Analysis of the RNA virome of basal hexapods

Insight Into ◽

The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered 40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades.

Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the Northeast Pacific Ocean, and implications for conservation

10.5194/bg-2019-360 ◽

2019 ◽

Cited By ~ 1

Author(s):

Magdalini Christodoulou ◽

Timothy O'Hara ◽

Andrew Hugall ◽

Sahar Khodami ◽

Clara F. Rodrigues ◽

...

Keyword(s):

Pacific Ocean ◽

Deep Sea ◽

Common Species ◽

Mineral Deposits ◽

Species Delineation ◽

Polymetallic Nodule ◽

Ne Pacific ◽

Functional Analyses ◽

Insight Into ◽

Abstract. The largest and commercially appealing mineral deposits can be found in the abyssal seafloor of the Clarion-Clipperton Zone (CCZ), a polymetallic nodule province, in the NE Pacific Ocean, where experimental mining is due to take place. In anticipation of deep-sea mining impacts, it has become essential to rapidly and accurately assess biodiversity. For this reason, ophiuroid material collected during seven scientific cruises from five exploration license areas within CCZ, one area protected from mining (APEI3, Area of Particular Environmental Interest) in the periphery of CCZ and the DIS-turbance and re-COLonisation (DISCOL) Experimental Area (DEA), in the SE Pacific Ocean, was examined. Specimens were genetically analysed using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI). Maximum Likelihood and Neighbour Joining trees were constructed, while four tree-based and distance-based methods of species delineation (ABGD, BINs, GMYC, mPTP) were employed to propose Secondary Species Hypotheses (SSHs) within the ophiuroids collected. The species delimitations analyses concordant results revealed the presence of 43 deep-sea brittle stars SSHs, revealing an unexpectedly high diversity and showing that the most conspicuous invertebrates in abyssal plains have been so far considerably under-estimated. The number of SSHs found in each area varied from 5 (IFREMER area) to 24 (BGR area), while 13 SSHs were represented by singletons. None of the SSHs was found to be present in all 7 areas, while the majority of species (44.2 %) had a single-area presence (19 SSHs). The most common species were Ophioleucidae sp. (Species 29), Amphioplus daleus (Species 2) and Ophiosphalma glabrum (Species 3), present in all areas except APEI3. The biodiversity patterns could be mainly attributed to POC fluxes that could explain the highest species numbers found in BGR (German contractor area) and UKSRL (UK contractor area) areas. The five exploration contract areas belong to a mesotrophic province, while in contrary the APEI3 is located in an oligotrophic province which could explain the lowest diversity as well as very low similarity with the other six study areas. Based on these results the representativeness and the appropriateness of APEI3 to meet its purpose of preserving the biodiversity of the CCZ fauna are questioned. Finally, this study provides the foundation for biogeographic and functional analyses that will provide insight into the drivers of species diversity and its role in ecosystem function.

Patent Insight into the Development of Therapeutic Strategies against Coronaviruses

The Open COVID Journal ◽

10.2174/2666958702101010093 ◽

2021 ◽

Vol 1 (1) ◽

pp. 93-100

Author(s):

Hai-Long Zhang ◽

Ai-Feng Zhou ◽

Yiqian Li

Keyword(s):

Therapeutic Strategy ◽

Vaccine Development ◽

Rna Viruses ◽

Therapeutic Strategies ◽

Peptide Drugs ◽

Leading Role ◽

Global Pandemic ◽

Effective Therapeutic Strategy ◽

Insight Into ◽

Development And Evolution

Coronaviruses are a group of RNA viruses, which cause diseases in humans. The emergence of COVID-19, has caused a global pandemic. It is focused on developing an effective therapeutic strategy against COVID-19. To better understand the development and evolution of therapeutic strategies against coronaviruses, we conducted US granted patents analysis. The results showed vaccines played a leading role in therapies against coronaviruses. Both attenuated vaccines and recombinant genetic vaccines were very important approaches in vaccine development against coronaviruses. It is not a rapid approach to develop peptide drugs against COVID-19 or future novel coronaviruses. The study was the first one to show the development and evolution in therapeutic strategies against coronaviruses based on patent insight. The present study provides a new insight into the development of therapeutic strategies against coronaviruses.

