Novel RNA viruses associated with avian haemosporidian parasites

Avian haemosporidian parasites can cause malaria-like symptoms in their hosts and have been implicated in the demise of some bird species. The newly described Matryoshka RNA viruses (MaRNAV1 and MaRNAV2) infect parasites that in turn infect their vertebrate hosts. MaRNAV2 was the first RNA virus discovered associated with parasites of the genus Leucocytozoon. By analyzing metatranscriptomes from the NCBI SRA database with local sequence alignment tools, we detected two novel RNA viruses; we describe them as MaRNAV3 associated with Leucocytozoon and MaRNAV4 associated with Parahaemoproteus. These had ~40-60% amino acid identity to the RNA-dependent RNA-polymerase (RdRp) of MaRNAV1 and 2, respectively. These findings lead us to hypothesize that MaRNAV_like viruses are widespread and tightly associated with the order Haemosporida since they have been described in human Plasmodium vivax, and now two genera of avian haemosporidians.

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Diversity and host assemblage of avian haemosporidians in different terrestrial ecoregions of Peru

Current Zoology ◽

10.1093/cz/zoab030 ◽

2021 ◽

Author(s):

Luz Garcia-Longoria ◽

Jaime Muriel ◽

Sergio Magallanes ◽

Zaira Hellen Villa-Galarce ◽

Leonila Ricopa ◽

...

Keyword(s):

Amazon Basin ◽

Evolutionary Dynamics ◽

Bird Species ◽

Host Community ◽

Bird Diversity ◽

New Host ◽

Parasite Richness ◽

Haemosporidian Parasites ◽

Avian Haemosporidians ◽

Host Parasite

Abstract Characterizing the diversity and structure of host-parasite communities is crucial to understanding their eco-evolutionary dynamics. Malaria and related haemosporidian parasites are responsible for fitness loss and mortality in bird species worldwide. However, despite exhibiting the greatest ornithological biodiversity, avian haemosporidians from Neotropical regions are quite unexplored. Here, we analyse the genetic diversity of bird haemosporidian parasites (Plasmodium and Haemoproteus) in 1,336 individuals belonging to 206 bird species to explore for differences in diversity of parasite lineages and bird species across five well-differentiated Peruvian ecoregions. We detected 70 different haemosporidian lineages infecting 74 bird species. We showed that 25 out of the 70 haplotypes had not been previously recorded. Moreover, we also identified 81 new host – parasite interactions representing new host records for these haemosporidian parasites. Our outcomes revealed that the effective diversity (as well as the richness, abundance, and Shannon-Weaver index) for both birds and parasite lineages was higher in Amazon basin ecoregions. Furthermore, we also showed that ecoregions with greater diversity of bird species also had high parasite richness, hence suggesting that host community is crucial in explaining parasite richness. Generalist parasites were found in ecoregions with lower bird diversity, implying that the abundance and richness of hosts may shape the exploitation strategy followed by haemosporidian parasites. These outcomes reveal that Neotropical region is a major reservoir of unidentified haemosporidian lineages. Further studies analysing host distribution and specificity of these parasites in the tropics will provide important knowledge about phylogenetic relationships, phylogeography, and patterns of evolution and distribution of haemosporidian parasites.

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Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses

mBio ◽

10.1128/mbio.01871-18 ◽

2018 ◽

Vol 9 (5) ◽

Cited By ~ 11

Author(s):

Natalie D. Collins ◽

Andrew S. Beck ◽

Steven G. Widen ◽

Thomas G. Wood ◽

Stephen Higgs ◽

...

Keyword(s):

