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At least 19 recordsLinked to original sources
PubMed1979

Increased integration of viral genome following chemical and viral treatment of hamster embryo cells.

Treatment of hamster embryo cells with diverse classes of chemical carcinogens enhances transformation by a carcinogenic simian adenovirus, SA7. Virus transformed foci selected from plates pretreated with 3-methyl-cholanthrene (MCA), methyl methanesulfonate (MMS) or 7,12-dimethylbenz[a]anthracene (DMBA) and established as cell lines in culture, contained equivalent amounts of SA7 viral genome. However, hamster embryo cultures treated with MMS or nickel sulfate had increased amounts of SA7 DNA integrated into cellular DNA when examined 2--9 days after chemical treatment and viral inoculation. An increased uptake of SA7 DNA was demonstrated in hamster cells treated with MMS during DNA repair synthesis in cells retricted in scheduled DNA synthesis by amino acid deprivation; addition of virus after the repair period did not result in an increased integration of viral DNA. These data suggest that enhancement of viral oncogenesis by chemical carcinogens or mutagens may be related to the formation of additional attachment sites in cellular DNA for insertion of viral DNA, thereby increasing the probability of viral transformation.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed2026

The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California.

In July 2021, the California Code of Regulations Title 17 required all laboratories performing SARS‑CoV‑2 whole genome sequencing (WGS) to report their sequencing results to the California Department of Public Health (CDPH). These viral genomic data and patient metadata were compiled into the Integrated Genomic Epidemiology Database (IGED). Linking anonymized viral sequences with patient‑level information enabled monitoring of infectiousness, pathogenicity, transmission dynamics, evolution, and vaccine evasion among emerging SARS‑CoV‑2 lineages. Laboratories performing SARS-CoV-2 WGS transmitted sequencing results to CDPH through Electronic Laboratory Reporting (ELR) and non-ELR pathways. CDPH applied uniform reporting requirements but allowed flexibility in specific data formats to accommodate diverse data systems. To preserve data quality and interoperability across heterogeneous sources, CDPH implemented standardization, validation, and deduplication protocols. Snowflake, a cloud‑based data storage and analytics platform, and Posit Connect, a cloud deployment and automation platform, supported the management, processing, and integration of data within the IGED. The IGED established links between SARS‑CoV‑2 WGS data and epidemiologic metadata for 801,418 sequences, representing 81.7% of all sequences reported in California. Lineages reported to the IGED showed strong concordance with lineage proportions in GISAID. Sequences reported to the IGED had average turnaround times longer than one month, and the majority of sequencing was performed in Southern California and Los Angeles. The IGED enhanced genomic surveillance through predictive modeling and monitoring concerning evolutionary trends such as recombination and saltations in persistent infections. Development of the IGED highlighted the need for standardized data requirements, sustained funding for sequencing, incentives for data submission, and interdisciplinary collaboration to build an effective genomic surveillance system. This framework for linking genomic and epidemiologic data has not only generated critical insights for SARS‑CoV‑2 but also provided the foundation for CDPH and other public health organizations to develop similar IGED‑like systems for other priority pathogens as genomic surveillance expands.

Journal Article↗
PubMed1975

Isolation of RNA transcripts from the entire Sendai viral genome.

Three classes of viral transcripts (18S, 24S, and 33S) were isolated from viral ribonucleoproteins in Sendai virus-infected cells. Hybridization studies with virion minus strand genome RNA demonstrated that the 18S RNA contained transcripts from 60% of the viral genome while the 33S RNA contained transcripts from the entire viral genome. Brief heat of ME2SO treatment of the 33S RNA demonstrated that this RNA was composed of two classes: RNA which continued to sediment at 33S (33S RNA) and 18S RNA aggregates (18S RNA). The 33S RNA was determined to be a transcript from the 40% of the viral genome not protected by the 18S RNA. The aggregated 18S RNA does not appear to be an artifact of isolation.

Culture Techniques↗
PubMed2012

Limitations of encapsidation of recombinant self-complementary adeno-associated viral genomes in different serotype capsids and their quantitation.

