The Application of CRISPR/Cas Systems for Antiviral Therapy

As CRISPR/Cas systems have been refined over time, there has been an effort to apply them to real world problems, such as developing sequence-targeted antiviral therapies. Viruses pose a major threat to humans and new tools are urgently needed to combat these rapidly mutating pathogens. Importantly, a variety of CRISPR systems have the potential to directly cleave DNA and RNA viral genomes, in a targeted and easily-adaptable manner, thus preventing or treating infections. This perspective article highlights recent studies using different Cas effectors against various RNA viruses causing acute infections in humans; a latent virus (HIV-1); a chronic virus (hepatitis B); and viruses infecting livestock and animal species of industrial importance. The outlook and remaining challenges are discussed, particularly in the context of tacking newly emerging viruses, such as SARS-CoV-2.

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Determinants of HIV-1 Late Presentation in Patients Followed in Europe

Pathogens ◽

10.3390/pathogens10070835 ◽

2021 ◽

Vol 10 (7) ◽

pp. 835

Author(s):

Mafalda N. S. Miranda ◽

Marta Pingarilho ◽

Victor Pimentel ◽

Maria do Rosário O. Martins ◽

Anne-Mieke Vandamme ◽

...

Keyword(s):

Late Presentation ◽

World Health ◽

Prevention Measures ◽

Demographic Information ◽

Late Presenters ◽

Major Threat ◽

Immunodeficiency Virus ◽

Mode Of Transmission ◽

Health Organization ◽

Hiv 1

To control the Human Immunodeficiency Virus (HIV) pandemic, the World Health Organization (WHO) set the 90-90-90 target to be reached by 2020. One major threat to those goals is late presentation, which is defined as an individual presenting a TCD4+ count lower than 350 cells/mm3 or an AIDS-defining event. The present study aims to identify determinants of late presentation in Europe based on the EuResist database with HIV-1 infected patients followed-up between 1981 and 2019. Our study includes clinical and socio-demographic information from 89851 HIV-1 infected patients. Statistical analysis was performed using RStudio and SPSS and a Bayesian network was constructed with the WEKA software to analyze the association between all variables. Among 89,851 HIV-1 infected patients included in the analysis, the median age was 33 (IQR: 27.0–41.0) years and 74.4% were males. Of those, 28,889 patients (50.4%) were late presenters. Older patients (>56), heterosexuals, patients originated from Africa and patients presenting with log VL >4.1 had a higher probability of being late presenters (p < 0.001). Bayesian networks indicated VL, mode of transmission, age and recentness of infection as variables that were directly associated with LP. This study highlights the major determinants associated with late presentation in Europe. This study helps to direct prevention measures for this population.

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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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TRIM22. A Multitasking Antiviral Factor

Cells ◽

10.3390/cells10081864 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1864

Author(s):

Isabel Pagani ◽

Guido Poli ◽

Elisa Vicenzi

Keyword(s):

Protein Interactions ◽

Influenza A ◽

Direct Interaction ◽

Type I Interferons ◽

Viral Gene ◽

Target Cells ◽

Type I ◽

Protein Protein Interactions ◽

Viral Genomes ◽

Dna And Rna

Viral invasion of target cells triggers an immediate intracellular host defense system aimed at preventing further propagation of the virus. Viral genomes or early products of viral replication are sensed by a number of pattern recognition receptors, leading to the synthesis and production of type I interferons (IFNs) that, in turn, activate a cascade of IFN-stimulated genes (ISGs) with antiviral functions. Among these, several members of the tripartite motif (TRIM) family are antiviral executors. This article will focus, in particular, on TRIM22 as an example of a multitarget antiviral member of the TRIM family. The antiviral activities of TRIM22 against different DNA and RNA viruses, particularly human immunodeficiency virus type 1 (HIV-1) and influenza A virus (IAV), will be discussed. TRIM22 restriction of virus replication can involve either direct interaction of TRIM22 E3 ubiquitin ligase activity with viral proteins, or indirect protein–protein interactions resulting in control of viral gene transcription, but also epigenetic effects exerted at the chromatin level.

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Acute Infections, Cost per Infection and Turnaround Time in Three United States Hospital Laboratories Using Fourth-Generation Antigen-Antibody Human Immunodeficiency Virus Immunoassays

