Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark

Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera—i.e., Pedacovirus, Nyctacovirus, and Myotacovirus—that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates—including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus—present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.

Download Full-text

Therapeutic Exploitation of Viral Interference

Infectious Disorders - Drug Targets ◽

10.2174/1871526519666190405140858 ◽

2020 ◽

Vol 20 (4) ◽

pp. 423-432 ◽

Cited By ~ 1

Author(s):

Imre Kovesdi ◽

Tibor Bakacs

Keyword(s):

Broad Spectrum ◽

Viral Infections ◽

Viral Vector ◽

Antiviral Treatment ◽

Type I ◽

Virus Infections ◽

Emerging Viruses ◽

Viral Interference ◽

Pathogenic Virus ◽

Hepatitis C Rna

: Viral interference, originally, referred to a state of temporary immunity, is a state whereby infection with a virus limits replication or production of a second infecting virus. However, replication of a second virus could also be dominant over the first virus. In fact, dominance can alternate between the two viruses. Expression of type I interferon genes is many times upregulated in infected epithelial cells. Since the interferon system can control most, if not all, virus infections in the absence of adaptive immunity, it was proposed that viral induction of a nonspecific localized temporary state of immunity may provide a strategy to control viral infections. Clinical observations also support such a theory, which gave credence to the development of superinfection therapy (SIT). SIT is an innovative therapeutic approach where a non-pathogenic virus is used to infect patients harboring a pathogenic virus. : For the functional cure of persistent viral infections and for the development of broad- spectrum antivirals against emerging viruses a paradigm shift was recently proposed. Instead of the virus, the therapy should be directed at the host. Such a host-directed-therapy (HDT) strategy could be the activation of endogenous innate immune response via toll-like receptors (TLRs). Superinfection therapy is such a host-directed-therapy, which has been validated in patients infected with two completely different viruses, the hepatitis B (DNA), and hepatitis C (RNA) viruses. SIT exerts post-infection interference via the constant presence of an attenuated non-pathogenic avian double- stranded (ds) RNA viral vector which boosts the endogenous innate (IFN) response. SIT could, therefore, be developed into a biological platform for a new “one drug, multiple bugs” broad-spectrum antiviral treatment approach.

Download Full-text

Genetic and Antigenic Characterization of Avian Avulavirus Type 6 (AAvV-6) Circulating in Canadian Wild Birds (2005–2017)

Viruses ◽

10.3390/v13040543 ◽

2021 ◽

Vol 13 (4) ◽

pp. 543

Author(s):

Tamiko Hisanaga ◽

Catherine Soos ◽

Nicola Lewis ◽

Oliver Lung ◽

Matthew Suderman ◽

...

Keyword(s):

Clinical Symptoms ◽

Fusion Gene ◽

Full Genome ◽

Genome Sequences ◽

Viral Shedding ◽

Genetic Groups ◽

Antigenic Characterization ◽

Specific Pathogen ◽

First Time

We describe for the first time the genetic and antigenic characterization of 18 avian avulavirus type-6 viruses (AAvV-6) that were isolated from wild waterfowl in the Americas over the span of 12 years. Only one of the AAvV-6 viruses isolated failed to hemagglutinate chicken red blood cells. We were able to obtain full genome sequences of 16 and 2 fusion gene sequences from the remaining 2 isolates. This is more than double the number of full genome sequences available at the NCBI database. These AAvV-6 viruses phylogenetically grouped into the 2 existing AAvV-6 genotype subgroups indicating the existence of an intercontinental epidemiological link with other AAvV-6 viruses isolated from migratory waterfowl from different Eurasian countries. Antigenic maps made using HI assay data for these isolates showed that the two genetic groups were also antigenically distinct. An isolate representing each genotype was inoculated in specific pathogen free (SPF) chickens, however, no clinical symptoms were observed. A duplex fusion gene based real-time assay for the detection and genotyping of AAvV-6 to genotype 1 and 2 was developed. Using the developed assay, the viral shedding pattern in the infected chickens was examined. The chickens infected with both genotypes were able to shed the virus orally for about a week, however, no significant cloacal shedding was detected in chickens of both groups. Chickens in both groups developed detectable levels of anti-hemagglutinin antibodies 7 days after infection.

Download Full-text

Full-Genome Sequences of Influenza A(H1N1)pdm09 Viruses Isolated from Finnish Patients from 2009 to 2013

Genome Announcements ◽

10.1128/genomea.01004-13 ◽

2014 ◽

Vol 2 (1) ◽

Cited By ~ 12

Author(s):

T. Lakspere ◽

J. Tynell ◽

M. Kaloinen ◽

M. Vanlede ◽

A. Parsons ◽

...

