Multiple Viral Genomes Research Articles

CTL Escape and Viral Fitness in HIV/SIV Infection

Cytotoxic T lymphocyte (CTL) responses exert a suppressive effect on HIV and simian immunodeficiency virus (SIV) replication. Under the CTL pressure, viral CTL escape mutations are frequently selected with viral fitness costs. Viruses with such CTL escape mutations often need additional viral genome mutations for recovery of viral fitness. Persistent HIV/SIV infection sometimes shows replacement of a CTL escape mutation with an alternative escape mutation toward higher viral fitness. Thus, multiple viral genome changes under CTL pressure are observed in the chronic phase of HIV/SIV infection. HIV/SIV transmission to HLA/MHC-mismatched hosts drives further viral genome changes including additional CTL escape mutations and reversions under different CTL pressure. Understanding of viral structure/function and host CTL responses would contribute to prediction of HIV evolution and control of HIV prevalence.

MfSAT: Detect simple sequence repeats in viral genomes.

Simple sequence repeats (SSRs) are ubiquitous short tandem repeats, which are associated with various regulatory mechanisms and have been found in viral genomes. Herein, we develop MfSAT (Multi-functional SSRs Analytical Tool), a new powerful tool which can fast identify SSRs in multiple short viral genomes and then automatically calculate the numbers and proportions of various SSR types (mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats). Furthermore, it also can detect codon repeats and report the corresponding amino acid.

Contributions of Nucleotide Excision Repair, DNA Polymerase η, and Homologous Recombination to Replication of UV-irradiated Herpes Simplex Virus Type 1

The effects of UV irradiation on herpes simplex virus type 1 (HSV-1) gene expression and DNA replication were examined in cell lines containing mutations inactivating the XPA gene product required for nucleotide-excision repair, the DNA polymerase eta responsible for translesion synthesis, or the Cockayne syndrome A and B (CSA and CSB) gene products required for transcription-coupled nucleotide excision repair. In the absence of XPA and CSA and CSB gene products, virus replication was reduced 10(6)-, 400-, and 100-fold, respectively. In DNA polymerase eta mutant cells HSV-1 plaque efficiency was reduced 10(4)-fold. Furthermore, DNA polymerase eta was strictly required for virus replication at low multiplicities of infection but dispensable at high multiplicities of infection. Knock down of Rad 51, Rad 52, and Rad 54 levels by RNA interference reduced replication of UV-irradiated HSV-1 150-, 100-, and 50-fold, respectively. We find that transcription-coupled repair efficiently supports expression of immediate early and early genes from UV-irradiated HSV-1 DNA. In contrast, the progression of the replication fork appears to be impaired, causing a severe reduction of late gene expression. Since the HSV-1 replisome does not make use of proliferating cell nuclear antigen, we attribute the replication defect to an inability to perform proliferating cell nuclear antigen-dependent translesion synthesis by polymerase switching at the fork. Instead, DNA polymerase eta may act during postreplication gap filling. Homologous recombination, finally, might restore the physical and genetic integrity of the virus chromosome.

Novel circular DNA viruses in stool samples of wild-living chimpanzees

Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem-loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (approximately 1 kb) plant nanovirus circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.

Mixed Infection and the Genesis of Influenza Virus Diversity

The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve to one capable of human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes coinfect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection with influenza virus is therefore central to understanding the emergence of pandemic, antigenic, and drug-resistant strains. To better understand the potential for such events, we explored patterns of intrahost genetic diversity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences sampled from individual influenza patients we reveal a high level of mixed infection, including diverse lineages of the same influenza virus subtype, drug-resistant and -sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza virus types (A and B). These results reveal that individuals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents.

