New insights into the genetic diversity of Leishmania RNA Virus 1 and its species-specific relationship with Leishmania parasites

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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A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States

Viruses ◽

10.3390/v14010104 ◽

2022 ◽

Vol 14 (1) ◽

pp. 104

Author(s):

Adam A. Capoferri ◽

Wei Shao ◽

Jon Spindler ◽

John M. Coffin ◽

Jason W. Rausch ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Rna Virus ◽

Viral Evolution ◽

The United States ◽

Virus Spread ◽

Immune Pressure ◽

Viral Genetic Diversity ◽

Genetic Sampling ◽

The U.S

COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs.

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Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0019 ◽

2015 ◽

Vol 370 (1662) ◽

pp. 20140019 ◽

Cited By ~ 29

Author(s):

T. M. Brooks ◽

A. Cuttelod ◽

D. P. Faith ◽

J. Garcia-Moreno ◽

P. Langhammer ◽

...

Keyword(s):

Genetic Diversity ◽

Threatened Species ◽

Phylogenetic Diversity ◽

Species Population ◽

Threatened Taxa ◽

Conservation Actions ◽

Ecosystem Diversity ◽

Species Specific ◽

A Site ◽

Specific Conservation

‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4 , 326–337. ( doi:10.1111/j.1752-4571.2010.00157.x )) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

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Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Plant Disease ◽

10.1094/pdis-11-21-2409-re ◽

2022 ◽

Author(s):

Rochelle de Bruyn ◽

Rachelle Bester ◽

Glynnis Cook ◽

Chanel Steyn ◽

Johannes Hendrik Jacobus Breytenbach ◽

...

Keyword(s):

South Africa ◽

Genetic Diversity ◽

Real Time ◽

South African ◽

High Throughput Sequencing ◽

Rna Virus ◽

Citrus Paradisi ◽

Virus Elimination ◽

Shoot Tip Grafting ◽

Citrus Production

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

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Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Diversity ◽

10.3390/d12080306 ◽

2020 ◽

Vol 12 (8) ◽

pp. 306

Author(s):

Maurizio Rossetto ◽

Peter D. Wilson ◽

Jason Bragg ◽

Joel Cohen ◽

Monica Fahey ◽

...

Keyword(s):

Genetic Diversity ◽

A Priori ◽

Genetic Data ◽

Environmental Data ◽

Specific Data ◽

Acacia Species ◽

Simple Observation ◽

Source Plant ◽

Species Specific

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

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Genetic diversity and species-specific PCR-based markers from AFLP analyses of Thai bananas

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2010.03.015 ◽

2010 ◽

Vol 38 (3) ◽

pp. 416-427 ◽

Cited By ~ 6

Author(s):

Sirapope Wongniam ◽

Jamorn Somana ◽

Sasivimon Swangpol ◽

Tosak Seelanan ◽

Piyarat Chareonsap ◽

...

Keyword(s):

Genetic Diversity ◽

Specific Pcr ◽

Species Specific

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Isolation and Characterization of a Novel Single-Stranded RNA Virus Infecting the Bloom-Forming Diatom Rhizosolenia setigera

Applied and Environmental Microbiology ◽

10.1128/aem.70.2.704-711.2004 ◽

2004 ◽

Vol 70 (2) ◽

pp. 704-711 ◽

Cited By ~ 89

Author(s):

Keizo Nagasaki ◽

Yuji Tomaru ◽

Noriaki Katanozaka ◽

Yoko Shirai ◽

Kensho Nishida ◽

...

Keyword(s):

Host Specificity ◽

Rna Virus ◽

Biological Properties ◽

Rna Molecules ◽

Isolation And Characterization ◽

Ssrna Virus ◽

Ecological Relationship ◽

Rhizosolenia Setigera ◽

Species Specific

ABSTRACT A novel single-stranded RNA (ssRNA) virus specifically infecting the bloom-forming diatom Rhizosolenia setigera (R. setigera RNA virus [RsRNAV]) was isolated from Ariake Sea, Japan. Viral replication occurred within the cytoplasm, and the virus particle was icosahedral, lacked a tail, and was 32 nm in diameter on average. The major nucleic acid extracted from the RsRNAV particles was an ssRNA molecule 11.2 kb in length, although smaller RNA molecules (0.6, 1.2, and 1.5 kb) were occasionally observed. The major structural proteins of RsRNAV were 41.5, 41.0, and 29.5 kDa. Inter- and intraspecies host specificity tests revealed that RsRNAV is not only species specific but also strain specific and that its intraspecies host specificity is diverse among virus clones. The latent period of RsRNAV was 2 days, and the burst sizes were 3,100 and 1,010 viruses per host cell when viruses were inoculated into the host culture at the exponential and stationary growth phases, respectively, at 15°C under a 12-h-12-h light-dark cycle of ca. 110 μmol of photons m−2 s−1 with cool white fluorescent illumination. To our knowledge, this is the first report describing the biological properties of a virus infecting a diatom. Further studies on RsRNAV will be helpful in understanding the ecological relationship between diatoms and viruses in nature.

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Tree establishment and microhabitat relationships in north Swedish peatlands

Canadian Journal of Forest Research ◽

10.1139/x92-244 ◽

1992 ◽

Vol 22 (12) ◽

pp. 1869-1877 ◽

Cited By ~ 58

Author(s):

Mikael Ohlson ◽

Olle Zackrisson

Keyword(s):

Tree Species ◽

Coniferous Tree ◽

Northern Sweden ◽

Seedling Mortality ◽

Tree Establishment ◽

Specific Relationship ◽

Different Types ◽

Coniferous Tree Species ◽

Species Specific

We sowed seeds of Pinussylvestris L., Pinuscontorta Dougl, Piceaabies (L.) Karst., and Piceamariana (Mill.) B.S.P. at five different virgin peatland sites in northern Sweden. Seeds were sown in 1987, 1988, 1989, and 1990. The seeds were sown in three different types of microhabitat, viz Pleurozium, Sphagnumfuscum, and Sphagnumangustifolium. Germination and seedling mortality were monitored each year. Both germination and mortality were significantly affected by the micro-habitat. Sphagnumangustifolium microhabitats were most favourable and Pleurozium microhabitats were least favourable for germination of all tree species. In contrast, the mortality for all tree species was highest in Sphagnumangustifolium microhabitats and lowest in Pleurozium microhabitats. Lowest average mortality was found among the nonindigenous Pinuscontorta and Piceamariana. The coniferous tree species had a species-specific relationship with the microhabitat. Pinussylvestris seeds were the most able to germinate in the Pleurozium microhabitats, and seedling mortality was strongly affected by the microhabitat. Piceaabies was the least affected by the microhabitat, and seedling mortality was high irrespective of microhabitat.

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