed in vivo provides an efficient way to identify clinically relevant drug resistance.

molecular biology↗

bioRxiv2019

TRIM5α restricts flavivirus replication by targeting the viral protease for proteasomal degradation.

Tripartite motif-containing protein 5 (TRIM5) functions as a cellular antiviral restriction factor with exquisite specificity towards the capsid lattices of retroviruses. The relative avidity of TRIM5 binding to retrovirus capsids directly impacts primate species susceptibility to infection, but the antiviral role of TRIM5 is thought limited to retroviruses. In contrast to this current understanding, here we show that both human and rhesus TRIM5 possess potent antiviral function against specific flaviviruses through interaction with the viral protease (NS2B/3) to inhibit virus replication. Importantly, TRIM5 was essential for the antiviral function of IFN-I against sensitive flaviviruses in human cells. However, TRIM5 was ineffective against mosquito-borne flaviviruses (yellow fever, dengue, and Zika viruses) that establish transmission cycles in humans following emergence from non-human primates. Thus, TRIM5 is revealed to possess remarkable plasticity in recognition of diverse virus families, with potential to influence human susceptibility to emerging flaviviruses of global concern.

microbiology↗