We previously reported that self-complementary adeno-associated virus (scAAV) type 2 genomes of up to 3.3 kb can be successfully encapsidated into AAV2 serotype capsids. Here we report that such oversized AAV2 genomes fail to undergo packaging in other AAV serotype capsids, such as AAV1, AAV3, AAV6, and AAV8, as determined by Southern blot analyses of the vector genomes, although hybridization signals on quantitative DNA slot-blots could still be obtained. Recently, it has been reported that quantitative real-time PCR assays may result in substantial differences in determining titers of scAAV vectors depending on the distance between the primer sets and the terminal hairpin structure in the scAAV genomes. We also observed that the vector titers determined by the standard DNA slot-blot assays were highly dependent on the specific probe being used, with probes hybridizing to the ends of viral genomes being significantly overrepresented compared with the probes hybridizing close to the middle of the viral genomes. These differences among various probes were not observed using Southern blot assays. This overestimation of titer is a systemic error during scAAV genome quantification, regardless of viral genome sequences and capsid serotypes. Furthermore, different serotypes capsid and modification of capsid sequence may affect the ability of packaging intact, full-length AAV genomes. Although the discrepancy is modest with wild-type serotype capsid and short viral genomes, the measured titer could be as much as fivefold different with capsid mutant vectors and large genomes. Thus, based on our data, we suggest that Southern blot analyses should be performed routinely to more accurately determine the titers of recombinant AAV vectors. At the very least, the use of probes/primers hybridizing close to the mutant inverted terminal repeat in scAAV genomes is recommended to avoid possible overestimation of vector titers.

Blotting, Southern↗
PubMed2026

VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.

MOTIVATION: Metagenomic Hi-C provides in situ proximity signals that can improve genome binning and enable virus-host-association analysis. However, viral genome recovery remains difficult because virus-virus Hi-C contact matrices are extremely sparse. Viral genomes are small, often low-abundance, and frequently assemble into short contigs, leaving many true within-genome links unobserved and causing viral bins to fragment. RESULTS: We present VirBinn, a graph-diffusion framework for viral binning from metagenomic Hi-C. VirBinn enhances virus-virus connectivity through two complementary mechanisms: random-walk-with-restart enhancement on the sparse virus-virus contact graph and host-guided diffusion that propagates viral seeds through the host network to infer indirect virus-virus associations. The enhanced views are integrated and clustered using Leiden community detection to produce viral metagenome-assembled genomes (vMAGs). On dataset-specific simulation benchmarks with ground truth, VirBinn consistently recovers more high-quality vMAGs than Hi-C-based and shotgun-based baselines and substantially increases the number of near-complete genomes. On four real metagenomic Hi-C datasets spanning human gut, pig gut, sheep gut (long-read assembly), and wastewater, VirBinn yields more high-completeness vMAGs under CheckV and produces bins with strong within-cluster contact support. Finally, host linkage analysis using reconstructed host MAGs reveals habitat-specific host-association patterns and plausible host taxonomic profiles. AVAILABILITY AND IMPLEMENTATION: VirBinn is available at https://github.com/dyxstat/VirBinn. The scripts to reproduce the results and figures in this article are available at https://github.com/dyxstat/Reproduce_VirBinn.

Genome, Viral↗
PubMed2026

Longitudinal analysis of high-risk HPV infections reveals within-host viral genome changes over time.