Neuralized E3 Ubiquitin Protein Ligase 3 Is an Inducible Antiviral Effector That Inhibits Hepatitis C Virus Assembly by Targeting Viral E1 Glycoprotein

Journal of Virology ◽

10.1128/jvi.01123-18 ◽

2018 ◽

Vol 92 (21) ◽

Cited By ~ 3

Author(s):

Yanan Zhao ◽

Xuezhi Cao ◽

Mingzhe Guo ◽

Xuesong Wang ◽

Tao Yu ◽

...

Keyword(s):

Innate Immunity ◽

Hepatitis C ◽

Envelope Glycoprotein ◽

Biological Function ◽

Rna Viruses ◽

Innate Immune ◽

Hcv Infection ◽

Ubiquitin Protein Ligase ◽

Host Innate Immunity ◽

Insight Into

ABSTRACTHepatitis C virus (HCV) infection is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV can be sensed by host innate immunity to induce expression of interferons (IFNs) and a number of antiviral effectors. In this study, we found HCV infection induced the expression of neuralized E3 ubiquitin protein ligase 3 (NEURL3), a putative E3 ligase, in a manner that requires the involvement of innate immune sensing but is independent of the IFN action. Furthermore, we showed that NEURL3 inhibited HCV infection while it had little effect on other RNA viruses, including Zika virus (ZIKV), dengue virus (DENV), and vesicular stomatitis virus (VSV). Mechanistic studies demonstrated that NEURL3 inhibited HCV assembly by directly binding HCV envelope glycoprotein E1 to interfere with the E1/E2 heterodimerization, an important prerequisite for virion morphogenesis. Finally, we showed that knockout of NEURL3 significantly enhanced HCV infection. In summary, we identified NEURL3 as a novel inducible antiviral host factor that suppresses HCV assembly. Our results not only shed new insight into how host innate immunity acts against HCV but also revealed a new important biological function for NEURL3.IMPORTANCEThe exact biological function of NEURL3, a putative E3 ligase, remains largely unknown. In this study, we found that NEURL3 could be upregulated upon HCV infection in a manner dependent on pattern recognition receptor-mediated innate immune response. NEURL3 inhibits HCV assembly by directly binding viral E1 envelope glycoprotein to disrupt its interaction with E2, an action that requires its Neuralized homology repeat (NHR) domain but not the RING domain. Furthermore, we found that NEURL3 has a pangenotypic anti-HCV activity and interacts with E1 of genotypes 2a, 1b, 3a, and 6a but does not inhibit other closely related RNA viruses, such as ZIKV, DENV, and VSV. To our knowledge, our study is the first report to demonstrate that NEURL3 functions as an antiviral host factor. Our results not only shed new insight into how host innate immunity acts against HCV, but also revealed a new important biological function for NEURL3.

Control of RNA viruses in mosquito cells through the acquisition of vDNA and endogenous viral elements

eLife ◽

10.7554/elife.41244 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 26

Author(s):

Michel Tassetto ◽

Mark Kunitomi ◽

Zachary J Whitfield ◽

Patrick T Dolan ◽

Irma Sánchez-Vargas ◽

...

Keyword(s):

High Resolution ◽

Adaptive Immunity ◽

Virus Replication ◽

Genomic Sequence ◽

Rna Viruses ◽

Viral Persistence ◽

Mosquito Cells ◽

Infected Cells ◽

Antiviral Mechanism

Aedes aegypti transmit pathogenic arboviruses while the mosquito itself tolerates the infection. We examine a piRNA-based immunity that relies on the acquisition of viral derived cDNA (vDNA) and how this pathway discriminates between self and non-self. The piRNAs derived from these vDNAs are essential for virus control and Piwi4 has a central role in the pathway. Piwi4 binds preferentially to virus-derived piRNAs but not to transposon-targeting piRNAs. Analysis of episomal vDNA from infected cells reveals that vDNA molecules are acquired through a discriminatory process of reverse-transcription and recombination directed by endogenous retrotransposons. Using a high-resolution Ae. aegypti genomic sequence, we found that vDNAs integrated in the host genome as endogenous viral elements (EVEs), produce antisense piRNAs that are preferentially loaded onto Piwi4. Importantly, EVE-derived piRNAs are specifically loaded onto Piwi4 to inhibit virus replication. Thus, Ae. aegypti employs a sophisticated antiviral mechanism that promotes viral persistence and generates long-lasting adaptive immunity.