In silico microarray probe design for diagnosis of multiple pathogens

BackgroundWith multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as well as fingerprints that are unique to each individual genome. We present algorithmic enhancements to an existing single-genome pipeline that allows for efficient design of microarray probes common to groups of target genomes. The enhanced pipeline takes advantage of the similarities in the input genomes to narrow the search to short, nonredundant regions of the target genomes and, thereby, significantly reduces the computation time. The pipeline also computes a three-state hybridization matrix, which gives the expected hybridization of each probe with each target.ResultsDesign of microarray probes for eight pathogenic Burkholderia genomes shows that the multiple-genome pipeline is nearly four-times faster than the single-genome pipeline for this application. The probes designed for these eight genomes were experimentally tested with one non-target and three target genomes. Hybridization experiments show that less than 10% of the designed probes cross hybridize with non-targets. Also, more than 65% of the probes designed to identify all Burkholderia mallei and B. pseudomallei strains successfully hybridize with a B. pseudomallei strain not used for probe design.ConclusionThe savings in runtime suggest that the enhanced pipeline can be used to design fingerprints for tens or even hundreds of related genomes in a single run. Hybridization results with an unsequenced B. pseudomallei strain indicate that the designed probes might be useful in identifying unsequenced strains of B. mallei and B. pseudomallei.

Size and stability of the Epstein-Barr virus major internal repeat (IR-1) in Burkitt's lymphoma and lymphoblastoid cell lines

We have used field inversion gel electrophoresis to survey EBV strains for the size of the major internal repeat, IR-1, and estimate the number of 3.1-kb repeat units present. The B95-8 strain of EBV was estimated to contain 8.6 repeats. The repeat number varies considerably among naturally occurring isolates around a mean of six repeats. Some cell lines harbored multiple viral genomes with differing numbers of repeats and our results suggest that the repeat number in IR-1 is more likely to change during lytic replication than during latency. The Jijoye strain had 6.6 repeats and the Jijoye deletion mutant clone P3HR-1 retained 5.9 repeats setting the size of the P3HR-1 deletion at 6.8 kb. Thus, the nonimmortalizing mutant has retained all of the W1 and W2 exons of the immortalizing parent and has lost only the 3′ unique exons of EBNA4 and all of EBNA2.

Repair of psoralen-induced crosslinks in cells multiply infected with SV40.

Experiments were conducted to study the relationship between the production of interstrand crosslinks by 4,5',8-trimethylpsoralen (psoralen) in simian virus 40 DNA and the ability of psoralen to inactivate the virus. Under conditions where only single viral particles enter a given host cell, approximately one crosslink was lethal to the virus and could not be repaired. In contrast, when multiple viral genomes infected a host cell, psoralen-induced crosslinks were repaired (multiplicity reactivation). A model is proposed for multiplicity reactivation which involves genetic recombination between damaged viral genomes.

DNA repair in cultured human fibroblasts does not decline with donor age

Human fibroblasts from young (3 days to 3 years) and old (84–94 years) donors were tested for their ability to repair DNA damage by measuring survival of colony formation following irradiation with ultraviolet (UV) light. Repair was also measured by the ability to reactivate herpes simplex virus following treatment of the virus with UV light, methyl methane sulfonate or 4,5′,8-trimethylpsoralen plus light. This virus was used as a probe of cellular repair capacity because survival of damaged virus is lower in repair-deficient cell lines [1]. Cell lines from both age groups exhibited comparable survivals following UV irradiation and failed to show increased sensitivity to irradiation in the presence of caffeine. Cells from both groups repaired damaged virus to equal extents. Proficient viral repair was observed under conditions in which cells were infected by either single or multiple viral genomes. These results suggest that DNA repair mechanisms which act on a variety of lesions (e.g. pyrimidine dimers, apurinic sites, alkylated bases, cross-links, etc.) do not decline with age. A model for biological aging resulting from the accumulation with age of unrepaired DNA damage is discussed.

Infection of rat cells by avian sarcoma virus: Factors affecting transformation and subsequent reversion