Genetic Diversity ◽

Yellow Fever ◽

Yellow Fever Virus ◽

Rna Viruses ◽

Rna Virus ◽

Infectious Clone ◽

Vaccine Virus ◽

Wild Type ◽

Rna Dependent Rna Polymerase ◽

Replication Complex

ABSTRACT One paradigm to explain the complexity of viral RNA populations is that the low fidelity of the RNA-dependent RNA polymerase (RdRp) drives high mutation rates and consequently genetic diversity. Like most RNA viruses, wild-type yellow fever virus (YFV) replication is error-prone due to the lack of proofreading by the virus-encoded RdRp. However, there is evidence that replication of the live attenuated YF vaccine virus 17D, derived from wild-type strain Asibi, is less error-prone than wild-type RNA viruses. Recent studies comparing the genetic diversity of wild-type Asibi and 17D vaccine virus found that wild-type Asibi has the typical heterogeneous population of an RNA virus, while there is limited intra- and interpopulation variability of 17D vaccine virus. Utilizing chimeric and mutant infectious clone-derived viruses, we show that high and low genetic diversity profiles of wild-type Asibi virus and vaccine virus 17D, respectively, are multigenic. Introduction of either structural (pre-membrane and envelope) genes or NS2B or NS4B substitutions into the Asibi and 17D backbone resulted in altered variant population, nucleotide diversity, and mutation frequency compared to the parental viruses. Additionally, changes in genetic diversity of the chimeric and mutant viruses correlated with the phenotype of multiplication kinetics in human alveolar A549 cells. Overall, the paradigm that only the error-prone RdRp controls genetic diversity needs to be expanded to address the role of other genes in genetic diversity, and we hypothesize that it is the replication complex as a whole and not the RdRp alone that controls genetic diversity. IMPORTANCE With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity can contribute to both attenuation and virulence and the paradigm is that this is controlled by the error-prone RNA-dependent RNA polymerase (RdRp). Since wild-type yellow fever virus (YFV) strain Asibi has genetic diversity typical of a wild-type RNA virus, while 17D virus vaccine has limited diversity, it provides a unique opportunity to investigate RNA population theory in the context of a well-characterized live attenuated vaccine. Utilizing infectious clone-derived viruses, we show that genetic diversity of RNA viruses is complex and that multiple genes, including structural genes and NS2B and NS4B genes also contribute to genetic diversity. We suggest that the replication complex as a whole, rather than only RdRp, drives genetic diversity, at least for YFV.

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Late Male-Killing Viruses in Homona magnanima Identified as Osugoroshi Viruses, Novel Members of Partitiviridae

Frontiers in Microbiology ◽

10.3389/fmicb.2020.620623 ◽

2021 ◽

Vol 11 ◽

Author(s):

Ryosuke Fujita ◽

Maki N. Inoue ◽

Takumi Takamatsu ◽

Hiroshi Arai ◽

Mayu Nishino ◽

...

Keyword(s):

Mathematical Modeling ◽

Rna Polymerase ◽

Rna Viruses ◽

Rna Virus ◽

Horizontal Transmission ◽

Rna Dependent Rna Polymerase ◽

Double Stranded Rna ◽

First Report ◽

Male Killing ◽

Male Specific

Late male-killing, a male-specific death after hatching, is a unique phenotype found in Homona magnanima, oriental tea tortrix. The male-killing agent was suspected to be an RNA virus, but details were unknown. We herein successfully isolated and identified the putative male-killing virus as Osugoroshi viruses (OGVs). The three RNA-dependent RNA polymerase genes detected were phylogenetically related to Partitiviridae, a group of segmented double-stranded RNA viruses. Purified dsRNA from a late male-killing strain of H. magnanima revealed 24 segments, in addition to the RdRps, with consensus terminal sequences. These segments included the previously found male-killing agents MK1068 (herein OGV-related RNA16) and MK1241 (OGV-related RNA7) RNAs. Ultramicroscopic observation of purified virions, which induced late male-killing in the progeny of injected moths, showed sizes typical of Partitiviridae. Mathematical modeling showed the importance of late male-killing in facilitating horizontal transmission of OGVs in an H. magnanima population. This study is the first report on the isolation of partiti-like virus from insects, and one thought to be associated with late male-killing, although the viral genomic contents and combinations in each virus are still unknown.

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Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing

Viruses ◽

10.3390/v13061042 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1042

Author(s):

Xin-Xin Chen ◽

Wei-Chen Wu ◽

Mang Shi

Keyword(s):

Rna Sequencing ◽

Rna Viruses ◽

Rna Virus ◽

Acute Infection ◽

Sufficient Information ◽

Lower Vertebrate ◽

Diverse Range ◽

New Findings ◽

Active Transcription ◽

Vertebrate Hosts

In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total “infectome” within a diverse range of vertebrate hosts.