High Diversity of RNA Viruses in Rodents, Ethiopia

Emerging Infectious Diseases ◽

10.3201/eid1812.120596 ◽

2012 ◽

Vol 18 (12) ◽

pp. 2047-2050 ◽

Cited By ~ 28

Author(s):

Yonas Meheretu ◽

Dagmar Čížková ◽

Jana Těšíková ◽

Kiros Welegerima ◽

Zewdneh Tomas ◽

...

Keyword(s):

Rna Viruses ◽

Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan

Viruses ◽

10.3390/v11040356 ◽

2019 ◽

Vol 11 (4) ◽

pp. 356 ◽

Cited By ~ 2

Author(s):

Mendenhall ◽

Kerimbayev ◽

Strochkov ◽

Sultankulova ◽

Kopeyev ◽

...

Keyword(s):

South Africa ◽

Rna Viruses ◽

Phylogenetic Reconstruction ◽

Gastrointestinal Illness ◽

The World ◽

Human Coronaviruses ◽

Collaborative Efforts ◽

Bat Coronavirus ◽

Coronaviruses are positive-stranded RNA viruses that infect a variety of hosts, resulting in a range of symptoms from gastrointestinal illness to respiratory distress. Bats are reservoirs for a high diversity of coronaviruses, and focused surveillance detected several strains genetically similar to MERS-coronavirus, SARS-coronavirus, and the human coronaviruses 229E and NL63. The bat fauna of central Asia, which link China to eastern Europe, are relatively less studied than other regions of the world. Kazakhstan is the world’s ninth largest country; however, little is understood about the prevalence and diversity of bat-borne viruses. In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. Our phylogenetic reconstruction indicates these are novel bat coronaviruses that belong to the genus Alphacoronavirus. In addition, two distinct lineages of Kazakhstan bat coronaviruses were detected. Both lineages are closely related to bat coronaviruses from China, France, Spain, and South Africa, suggesting that co-circulation of coronaviruses is common in multiple bat species with overlapping geographical distributions. Our study highlights the need for collaborative efforts in understudied countries to increase integrated surveillance capabilities toward better monitoring and detection of infectious diseases.

Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons

10.1101/825315 ◽

2019 ◽

Cited By ~ 1

Author(s):

Sylvia E. J. Fischer ◽

Gary Ruvkun

Keyword(s):

Transposable Elements ◽

Viral Infection ◽

Endogenous Retroviruses ◽

Ltr Retrotransposons ◽

C Elegans ◽

Viral Genes ◽

Common Response ◽

Different Types ◽

Insight Into

ABSTRACTEndogenous retroviruses and LTR retrotransposons are mobile genetic elements that are closely related to retroviruses. Desilenced endogenous retroviruses are associated with human autoimmune disorders and neurodegenerative diseases. C. elegans and related Caenorhabdites contain LTR retrotransposons and, as described here, numerous integrated viral genes including viral envelope genes that are part of LTR retrotransposons. We found that both LTR retrotransposons and endogenous viral elements are silenced by ADARs (adenosine deaminases acting on double-stranded RNA (dsRNA)) together with the endogenous RNAi factor ERI-6/7, a homolog of Mov10 helicase, a retrotransposon and retrovirus restriction factor in human. siRNAs corresponding to integrated viral genes and LTR retrotransposons, but not to DNA transposons, are dependent on the ADARs and ERI-6/7; on the contrary, siRNAs corresponding to palindromic repeats are increased in adar-eri mutants because of an antiviral RNAi response to dsRNA. Silencing of LTR retrotransposons is dependent on downstream RNAi factors and P granule components but is independent of the viral sensor DRH-1/RIG-I and the nuclear Argonaute NRDE-3. The activation of retrotransposons in the ADAR- and ERI-6/7/MOV10-defective mutant is associated with the induction of the Unfolded Protein Response (UPR), a common response to viral infection. The overlap between genes induced upon viral infection and infection with intracellular pathogens, and genes co-expressed with retrotransposons, suggests that there is a common response to different types of foreign elements that includes a response to proteotoxicity presumably caused by the burden of replicating pathogens and expressed retrotransposons.SIGNIFICANCESilencing of transposable elements and viruses is critical for the maintenance of genome integrity, cellular homeostasis and organismal health. Here we describe multiple factors that control different types of transposable elements, providing insight into how they are regulated. We also identify stress response pathways that are triggered upon mis-regulation of these transposable elements. The conservation of these factors and pathways in human suggests that our studies in C. elegans can provide general insight into the regulation of and response to transposable elements and viruses.