We have investigated factors that influence (1) the initial incidence of transformation in rat cells infected by avian sarcoma virus B77 and (2) the transformed phenotype of the cell and its stability. Transformation is not limited to a genetically highly competent subpopulation of either viruses or cells but can potentially involve any of the viruses or hosts. The kinetics of transformation are one-hit, even at input virus multiplicities of infection (m.o.i.) of 1 to 10, suggesting that a single virus particle is sufficient to induce transformation and that there is not a physiologically highly susceptible cell population whose response reaches a plateau at high m.o.i. However, as judged by levels of virus recovery and morphological reversion, transformed clones obtained after infection at high m.o.i. show a more uniform virus expression than those obtained at low m.o.i. Moreover, analysis of integrated proviral DNA in cloned transformed cells indicated that seven clones transformed at low (0.01) m.o.i. contain only single proviruses whereas five clones derived from high (1 or 7.5) m.o.i. infections each bear a minimum of three integrated proviruses. These findings suggest that, in the high m.o.i. transformants, multiple viral genome copies contribute to the transformed cell phenotype, making it unlikely that transformation is due simply to randomly occurring virus-cell interactions. Studies on transformants obtained at low m.o.i. show that heterogeneity in virus recovery and morphological reversion can be stable but is not, in most cases, due to virus mutants. Since levels of virus recovery and morphological reversion in these clones did not show a uniform inverse relationship, it is also unlikely that their phenotypic variability is due simply to modulations in overall levels of virus expression. Most revertants isolated from clones transformed at low m.o.i. show decreased but detectable rescuability of transforming virus, suggesting that virus expression is reduced, but reversion by other mechanisms has also been detected in these clones (Varmus et al., 1980).

Conformation of Moloney murine leukaemia proviral sequences in chromatin from leukaemic and nonleukaemic cells.

THE structure of transcriptionally active and inert regions of eukaryotic chromatin can be differentiated on the basis of their sensitivity towards nuclease digestion. Whereas DNase I preferentially digests transcriptionally active genes into fragments too small to form stable hybrids, micrococcal nuclease shows no preferential digestion of specific nuclear DNA sequences1–6. We report here experiments in which the structure of Moloney murine leukaemia proviral DNA sequences in chromatin of target cells expressing the viral genome and of non-target cells in which the same sequences are repressed were examined by digestion with DNase I and microccoccal nuclease. It is shown that the Moloney murine leukaemia virus (M-MuLV) genomes in target and non-target cells of BALB/Mo mice are integrated into the host cell genome and organised in nucleosome-like structures. The difference in transcriptional activity of viral genomes in target and non-target cells is reflected by a difference in DNase I sensitivity. A partial resistance to DNase I of M-MuLV sequences in target cells suggests that the multiple viral genome copies in these cells are integrated at different sites and have different transcriptional activity.

Antigen-Inducing Ability of Herpesvirus Papio in Human and Baboon Lymphoma Lines, Compared to Epstein-Barr Virus

Herpesvirus papio(HVP)-carrying baboon lymphoblastoid lines do not express a nuclear antigen like the Epstein-Barr virus(EBV)-determined nuclear antigen (EBNA), as judged by in situ anticomplement fluorescence staining, although the carry multiple viral genomes and, in the case of producerlines, early antigen (EA) and viral capsid antigen (VCA) that cross-react with the corresponding human EBV-determined antigens. To test whether the lack of in situ nuclear antigen expression is a property innate to the baboon virus or the baboon cell, nonproducer HVP-carrying baboon lymphoid cells of the 26 CB-1 line were superinfected with two human EBV strains. B95-8-derived EBV induced brilliant EBNA staining, proving that the baboon lymphoid cell was competent to synthesize EBNA. In the mirror experiment, HVP derived from the 9B or the 18C baboon line was added to the EBV-carrying Raji line, the EBV-negative Ramos and BJAB lines and the HVP-carrying nonproducer 26 CB-1 line, respectively. HVP induced EA and VCA in Raji, and EA in BJAB and 26 CB-1. EBNA was not induced in any of the three EBNA-negative lines, BJAB, Ramos and 26 CB-1. It is concluded that the lack of in situ nuclear staining in HVP-carrying baboon lines is a HVP-associated property and is not due to any innate inability of the baboon lymphoid cell to synthesize an antigen of the EBNA type.

Analysis of multiple viral genome fragments in adenovirus 7-transformed hamster cells.

The presence of multiple copies of a portion of the viral genome was demonstrated in Ad7-transformed cells by a new method based on the kinetic analysis of labeled viral DNA reassociation in the presence of unlabeled transformed cell DNA. DNA-DNA homology measurement utilizing defined DNA fragments (restriction endonuclease digests) as labeled probes supported the above conclusion.