Persistent infection with high-risk (HR)-HPV causes cervical cancer, however, it is unclear why most infections resolve while a minority progress. We deep sequenced the HPV genomes of 1,228 HR-HPV-positive serial samples from 351 women with persistent infections (2-10 serial samples per woman over 1-8 years), including 279 controls and 72 precancer/cancer cases, to assess HR-HPV genome changes during infection and relation to infection outcomes. Seventy-seven percent of persistent infections (45-97% by HPV type) were infections with the same exact viral genome isolate; for HPV16, only 52% were persistent with the same isolate. This may suggest some infections include a type-specific isolate switch or new isolate infection during persistence. We additionally observed within-host change to the HPV genome estimated as gradual changes to intrahost single nucleotide variant (iSNV) frequency, and changes varied by HPV type, with HPV33 infections showing the most iSNV changes. Cases exhibited fewer viral genome changes during infection compared to controls (OR = 0.31, 95% CI = 0.1 - 0.86, p = 0.019), suggesting a more stable and clonal viral genome in cases. By viral gene, E7 had fewer nonsynonymous mutations in the cases compared to controls that cleared within 2 years of infection (p = 0.012), which confirms the importance of E7 conservation and suggests mutations to E7 reduce persistence associated with progression. There was a similar pattern in E4 (p = 0.013), while E5 had more changes in the cases (p = 0.008). A subset of 28 infections had an intervening HPV-negative sample between HPV-positive visits; 93% of these infections had the same exact viral genome isolate in the samples before and after the negative, consistent with subclinical persistence and subsequent re-detection. Our data suggests that HR-HPV type-persistence can include a collection of viral isolates, and viral mutations during infection, particularly in E7, reduce HR-HPV persistence and thus carcinogenic potential.

Humans↗
PubMed2026

A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.

The rapid growth of genomic sequencing demands fast, accurate, and scalable analysis methods. In viral genomic classification, expanding labeled reference collections can make supervised models costly to update and dependent on fixed label sets, motivating retrieval-based genomic classification as a simpler, more flexible alternative. We present a unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification across three viral classification tasks: hepatitis C virus (HCV) genotyping, COVID-19 discrimination, and human papillomavirus (HPV) genotyping. We compare standard sequence encodings (one-hot, k-mers, FCGR) with dense embeddings (dna2vec, DNABERT). For each representation, we evaluate supervised classifiers (Random Forest, Decision Tree, XGBoost) and retrieval-based classification, where sequence vectors are indexed with FAISS and labels are assigned via similarity-weighted k-NN. Furthermore, we benchmark multiple FAISS index types (Flat, IVF, HNSW, IVFPQ, OPQ) to characterize accuracy-speed-memory trade-offs at scale. The results show that XGBoost and retrieval using Flat or IVF indexes achieve strong classification performance under different computational profiles. Compressed indexes such as IVFPQ and OPQ substantially reduce memory usage, although their accuracy loss depends on the dataset and representation. Overall, supervised XGBoost provides a favorable accuracy-size trade-off, while retrieval-based classification remains competitive and allows labeled reference sequences to be incorporated without retraining a global classifier. This benchmark provides practical guidance for selecting sequence representations, classifiers, and vector-search indexes under different accuracy, memory, and update requirements.

Genome, Viral↗
PubMed1977

Polyoma-induced stimulation of cellular RNA synthesis is paralleled by changed expression of the viral genome.

We studied synthesis of viral and cellular RNA in the presence and absence of 5-fluorodeoxyuridine (FdU, an inhibitor of DNA synthesis) during lytic infection with polyoma virus in confluent, primary mouse kidney cell cultures. In the presence of FdU, synthesis of early 19S polyoma mRNA and of polyoma tumor (T)-antigen, i.e. expression of the early viral gene, is rapidly followed by a mitogenic reaction of the host cell; it leads to an increase of 30 +/- 5% in cellular, mainly 28S and 18S rRNA, followed by activation of the cellular DNA-synthesizing apparatus. Polyoma-induced cellular RNA synthesis is paralleled by increased production of early 19S mRNA and begin of expression of the late viral genes, leading to synthesis of small amounts of late 19S and 16S mRNAs. Changed expression of the viral genome occurs in the absence of detectable synthesis of polyoma DNA I. Infection in the absence of FdU induces the same sequence of events; it is followed, however, by duplication of the mouse cell chromatin (S-phase) and production of progeny virus.

Cell Line↗
PubMed2026

AI-enabled viral genomics: from virus discovery to host prediction and emerging variant forecasting.

