Preparation and use of cDNA probes for detection of viral genomes

The properties of human herpesvirus-encoded enzymes are reviewed and the importance of sequence analysis of viral genomes as well as the experiments on characteristics of enzymes isolated from infected cell cultures are emphasized. The following enzymes are described in detail: DNA replication complex consisting of DNA polymerase, DNA helicase-primase, single-stranded DNA binding protein and origin binding protein, further thymidine kinase, ribonucleotide reductase, deoxyuridine triphosphatase as well as uracil-DNA-glycosylase, deoxyribonuclease and protein kinase. The importance of these enzymes from the point of view of antiviral chemotherapy is discussed.

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Latest Advances of Virology Research Using CRISPR/Cas9-Based Gene-Editing Technology and Its Application to Vaccine Development

Viruses ◽

10.3390/v13050779 ◽

2021 ◽

Vol 13 (5) ◽

pp. 779

Author(s):

Man Teng ◽

Yongxiu Yao ◽

Venugopal Nair ◽

Jun Luo

Keyword(s):

Biological Sciences ◽

Gene Therapy ◽

Genetic Engineering ◽

Gene Function ◽

Viral Genome ◽

Gene Editing ◽

Vaccine Development ◽

Future Prospects ◽

Dna Viruses ◽

Viral Genomes

In recent years, the CRISPR/Cas9-based gene-editing techniques have been well developed and applied widely in several aspects of research in the biological sciences, in many species, including humans, animals, plants, and even in viruses. Modification of the viral genome is crucial for revealing gene function, virus pathogenesis, gene therapy, genetic engineering, and vaccine development. Herein, we have provided a brief review of the different technologies for the modification of the viral genomes. Particularly, we have focused on the recently developed CRISPR/Cas9-based gene-editing system, detailing its origin, functional principles, and touching on its latest achievements in virology research and applications in vaccine development, especially in large DNA viruses of humans and animals. Future prospects of CRISPR/Cas9-based gene-editing technology in virology research, including the potential shortcomings, are also discussed.

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Persistent Human Papillomavirus Infection

Viruses ◽

10.3390/v13020321 ◽

2021 ◽

Vol 13 (2) ◽

pp. 321

Author(s):

Ashley N. Della Fera ◽

Alix Warburton ◽

Tami L. Coursey ◽

Simran Khurana ◽

Alison A. McBride

Keyword(s):

Human Papillomavirus ◽

Dna Replication ◽

Cellular Proliferation ◽

Basal Cells ◽

Viral Dna ◽

Viral Dna Replication ◽

Viral Genomes ◽

Cellular Environment ◽

E6 And E7 ◽

Cellular Replication

Persistent infection with oncogenic human papillomavirus (HPV) types is responsible for ~5% of human cancers. The HPV infectious cycle can sustain long-term infection in stratified epithelia because viral DNA is maintained as low copy number extrachromosomal plasmids in the dividing basal cells of a lesion, while progeny viral genomes are amplified to large numbers in differentiated superficial cells. The viral E1 and E2 proteins initiate viral DNA replication and maintain and partition viral genomes, in concert with the cellular replication machinery. Additionally, the E5, E6, and E7 proteins are required to evade host immune responses and to produce a cellular environment that supports viral DNA replication. An unfortunate consequence of the manipulation of cellular proliferation and differentiation is that cells become at high risk for carcinogenesis.

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Reovirus Low-Density Particles Package Cellular RNA

Viruses ◽

10.3390/v13061096 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1096

Author(s):

Timothy W. Thoner ◽

Xiang Ye ◽

John Karijolich ◽

Kristen M. Ogden

Keyword(s):

Rna Polymerase ◽

Viral Proteins ◽

Viral Rna ◽

Low Density ◽

Rna Packaging ◽

Genome Packaging ◽

Double Stranded Rna ◽

Viral Genomes ◽

Mammalian Orthoreovirus ◽

Insight Into

Packaging of segmented, double-stranded RNA viral genomes requires coordination of viral proteins and RNA segments. For mammalian orthoreovirus (reovirus), evidence suggests either all ten or zero viral RNA segments are simultaneously packaged in a highly coordinated process hypothesized to exclude host RNA. Accordingly, reovirus generates genome-containing virions and “genomeless” top component particles. Whether reovirus virions or top component particles package host RNA is unknown. To gain insight into reovirus packaging potential and mechanisms, we employed next-generation RNA-sequencing to define the RNA content of enriched reovirus particles. Reovirus virions exclusively packaged viral double-stranded RNA. In contrast, reovirus top component particles contained similar proportions but reduced amounts of viral double-stranded RNA and were selectively enriched for numerous host RNA species, especially short, non-polyadenylated transcripts. Host RNA selection was not dependent on RNA abundance in the cell, and specifically enriched host RNAs varied for two reovirus strains and were not selected solely by the viral RNA polymerase. Collectively, these findings indicate that genome packaging into reovirus virions is exquisitely selective, while incorporation of host RNAs into top component particles is differentially selective and may contribute to or result from inefficient viral RNA packaging.