Open Forum Infectious Diseases ◽

10.1093/ofid/ofv188 ◽

2015 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Laura G. Wesolowski ◽

Muazzam Nasrullah ◽

Robert W. Coombs ◽

Eric Rosenberg ◽

Steven F. Ethridge ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

South Carolina ◽

Massachusetts General Hospital ◽

Medical Center ◽

Fourth Generation ◽

Reference Laboratory ◽

Acute Infections ◽

Immunodeficiency Virus ◽

Antigen Antibody ◽

Hiv 1

Abstract Background. To improve clinical and public health outcomes through early human immunodeficiency virus (HIV) detection, fourth-generation antigen/antibody immunoassay (4IA) and supplemental testing results must be returned rapidly. Methods. We examined HIV testing data at Harborview Medical Center (HMC), Massachusetts General Hospital (MGH), and the Medical University of South Carolina (MUSC), which used 4IA and supplemental antibody and nucleic acid tests (NATs). At MGH and MUSC, HIV-1 Western blot (WB) and HIV-2 testing were conducted at a reference laboratory. We compared time from specimen collection to laboratory result for established (positive WB) and acute infections (reactive 4IA, negative/indeterminate WB, detectable NAT), and we calculated testing cost per positive-test result. Results. From 3731 (MUSC) to 19 774 (MGH) tests were conducted; 0.01% (MGH) to 0.05% (HMC) were acute infections. Each laboratory had reactive 4IA, WB-negative, or indeterminate specimens without NAT (ie, potential acute infections). Time to result was 1.5 (HMC) to 5.2 days (MGH) for acute and 1.0 (HMC) to 5.2 days (MGH) for established infections. Costs were $1054 (MGH) to $1521 (MUSC). Conclusions. Conducting supplemental testing in-house lowered turnaround times, which may be further reduced with rapid HIV-1/HIV-2 differentiation tests. Hospitals may benefit from quantitative NATs not requiring physician orders, so all potential acute infections receive NAT.

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Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510199112 ◽

2015 ◽

Vol 112 (33) ◽

pp. 10473-10478 ◽

Cited By ~ 128

Author(s):

Davide Corti ◽

Jincun Zhao ◽

Mattia Pedotti ◽

Luca Simonelli ◽

Sudhakar Agnihothram ◽

...

Keyword(s):

B Cells ◽

Neutralizing Antibodies ◽

Human Monoclonal Antibody ◽

Infected Individual ◽

Chinese Hamster ◽

Neutralizing Antibody ◽

Emerging Viruses ◽

Antiviral Therapies ◽

Human Infections ◽

First Time

Middle East Respiratory Syndrome (MERS) is a highly lethal pulmonary infection caused by a previously unidentified coronavirus (CoV), likely transmitted to humans by infected camels. There is no licensed vaccine or antiviral for MERS, therefore new prophylactic and therapeutic strategies to combat human infections are needed. In this study, we describe, for the first time, to our knowledge, the isolation of a potent MERS-CoV–neutralizing antibody from memory B cells of an infected individual. The antibody, named LCA60, binds to a novel site on the spike protein and potently neutralizes infection of multiple MERS-CoV isolates by interfering with the binding to the cellular receptor CD26. Importantly, using mice transduced with adenovirus expressing human CD26 and infected with MERS-CoV, we show that LCA60 can effectively protect in both prophylactic and postexposure settings. This antibody can be used for prophylaxis, for postexposure prophylaxis of individuals at risk, or for the treatment of human cases of MERS-CoV infection. The fact that it took only 4 mo from the initial screening of B cells derived from a convalescent patient for the development of a stable chinese hamster ovary (CHO) cell line producing neutralizing antibodies at more than 5 g/L provides an example of a rapid pathway toward the generation of effective antiviral therapies against emerging viruses.

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Localization and genotyping of canine papillomavirus in canine inverted papillomas

Journal of Veterinary Diagnostic Investigation ◽

10.1177/10406387211035799 ◽

2021 ◽

pp. 104063872110357

Author(s):

Margherita Orlandi ◽

Maurizio Mazzei ◽

Marta Vascellari ◽

Erica Melchiotti ◽

Claudia Zanardello ◽

...

Keyword(s):

In Situ Hybridization ◽

Inclusion Bodies ◽

Animal Species ◽

Viral Etiology ◽

Molecular Approaches ◽

Dna And Rna ◽

Promising Tool ◽

First Choice ◽

Inverted Papillomas

Numerous canine papillomaviruses (CPVs) have been identified (CPV1–23). CPV1, 2, and 6 have been associated with inverted papillomas (IPs). We retrieved 19 IPs from 3 histopathology archives, and evaluated and scored koilocytes, inclusion bodies, giant keratohyalin granules, cytoplasmic pallor, ballooning degeneration, and parakeratosis. IHC targeting major capsid proteins of PV was performed, and CPV genotyping was achieved by PCR testing. Tissue localization of CPV DNA and RNA was studied by chromogenic and RNAscope in situ hybridization (DNA-CISH, RNA-ISH, respectively). IPs were localized to the limbs (50%), trunk (30%), and head (20%), mainly as single nodules (16 of 19). In 15 of 19 cases, immunopositivity was detected within the nuclei in corneal and subcorneal epidermal layers. PCR revealed CPV1 in 11 IPs and CPV2 DNA in 3 IPs. Overall, 14 of 17 cases were positive by both DNA-CISH and RNA-ISH, in accord with PCR results. A histologic score >5 was always obtained in cases in which the viral etiology was demonstrated by IHC, DNA-CISH, and RNA-ISH. IHC and molecular approaches were useful to ascertain the viral etiology of IPs. Although IHC is the first choice for diagnostic purposes, ISH testing allows identification of PV type and the infection phase. RNA-ISH seems a promising tool to deepen our understanding of the pathogenesis of different PV types in animal species.