The rapid expansion of metagenomic sequencing has generated vast repositories of viral sequence data that far outpace our capacity to interpret them using conventional approaches. Highly divergent sequences, sparse functional annotation, and taxonomically uneven sampling present fundamental challenges for reference-dependent methods, which lose sensitivity precisely for novel and understudied viruses with high public health relevance. Artificial intelligence (AI) provides a new avenue to address these challenges by enabling predictive inference from viral genomes and proteins while reducing dependence on sequence similarity. In this Review, we discuss representative advances in AI for virus discovery, taxonomic classification and functional annotation, prediction of host range and zoonotic potential, and efforts toward forecasting emerging variants. These advances are transforming viral genomics from a largely descriptive discipline into one with increasing predictive capability. We also critically assess the major challenges that constrain current approaches, including the availability of high-quality and representative datasets, rigorous model evaluation, biological interpretability and responsible governance for increasingly capable AI models.

Artificial Intelligence↗
PubMed1978

Abortive growth of human lymphocytes carrying a dormant Epstein-Barr viral genome.

When P3HR-1 lymphoblastoid cells expressing Epstein-Barr virus (EBV)-related antigens at very low frequency were cocultivated with human umbilical cord blood lymphocytes and the cell-free mixed culture fluid was applied to fresh cord lymphocytes, cells morphologically distinct from normal lymphocytes became evident after one to two weeks' exposure. The abnormal cells became abundant after one month and were easily identified by B-cell markers and a variety of morphologic abnormalities. Such abnormal B-lymphocytes appeared to be negative for EBV-determined nuclear antigen (EBNA), but when the immunofluorescence-negative cells were exposed to pokeweed mitogen and 5-iododeoxyuridine, a striking EBNA induction occurred. The growth of these abnormal cells was limited and they could be maintained for no more than three months. The implications of these findings are discussed in relation to the biological activity of EBV.

B-Lymphocytes↗
PubMed1976

Persistence of the viral genome in interferon-treated cells infected with oncogneic or nononcogenic viruses.

In AKR mouse cells chronically infected with a murine leukemia virus, treatment with interferon for nine days resulted in sustained inhibition of extracellular production of murine leukemia virus but no inhibition of viral intracellular p30 antigen or of reverse transcriptase. Removal of interferon resulted in rapid reversal of these effects. Interferon-treated mouse L-cells were infected with high multiplicities of vesicular stomatitis virus or herpes simplex virus type 1. Infectious virus and intracellular viral antigen were rapidly eliminated from the interferon-treated cultures infected with herpes simplex virus. In cultures infected with vesicular stomatitis virus, titers of virus remained low in interferon-treated cells, but after about two weeks they rose rapidly and the cultures were destroyed. If treatment with interferon was reinstituted as late as nine days after primary infection, infectious vesicular stomatitis virus was eliminated, and there was no evidence for survival of the viral genome in these cultures. In the cultures infected with murine leukemia virus, inhibition of production of virus by treatment with interferon was possible, but the viral genome was not eliminated. In cells acutely infected with vesicular stomatitis virus or herpes simplex virus, however, the viral genomes were apparently eliminated from cultures treated with interferon.

Animals↗
PubMed2025

ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution.

MOTIVATION: Tumor viruses account for ∼10% of cancer diagnoses. Virally induced tumorigenesis is understood as direct signaling through oncogenes such as E6 and E7 genes in the case of human papillomavirus. Furthermore, pathogen characteristics such as viral oncogene dose may impact the disease course. To our knowledge, no tool has been proposed to assess the intra-viral copy number alterations that define the gene dose of viral oncogenes and associated suppressive pathways native to the pathogen's normal life cycle. RESULTS: We propose an R package, "ELViS," that analyzes viral copy number changes from DNA sequencing of whole viral genomes. The method adjusts for viral load with 2D transformation and segmentation to offer the relative viral gene doses. AVAILABILITY AND IMPLEMENTATION: The ELViS R package is available from https://bioconductor.org/packages/ELViS. This article used controlled access data from dbGaP (phs001713.v1.p1).