Keyword(s):

Influenza A ◽

Full Genome ◽

Genome Sequences ◽

Influenza A H1n1

Download Full-text

Whole-genome sequences of Odocoileus hemionus deer adenovirus isolates from deer, moose and elk are highly conserved and support a new species in the genus Atadenovirus

Journal of General Virology ◽

10.1099/jgv.0.000880 ◽

2017 ◽

Vol 98 (9) ◽

pp. 2320-2328 ◽

Cited By ~ 7

Author(s):

Myrna M. Miller ◽

Todd E. Cornish ◽

Terry E. Creekmore ◽

Karen Fox ◽

Will Laegreid ◽

...

Keyword(s):

New Species ◽

Odocoileus Hemionus ◽

Whole Genome ◽

Genome Sequences ◽

A New Species

Download Full-text

Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

Genome Announcements ◽

10.1128/genomea.00326-16 ◽

2016 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

Steven Van Borm ◽

Toon Rosseel ◽

Andy Haegeman ◽

Mpolokang Elliot Fana ◽

Latoa Seoke ◽

...

Keyword(s):

Genome Sequencing ◽

Complete Genome ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

Clinical Samples ◽

Full Genome ◽

Full Genome Sequencing ◽

Genome Sequences ◽

Foot And Mouth

The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.

Download Full-text

Introduction

Viruses: A Very Short Introduction ◽

10.1093/actrade/9780198811718.003.0001 ◽

2018 ◽

pp. 1-1

Author(s):

Dorothy H. Crawford

Keyword(s):

Immune System ◽

Infected Individual ◽

The Body ◽

Virus Infections ◽

Emerging Viruses ◽

The Future

The Introduction outlines the structure of this VSI. The first two chapters introduce viruses, their structure and diversity, how they live, and their effects. Then the constant battle between viruses and the immune system of the infected individual is outlined, followed by chapters about infection by emerging viruses, epidemic viruses, pandemic viruses, and those that persist in the body for a lifetime. Later chapters look at how our knowledge of viruses has advanced through the ages and how the recent molecular revolution has enhanced our ability to isolate new viruses and to diagnose and treat virus infections. The final chapter speculates about how humans and viruses might interact in the future.

Download Full-text

Screening for Anti-Influenza Actives of Prefractionated Traditional Chinese Medicines

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/4979850 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7

Author(s):

Qianli Kang ◽

Yanyan Wang ◽

Qinghua Cui ◽

Lili Gong ◽

Yong Yang ◽

...

Keyword(s):

Influenza Virus ◽

Ebola Virus ◽

Antiviral Treatment ◽

Traditional Chinese Medicines ◽

Virus Infections ◽

Clinical Practices ◽

Emerging Viruses ◽

Gaussia Luciferase ◽

Chinese Medicines ◽

Antiviral Activities

Traditional Chinese medicines (TCMs) have proven to possess advantages in counteracting virus infections according to clinical practices. It’s therefore of great value to discover novel antivirals from TCMs. In this paper, One hundred medicinal plants which have been included in TCM prescriptions for antiviral treatment were selected and prefractionated into 5 fractions each by sequentially using cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water. 500 TCM-simplified extracts were then subjected to a phenotypic screening using a recombinant IAV expressing Gaussia luciferase. Ten TCM fractions were identified to possess antiviral activities against influenza virus. The IC50’s of the hit fractions range from 1.08 to 6.45 μg/mL, while the SIs, from 7.52 to 98.40. Furthermore, all the ten hit fractions inhibited the propagation of progeny influenza virus significantly at 20 μg/mL. The hit TCM fractions deserve further isolation for responsible constituents leading towards anti-influenza drugs. Moreover, a library consisting of 500 simplified TCM extracts was established, facilitating antiviral screening in quick response to emerging and re-emerging viruses such as Ebola virus and current SARS-CoV-2 pandemic.

Download Full-text

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group

Microbiology Resource Announcements ◽

10.1128/mra.00505-20 ◽

2020 ◽

Vol 9 (28) ◽

Author(s):

Giselle S. Cavalcanti ◽

Jessica Wasserscheid ◽

Ken Dewar ◽

Nicholas J. Shikuma

Keyword(s):

New Species ◽

Complete Genome ◽

Genome Sequences ◽

Marine Biofilm ◽

Roseobacter Group ◽

Genome Assemblies ◽

One New Species

ABSTRACT Here, we report the complete-genome assemblies of biofilm isolates 201A and 204H. They possess six and seven plasmids, respectively, with a size ranging from 44 kb to 159 kb. Genomic comparisons place the two strains into one new species belonging to the genus Leisingera as novel representatives of the Roseobacter group.

Download Full-text

Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach

Genes ◽

10.3390/genes11010028 ◽

2019 ◽

Vol 11 (1) ◽

pp. 28

Author(s):

Nabil Abid ◽

Giovanni Chillemi ◽

Marco Salemi

Keyword(s):

Statistical Approach ◽

Viral Proteins ◽

Viral Fitness ◽

Interaction Networks ◽

Full Genome ◽

Genome Sequences ◽

Potential Effectiveness ◽

Genome Wide ◽

Coevolution Analysis ◽

Infants And Young Children

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.

Download Full-text