Author response: Control of RNA viruses in mosquito cells through the acquisition of vDNA and endogenous viral elements

10.7554/elife.41244.026 ◽

2019 ◽

Cited By ~ 3

Author(s):

Michel Tassetto ◽

Mark Kunitomi ◽

Zachary J Whitfield ◽

Patrick T Dolan ◽

Irma Sánchez-Vargas ◽

...

Keyword(s):

Rna Viruses ◽

Author Response ◽

Response Control ◽

Mosquito Cells ◽

Endogenous Viral Elements

Endogenous viral elements are widespread in arthropod genomes and commonly give rise to piRNAs

10.1101/396382 ◽

2018 ◽

Cited By ~ 2

Author(s):

Anneliek M. ter Horst ◽

Jared C. Nigg ◽

Bryce W. Falk

Keyword(s):

Viral Infection ◽

Small Rna ◽

Rna Viruses ◽

Mosquito Species ◽

Small Rna Sequencing ◽

Arthropod Species ◽

Ping Pong ◽

And Function ◽

Genome Assemblies

ABSTRACTArthropod genomes contain sequences derived from integrations of DNA and non-retroviral RNA viruses. These sequences, known as endogenous viral elements (EVEs), have been acquired over the course of evolution and have been proposed to serve as a record of past viral infection. Recent evidence indicates that EVEs can function as templates for the biogenesis of PIWI-interacting RNAs (piRNAs) in some mosquito species and cell lines, raising the possibility that EVEs may function as a source of immunological memory in these organisms. However, whether EVEs are capable of acting as templates for piRNA production in other arthropod species is unknown. Here we used publically available genome assemblies and small RNA sequencing datasets to characterize the repertoire and function of EVEs across 48 arthropod genomes. We found that EVEs are widespread in arthropod genomes and primarily correspond to unclassified ssRNA viruses and viruses belonging to the Rhabdoviridae and Parvoviridae families. Additionally, EVEs were enriched in piRNA clusters in a majority of species and we found that production of primary piRNAs from EVEs is common, particularly for EVEs located within piRNA clusters. While we found evidence suggesting that piRNAs mapping to a number of EVEs are produced via the ping-pong cycle, potentially pointing towards a role for EVE-derived piRNAs during viral infection, limited nucleotide identity between currently described viruses and EVEs identified here likely limits the extent to which this process plays a role during infection with known viruses.

Comparative Domain-Fold Analysis of the SARS-CoV-2 ORF1ab Polyprotein: Insight into Co-Evolution, Conservation of Folding Patterns, Potential Therapeutic Strategies, and the Possibility of Reemergence

10.20944/preprints202004.0286.v1 ◽

2020 ◽

Author(s):

Srijeeb Karmakar ◽

Sachin Kumar ◽

Vimal Katiyar

Keyword(s):

Natural Selection ◽

Amino Acid ◽

Amino Acid Sequence ◽

Rna Viruses ◽

Small Variation ◽

Therapeutic Strategies ◽

Domain Specific ◽

In Silico Study ◽

Protein Functions ◽

Insight Into

The high transmissibility and replication of SARS-CoV-2 have been attributed to enhanced protein functions which are dependent on protein folding. Our in silico study endeavored to scrutinize SARS-CoV-2 ORF1ab by analyzing the conserved folding patterns of its transcribed proteins. Accordingly, the findings indicated that SARS-CoV-2 ORF1ab shares domain-specific fold-fingerprints with a spectrum of unrelated organisms. Closer observation revealed slight changes in folding patterns engendered with small variation in the intrinsic amino acid sequence. By correlating with the evolvability-potential of RNA-viruses and COVID-19 pandemic, we hypothesize that SARS-CoV-2 could undergo fast recombination with the host, SARS-CoV-2 minor variants and other viral species resulting in a reservoir of SARS-CoV-2 quasispecies. It is highly possible that natural selection will cause a future emergence of evolved SARS-CoV-2-descendants. Nonetheless, we hope that this insightful study will assist in elucidating SARS-CoV-2 protein functionalities, development of vaccines, and the possibility and nature of future emergence.