Software↗
PubMed2025

A Respiratory Syncytial Virus trailer sequence modulates viral replication and copy-back defective viral genome generation and propagation kinetics.

Copy-back defective viral genomes (cbDVGs) are key inducers of antiviral responses during negative-sense RNA virus infection. Once considered byproducts of in vitro viral replication, cbDVGs have since been detected in clinical specimens and implicated in affecting infection outcomes. The molecular mechanism of cbDVG generation remains unclear, thereby hindering our ability to manipulate cbDVG production during infection for therapeutic gain. Previous work showed that respiratory syncytial virus (RSV) cbDVG re-initiation sites cluster in trailer-end hotspots R1, R2, and R3, and that a poly-U mutation in R1 selectively reduced cbDVG formation at the mutated region. Here, we reported that a 10U mutation in R2 drastically reduced cbDVGs in this region in both minigenome and recombinant virus systems. Furthermore, during high-MOI passaging of the R2-10U virus, we observed delayed detection of cbDVGs with re-initiation sites in R1-R3 (trailer cbDVGs) compared to WT, while no differences in virus titers were observed. Interestingly, we observed the rapid emergence and accumulation of a viral variant bearing a 2-ribonucleotide deletion (R2-8U) within the R2-10U mutation sequence as early as P0. Compared to R2-10U, the R2-8U virus was stable, displayed faster generation and accumulation of trailer cbDVGs, restored cbDVGs with R2 re-initiation sites, and exhibited enhanced genomic replication. Overall, our data identify a sequence in the RSV trailer whose mutation critically modulates both viral replication and the generation/propagation of trailer cbDVGs. Our data also suggest that cbDVG generation, particularly near the trailer, may be an evolutionary tradeoff for more rapid virus genomic replication.

defective viral genome generation and accumulation↗
PubMed2025

Epstein-barr virus (EBV) in cervical carcinoma detected by in situ hybridization targeting ebers and the viral genome.

Epstein-Barr virus (EBV) infection has been suggested as a potential cofactor for the development and progression of cervical cancer, collaborating with high-risk Human Papillomavirus (HR-HPV). In situ hybridization (ISH) has been considered the gold standard in the investigation of EBV in neoplasms. This study aimed to detect EBV in cervical carcinoma samples using ISH targeting EBERs (EBER-ISH) and the BamHI-W region of the viral genome (BamHI-W-ISH), and compare the results of both targets. Of the 88 cases collected, 9 were EBER-ISH positive (10.2%), while 33 (37.5%) cases were positive for EBV by BamHI-W-ISH, all showing staining in the nuclei of the malignant cells. No statistically significant results were found between the presence of EBV and carcinoma type, differentiation grade or tumor staging. The kappa agreement index between the two targets was 0.092. Only 4 cases were EBER-ISH(+) and BamHI-W-ISH(-). On the other hand, 28 cases were BamHI-W-ISH(+) and EBER-ISH(-). Altogether, 37/88 (42%) cases were EBV-positive by one or both targets. Infected lymphocytes were verified in 9 (10.2%) and 34 (38.6%) cases, by EBER-ISH and BamHI-W-ISH, respectively. The slight agreement demonstrated between the targets may be due to the lack of expression of EBERs, suggesting that EBV may present a distinct latency pattern in the cervical mucosa, or that it has entered the replicative cycle in some of these tumors, in both cases, explaining the low positivity rate verified through EBER-ISH, while calling into question the latter's gold standard status in the detection of EBV in malignancies. Our findings also indicate that the chosen viral genomic target may represent a suitable candidate for EBV detection by ISH.

Humans↗
PubMed2026

hnRNPC facilitates coronavirus replication by directly binding the frameshift-stimulatory element of viral genomic RNA.