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Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1

Viruses ◽

10.3390/v14010146 ◽

2022 ◽

Vol 14 (1) ◽

pp. 146

Author(s):

Angelo Pavesi ◽

Fabio Romerio

Keyword(s):

De Novo ◽

Point Mutations ◽

Selective Advantage ◽

Genomic Region ◽

Fine Tuning ◽

Sequence Evolution ◽

Viral Genomes ◽

Stop Codons ◽

Hiv 1

Gene overprinting occurs when point mutations within a genomic region with an existing coding sequence create a new one in another reading frame. This process is quite frequent in viral genomes either to maximize the amount of information that they encode or in response to strong selective pressure. The most frequent scenario involves two different reading frames in the same DNA strand (sense overlap). Much less frequent are cases of overlapping genes that are encoded on opposite DNA strands (antisense overlap). One such example is the antisense ORF, asp in the minus strand of the HIV-1 genome overlapping the env gene. The asp gene is highly conserved in pandemic HIV-1 strains of group M, and it is absent in non-pandemic HIV-1 groups, HIV-2, and lentiviruses infecting non-human primates, suggesting that the ~190-amino acid protein that is expressed from this gene (ASP) may play a role in virus spread. While the function of ASP in the virus life cycle remains to be elucidated, mounting evidence from several research groups indicates that ASP is expressed in vivo. There are two alternative hypotheses that could be envisioned to explain the origin of the asp ORF. On one hand, asp may have originally been present in the ancestor of contemporary lentiviruses, and subsequently lost in all descendants except for most HIV-1 strains of group M due to selective advantage. Alternatively, the asp ORF may have originated very recently with the emergence of group M HIV-1 strains from SIVcpz. Here, we used a combination of computational and statistical approaches to study the genomic region of env in primate lentiviruses to shed light on the origin, structure, and sequence evolution of the asp ORF. The results emerging from our studies support the hypothesis of a recent de novo addition of the antisense ORF to the HIV-1 genome through a process that entailed progressive removal of existing internal stop codons from SIV strains to HIV-1 strains of group M, and fine tuning of the codon sequence in env that reduced the chances of new stop codons occurring in asp. Altogether, the study supports the notion that the HIV-1 asp gene encodes an accessory protein, providing a selective advantage to the virus.

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Recent responses to climate change reveal the drivers of species extinction and survival

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1913007117 ◽

2020 ◽

Vol 117 (8) ◽

pp. 4211-4217 ◽

Cited By ~ 21

Author(s):

Cristian Román-Palacios ◽

John J. Wiens

Keyword(s):

Climate Change ◽

Animal Species ◽

Biodiversity Loss ◽

Climatic Changes ◽

Important Work ◽

Species Extinction ◽

Major Threat ◽

Niche Shifts ◽

Local Extinctions ◽

Over Time

Climate change may be a major threat to biodiversity in the next 100 years. Although there has been important work on mechanisms of decline in some species, it generally remains unclear which changes in climate actually cause extinctions, and how many species will likely be lost. Here, we identify the specific changes in climate that are associated with the widespread local extinctions that have already occurred. We then use this information to predict the extent of future biodiversity loss and to identify which processes may forestall extinction. We used data from surveys of 538 plant and animal species over time, 44% of which have already had local extinctions at one or more sites. We found that locations with local extinctions had larger and faster changes in hottest yearly temperatures than those without. Surprisingly, sites with local extinctions had significantly smaller changes in mean annual temperatures, despite the widespread use of mean annual temperatures as proxies for overall climate change. Based on their past rates of dispersal, we estimate that 57–70% of these 538 species will not disperse quickly enough to avoid extinction. However, we show that niche shifts appear to be far more important for avoiding extinction than dispersal, although most studies focus only on dispersal. Specifically, considering both dispersal and niche shifts, we project that only 16–30% of these 538 species may go extinct by 2070. Overall, our results help identify the specific climatic changes that cause extinction and the processes that may help species to survive.

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Virome of Bat Guano from Nine Northern California Roosts

Journal of Virology ◽

10.1128/jvi.01713-20 ◽

2020 ◽

Author(s):

Yanpeng Li ◽

Eda Altan ◽

Gabriel Reyes ◽

Brian Halstead ◽

Xutao Deng ◽

...

Keyword(s):

Animal Species ◽

Amino Acid Identity ◽

Wide Distribution ◽

Mouse Kidney ◽

Northern California ◽

Dna Viruses ◽

Viral Genomes ◽

In The Wild ◽

Close Relatives ◽

Viral Sequences

Bats are hosts to a large variety of viruses, including many capable of cross species transmissions to other mammals or humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Near or complete genomes of a novel parvovirus, astrovirus, nodavirus, CRESS-DNA viruses and densoviruses and more partial genomes of a novel alphacoronavirus, and bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found likely reflecting their wide distribution among different bats. Unexpectedly a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR possibly originating from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent indicating that numerous viruses still remain to be characterized even from such a heavily investigated order as Chiroptera. IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected whose presence are likely the result of contamination from defecation and urination atop guano and reflect the close interaction of these mammals in the wild.

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