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NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data

10.1101/2021.12.31.474423 ◽

2022 ◽

Author(s):

Shoichi Sakaguchi ◽

Syun-ichi Urayama ◽

Yoshihiro Takaki ◽

Hong Wu ◽

Youichi Suzuki ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Viruses ◽

Rna Virus ◽

Sequence Similarity ◽

Virus Detection ◽

Detection Methods ◽

Amino Acid Sequence Similarity ◽

Sequencing Data ◽

Rna Dependent Rna Polymerase ◽

Multiple Sequence

RNA viruses are distributed in various environments, and most RNA viruses have been recently identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify their sequences. Therefore, this study generated a dataset of RNA-dependent RNA polymerase (RdRp) domains essential for all RNA viruses belonging to Orthornavirae. Also, the collected genes with RdRp domains from various RNA viruses were clustered by amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than five. Using the 1,467 HMM profiles, we detected RdRp domains in the RefSeq RNA virus sequences, combined the hit sequences with the RdRp domains, and reconstructed the HMM profiles. As a result, 2,234 HMM profiles were generated from 12,316 RdRp domain sequences, and the dataset was named NeoRdRp. Additionally, using the UniProt dataset, we confirmed that almost all NeoRdRp HMM profiles could specifically detect RdRps in Orthornavirae. Furthermore, we compared the NeoRdRp dataset with two previously reported RNA virus detection methods to detect RNA virus sequences from metatranscriptome sequencing data. Our methods can identify most of the RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. The NeoRdRp can be improved by repeatedly adding new RdRp sequences and can be expected to be widely applied as a system for detecting various RNA viruses from metatranscriptome data.

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How Does Circadian Rhythm Shape Host-Parasite Associations? A Comparative Study on Infection Patterns in Diurnal and Nocturnal Raptors

Diversity ◽

10.3390/d13080338 ◽

2021 ◽

Vol 13 (8) ◽

pp. 338

Author(s):

Kai Gao ◽

Bing Zhou ◽

Li-Xing Yang ◽

Lu Dong ◽

Xi Huang ◽

...

Keyword(s):

Circadian Rhythm ◽

Classical Model ◽

Parasite Infection ◽

Haemosporidian Parasites ◽

Rescue Center ◽

Avian Haemosporidians ◽

Vertebrate Hosts ◽

Underlying Mechanisms ◽

Host Parasite ◽

Insight Into

Infection patterns of parasites, including their prevalence, diversity and host specificity, can be impacted by many biological and environmental factors, but no study has focused on the circadian rhythms of vertebrate hosts, which may affect susceptibilities and encounter rates between hosts and vectors and further shape host-parasite associations. In this study, we focused on avian haemosporidians, a classical model in studies of host-parasite associations, and investigated the infection patterns in rescued raptors brought to the Beijing Raptor Rescue Center during 2007–2020. We first assessed the association between prevalence and host biotic traits; haemosporidian prevalence was higher in the nocturnal raptors than in the diurnal raptors, and the prevalence of Haemoproteus and Leucocytozoon in the nocturnal raptors was significantly higher than that in the diurnal raptors. Furthermore, we analysed the phylogenetic relationship and host-parasite network-level differences of haemosporidian parasites in diurnal and nocturnal raptors, and demonstrated that the lineages infecting the diurnal and nocturnal raptors were not clearly separated, but the nocturnal lifestyle led to a more specialized host-parasite network structure. These variations in host-parasite associations may be driven by different susceptibilities of the hosts and the diversity or abundance of vectors during the day and night. Our study provides new insight into host-parasite associations shaped by circadian rhythm and calls for more studies on the underlying mechanisms of parasite infection.

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Prevalence and Genetic Diversity of Avian Haemosporidian Parasites in Southern Iran

Pathogens ◽

10.3390/pathogens10060645 ◽

2021 ◽

Vol 10 (6) ◽

pp. 645

Author(s):

Vajiheh Ghaemitalab ◽

Omid Mirshamsi ◽

Gediminas Valkiūnas ◽

Mansour Aliabadian

Keyword(s):