Translation of key viral replicative proteins in coronaviruses requires a programmed -1 ribosomal frameshifting (-1 PRF) event controlled by the viral frameshift-stimulatory element (FSE). Although previous studies have analyzed host factor dependencies of coronaviruses, how host cellular factors alter -1 PRF efficiency and affect viral replication remains poorly understood. Here, using RNA pull-down combined with LC-MS/MS analysis, we identified heterogeneous nuclear ribonucleoprotein C (hnRNPC) as a major interacting protein of FSE RNA. Coronavirus infection triggers hnRNPC mRNA decay, alters hnRNPC protein levels, and induces its cytoplasmic relocalization, where it appears to bind directly to FSE RNA through residues Asn7 and Asn83. This binding is associated with increased -1 PRF efficiency and may facilitate coronavirus replication. Deletion mapping analysis shows that hnRNPC preferentially binds U-rich regions of the FSE RNA. Finally, we demonstrated that the small molecule Elbasvir directly binds hnRNPC, disrupting the interaction between hnRNPC and FSE RNA and inhibiting coronavirus replication by decreasing -1 PRF efficiency. Collectively, our study identifies hnRNPC as a key host cofactor for coronaviruses and provides a novel target for broad-spectrum antiviral drug development.

RNA, Viral↗
PubMed1979

Viral genome RNA serves as messenger early in the infectious cycle of murine leukemia virus.

When NIH/3T3 mouse fibroblasts were infected with the Moloney strain of murine leukemia virus, part of the viral genome RNA molecules were detected in polyribosomes of the infected cells early in the infectious cycle. The binding appears to be specific, since we could demonstrate the release of viral RNA from polyribosomes with EDTA. Moreover, when infection occurred in the presence of cycloheximide, most viral RNA molecules were detected in the free cytoplasm. Size analysis on polyribosomal viral RNA molecules indicated that two size class molecules, 38S and 23S, are present in polyribosomes at 3 h after infection. Analysis of the polyriboadenylate [poly(rA)] content of viral RNA extracted from infected polyribosomes demonstrated that such molecules bind with greatest abundance at 3 h after infection, as has been detected with total viral RNA. No molecules lacking poly(rA) stretches could be detected in polyribosomes. Furthermore, when a similar analysis was performed on unbound molecules present in the free cytoplasm, identical results were obtained. We conclude that no selection towards poly(rA)-containing viral molecules is evident on binding to polyribosomes. These findings suggest that the incoming viral genome of the Moloney strain of murine leukemia virus may serve as a messenger for the synthesis of one or more virus-specific proteins early after infection of mouse fibroblasts.

Animals↗
PubMed1979

Method for determining the extent and copy number of overlapping and nonoverlapping segments of integrated viral genomes.

We analyzed the method of exhaustive hybridization of single-stranded DNA and derived a general relationship between the fraction of the probe DNA hybridized and the sizes and copy numbers of the segments of the viral genome integrated in cellular DNA. The equations employed can be used to analyze integrated DNA comprised of overlapping and nonoverlapping segments of the viral genome. Using these equations, we analyzd the adenovirus type 2 DNA content of a series of hamster cell lines transformed by adenovirus type 2 and several adenovirus type 2-simian virus 40 hybrid viruses. We found no eividence that the integrated viral DNA is comprised of overlapsping segments. However, the number of copies of the integrated segments varies between lines cloned from the same transformed isolate, and copy numbers change during in vivo passage of transformed cells.

Adenoviruses, Human↗
PubMed1977

Incomplete viral genome in a non-virogenic mouse tumour cell line (RVP3) transformed by Prague strain of avian sarcoma virus.

Two cell lines, RVP3 and RVA4, derived originally from mouse tumors induced by the Prague and Schmidt-Ruppin strain of RSV, respectively, were studied. tall attempts failed to induce infectious virus production in RVP3 cells by fusion with chicken fibroblasts even if the cells were infected with avian leukosis viruses. Also, attempts to rescue the viral genome by transfection were unsuccessful. RVP3 cells harboured 31-45% of the viral genome sequences, as was shown by molecular hybridization, and therefore they were designated cryptovirogenic. The tumour cell line RVA4 did not contain any detectable viral sequences. The significance of the detection of the incomplete Rous virus genome sequences in mammalian cells is discussed.

Animals↗