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SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection

Clinical Infectious Diseases ◽

10.1093/cid/ciab380 ◽

2021 ◽

Author(s):

Manish C Choudhary ◽

Charles R Crain ◽

Xueting Qiu ◽

William Hanage ◽

Jonathan Z Li

Keyword(s):

Persistent Infection ◽

Viral Evolution ◽

Phylogenetic Reconstruction ◽

Geographic Region ◽

Antibody Treatment ◽

Viral Genomes ◽

Monoclonal Antibody Treatment ◽

Viral Sequences ◽

Sequence Characteristics ◽

Baseline Health

Abstract Background Both SARS-CoV-2 reinfection and persistent infection have been reported, but sequence characteristics in these scenarios have not been described. We assessed published cases of SARS-CoV-2 reinfection and persistence, characterizing the hallmarks of reinfecting sequences and the rate of viral evolution in persistent infection. Methods A systematic review of PubMed was conducted to identify cases of SARS-CoV-2 reinfection and persistence with available sequences. Nucleotide and amino acid changes in the reinfecting sequence were compared to both the initial and contemporaneous community variants. Time-measured phylogenetic reconstruction was performed to compare intra-host viral evolution in persistent SARS-CoV-2 to community-driven evolution. Results Twenty reinfection and nine persistent infection cases were identified. Reports of reinfection cases spanned a broad distribution of ages, baseline health status, reinfection severity, and occurred as early as 1.5 months or >8 months after the initial infection. The reinfecting viral sequences had a median of 17.5 nucleotide changes with enrichment in the ORF8 and N genes. The number of changes did not differ by the severity of reinfection and reinfecting variants were similar to the contemporaneous sequences circulating in the community. Patients with persistent COVID-19 demonstrated more rapid accumulation of sequence changes than seen with community-driven evolution with continued evolution during convalescent plasma or monoclonal antibody treatment. Conclusions Reinfecting SARS-CoV-2 viral genomes largely mirror contemporaneous circulating sequences in that geographic region, while persistent COVID-19 has been largely described in immunosuppressed individuals and is associated with accelerated viral evolution.

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PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

Genome Biology ◽

10.1186/s13059-021-02307-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Maria Artesi ◽

Vincent Hahaut ◽

Basiel Cole ◽

Laurens Lambrechts ◽

Fereshteh Ashrafi ◽

...

Keyword(s):

Viral Genome ◽

Clonal Expansion ◽

Endogenous Retroviruses ◽

Viral Genomes ◽

Short Read Sequencing ◽

Long Reads ◽

Infected Cells ◽

Insertion Sites ◽

Viral Insertion ◽

Hiv 1

AbstractThe integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.

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Favipiravir antiviral efficacy against SARS-CoV-2 in a hamster model

Nature Communications ◽

10.1038/s41467-021-21992-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jean-Sélim Driouich ◽

Maxime Cochin ◽

Guillaume Lingas ◽

Grégory Moureau ◽

Franck Touret ◽

...

Keyword(s):

Clinical Trials ◽

Drug Exposure ◽

Clinical Evidence ◽

Antiviral Effect ◽

Dose Effect ◽

Plasma Drug ◽

Hamster Model ◽

Viral Genomes ◽

Antiviral Efficacy ◽

Repurposed Drugs

AbstractDespite no or limited pre-clinical evidence, repurposed drugs are massively evaluated in clinical trials to palliate the lack of antiviral molecules against SARS-CoV-2. Here we use a Syrian hamster model to assess the antiviral efficacy of favipiravir, understand its mechanism of action and determine its pharmacokinetics. When treatment is initiated before or simultaneously to infection, favipiravir has a strong dose effect, leading to reduction of infectious titers in lungs and clinical alleviation of the disease. Antiviral effect of favipiravir correlates with incorporation of a large number of mutations into viral genomes and decrease of viral infectivity. Antiviral efficacy is achieved with plasma drug exposure comparable with those previously found during human clinical trials. Notably, the highest dose of favipiravir tested is associated with signs of toxicity in animals. Thereby, pharmacokinetic and tolerance studies are required to determine whether similar effects can be safely achieved in humans.

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