Bird Species ◽

Geographic Area ◽

Haemosporidian Parasite ◽

New Host ◽

Haemosporidian Parasites ◽

Mitochondrial Cytochrome B ◽

Base Pair Fragment ◽

Avian Haemosporidians ◽

Resident Bird ◽

Local Transmission

Avian haemosporidians are widespread and diverse and are classified in the genera Plasmodium, Haemoproteus, Leucocytozoon, and Fallisia. These species are known to cause haemosporidiosis and decreased fitness of their hosts. Despite the high diversity of habitats and animal species in Iran, only few studies have addressed avian haemosporidians in this geographic area. This study was performed in the south and southeast of Iran during the bird breeding seasons in 2017 and 2018, with the aim to partly fill in this gap. Blood samples of 237 passerine birds belonging to 41 species and 20 families were collected. Parasite infections were identified using a nested PCR protocol targeting a 479-base-pair fragment of the mitochondrial cytochrome b (cytb) gene of Haemoproteus, Plasmodium and Leucocytozoon species. The overall prevalence of haemosporidian parasites was 51.1%, and 55 different lineages were identified, of which 15 cytb lineages were new globally. The lineages of Haemoproteus predominated (63.6% of all detected lineages), followed by Leucocytozoon and Plasmodium. Nineteen new host records of haemosporidian cytb lineages were identified, and the majority of them were found in resident bird species, indicating local transmission. Thirteen co-infections (9.8% of infected individuals) of Haemoproteus and Leucocytozoon parasites in seven host species were observed. This study shows the presence of active local transmission of parasites to resident bird species in the southeast of Iran and contributes to the knowledge on haemosporidian parasite biodiversity in this poorly studied region of the world.

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Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles

Journal of Virology ◽

10.1128/jvi.02921-15 ◽

2015 ◽

Vol 90 (5) ◽

pp. 2446-2454 ◽

Cited By ~ 35

Author(s):

Enzo Z. Poirier ◽

Bryan C. Mounce ◽

Kathryn Rozen-Gagnon ◽

Peter Jan Hooikaas ◽

Kenneth A. Stapleford ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Viruses ◽

Rna Virus ◽

Point Mutations ◽

Viral Fitness ◽

Dependent Manner ◽

Rna Dependent Rna Polymerase ◽

Live Attenuated Vaccine ◽

Defective Interfering Particles

ABSTRACTLow-fidelity RNA-dependent RNA polymerases for many RNA virus mutators have been shown to confer attenuated phenotypes, presumably due to increased mutation rates. Additionally, for many RNA viruses, replication to high titers results in the production of defective interfering particles (DIs) that also attenuate infection. We hypothesized that fidelity, recombination, and DI production are tightly linked. We show that a Sindbis virus mutator replicating at a high multiplicity of infection manifests an earlier and greater accumulation of DIs than its wild-type counterpart. The isolated DIs interfere with the replication of full-length virus in a dose-dependent manner. Importantly, the ability of the mutator virus to overproduce DIs could be linked to an increased recombination frequency. These data confirm that RNA-dependent RNA polymerase fidelity and recombination are inversely correlated for this mutator. Our findings suggest that defective interference resulting from higher recombination rates may be more detrimental to RNA virus mutators than the increase in mutational burden.IMPORTANCEReplication, adaptation, and evolution of RNA viruses rely in large part on their low-fidelity RNA-dependent RNA polymerase. Viruses artificially modified in their polymerases to decrease fidelity (mutator viruses) are attenuatedin vivo, demonstrating the important role of fidelity in viral fitness. However, attenuation was attributed solely to the modification of the viral mutation rate and the accumulation of detrimental point mutations. In this work, we described an additional phenotype of mutator viruses: an increased recombination rate leading to defective interfering particle (DI) overproduction. Because DIs are known for their inhibitory effect on viral replication, our work suggests that fidelity variants may be attenuatedin vivovia several mechanisms. This has important implications in the development of fidelity variants as live attenuated vaccine strains.

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Unmapped RNA Virus Diversity in Termites and Their Symbionts

Viruses ◽

10.3390/v12101145 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1145

Author(s):

Callum Le Lay ◽

Mang Shi ◽

Aleš Buček ◽

Thomas Bourguignon ◽

Nathan Lo ◽

...

Keyword(s):

Evolutionary History ◽

Phylogenetic Diversity ◽

Rna Viruses ◽

Rna Virus ◽

Amino Acid Identity ◽

Sampling Procedure ◽

Phylogenetic Position ◽

Virus Diversity ◽

Diverse Species ◽

Ecological Importance

Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae, Picobirnaviridae and Partitiviridae. However, all viruses identified were novel and divergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic diversity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the sampling procedure had the strongest association with virome composition, with greater RNA virome diversity in libraries prepared from whole termite bodies than those that only sampled heads.

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Structure Unveils Relationships between RNA Virus Polymerases

Viruses ◽

10.3390/v13020313 ◽

2021 ◽

Vol 13 (2) ◽

pp. 313

Author(s):

Heli A. M. Mönttinen ◽

Janne J. Ravantti ◽

Minna M. Poranen

Keyword(s):

Phylogenetic Tree ◽

Rna Viruses ◽

Rna Virus ◽

Sequence Similarity ◽

Protein Structures ◽

Structural Similarity ◽

Functional Differentiation ◽

Comparison Method ◽

Homologous Structure ◽

Biological Entities

RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.

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