Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.

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Streptomyces Species Associated with Fissure Scab of Potato in South Africa Including Description of S. Resiliuntiscabiei Sp. Nov.

10.21203/rs.3.rs-326303/v1 ◽

2021 ◽

Author(s):

Elsie Margaretha Cruywagen ◽

Rian Pierneef ◽

Kgothatso Andronicah Chauke ◽

Brightness Zama Nkosi ◽

David Labeda ◽

...

Keyword(s):

South Africa ◽

Culture Media ◽

Phylogenetic Analyses ◽

Housekeeping Genes ◽

Potato Tubers ◽

Streptomyces Species ◽

Culture Morphology ◽

New Type ◽

Genome Analyses ◽

Phenotypic Tests

Abstract Streptomyces species are the causal agents of several scab diseases on potato tubers. A new type of scab symptom, caused by Streptomyces species, was observed in South Africa from 2010 onwards. The disease was initially thought to be caused by a single Streptomyces species, however, subsequent isolations from similar symptoms on other potato tubers revealed diversity of the Streptomyces isolates. The objective of this study was to characterise these isolates in order to determine which species are involved in the disease. This was done by sequencing and phylogenetic analyses of the 16S rDNA as well as five housekeeping genes, investigation of growth on different culture media, standard phenotypic tests and scanning electron microscopy of culture morphology. The presence of the pathogenicity island (PAI) present in plant pathogenic Streptomyces species was also investigated. The genomes of eight isolates selected from the three main clades identified, were sequenced and annotated to further clarify species boundaries. Two isolates of each of the three main clades were also inoculated onto susceptible potato cultivars in order to establish the pathogenicity of the species. The results of the phylogenetic and genome analyses revealed that there are three main species involved, namely, S. werraensis, S. pseudogriseolus and a novel Streptomyces species that is described here as Streptomyces resiliuntiscabiei sp. nov. The glasshouse trial results showed that all three of the Streptomyces species are capable of producing fissure scab symptoms. None of the Streptomyces isolates from fissure scab contained the full PAI and the mechanism of disease initiation still needs to be determined.

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Complete Genome Sequences of Five Bluetongue Virus (BTV) Vaccine Strains from a Commercial Live Attenuated Vaccine, a BTV-4 Field Strain from South Africa, and a Reassortant Strain Isolated from Experimentally Vaccinated Cattle

Genome Announcements ◽

10.1128/genomea.00462-16 ◽

2016 ◽

Vol 4 (3) ◽

Cited By ~ 4

Author(s):

Carien van den Bergh ◽

Peter Coetzee ◽

Alan J. Guthrie ◽

Misha le Grange ◽

Estelle H. Venter

Keyword(s):

South Africa ◽

Complete Genome ◽

Bluetongue Virus ◽

Phylogenetic Analyses ◽

Field Strain ◽

Full Genome Sequencing ◽

Genome Sequences ◽

Live Attenuated Vaccine ◽

Live Virus ◽

Reassortant Strain

This is a report of the complete genome sequences of plaque-selected isolates of each of the five virus strains included in a South African commercial trivalent bluetongue virus (BTV) attenuated live virus vaccine, a BTV-4 field strain isolated from Rustenburg, South Africa, in 2011, and a bluetongue reassortant (bluetongue virus 4 strain 4/O. aries-tc/ZAF/11/OBP-115) isolated from experimentally vaccinated cattle. Full-genome sequencing and phylogenetic analyses show that the bluetongue virus 9 strain 9/B. taurus-tc/ZAF/15/Onderstepoort_B02b is a reassortant virus containing segments from both BTV-9 and BTV-8.

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Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection

10.1101/058875 ◽

2016 ◽

Author(s):

My VT Phan ◽

Pham Hong Anh ◽

Nguyen Van Cuong ◽

Bas B. Oude Munnink ◽

Lia van der Hoek ◽

...

Keyword(s):

Deep Sequencing ◽

Phylogenetic Analyses ◽

Mekong Delta ◽

Viral Gastroenteritis ◽

Human Patient ◽

Virus Diversity ◽

Genotype Constellation ◽

Group A ◽

Stool Samples ◽

Group B

AbstractCoordinated and synchronous virological surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus is an important cause of viral gastroenteritis in humans and animals. We have documented the rotavirus diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of 60 human rotaviruses (all group A) and 31 porcine rotaviruses (13 group A, 7 group B, 6 group C and 5 group H). Phylogenetic analyses showed the co-circulation of multiple distinct rotavirus group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C and H, none of which have been previously reported in Vietnam. Furthermore the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event

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Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing

Current Issues in Molecular Biology ◽

10.3390/cimb43030141 ◽

2021 ◽

Vol 43 (3) ◽

pp. 2048-2058

Author(s):

Chenghao Jia ◽

Tianyan Yang ◽

Takashi Yanagimoto ◽

Tianxiang Gao

Keyword(s):

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Economic Value ◽

Draft Genome ◽

Whole Genome ◽

Genome Sequences ◽

Genome Data ◽

Genome Survey ◽

Genome Wide ◽

Genome Analyses

Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.

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Evolution of DS-1-like human G2P[4] rotaviruses assessed by complete genome analyses

Journal of General Virology ◽

10.1099/vir.0.056788-0 ◽

2014 ◽

Vol 95 (1) ◽

pp. 91-109 ◽

Cited By ~ 33

Author(s):

Giovanni M. Giammanco ◽

Floriana Bonura ◽

Mark Zeller ◽

Elisabeth Heylen ◽

Marc Van Ranst ◽

...

Keyword(s):

Complete Genome ◽

Viral Gastroenteritis ◽

Archival Collection ◽

Antigenic Proteins ◽

Genotype Constellation ◽

Reassortant Strain ◽

Novel Variant ◽

Group A Rotaviruses ◽

Group A ◽

Genome Analyses

Group A rotaviruses (RVAs) are a leading cause of viral gastroenteritis in children, with G2P[4] RVA being one of the most common human strains worldwide. The complete genome sequences of nine G2P[4] RVA strains, selected from a 26-year archival collection (1985–2011) established in Palermo, Italy, were determined. A strain associated with a peak of G2P[4] RVA activity in 1996 resembled a reassortant strain identified in Kenya in 1982 and differed completely in genomic make up from more recent strains that circulated during 2004–2011. Conversely, the 2004–2011 G2P[4] RVAs were genetically more similar to contemporary RVA strains circulating globally. Recent G2P[4] strains possessed either single or multiple genome segments (VP1, VP3 and/or NSP4) likely derived from ruminant viruses through intra-genotype reassortment. Amino acid substitutions were selected and maintained over time in the VP7 and VP8* antigenic proteins, allowing the circulation of two contemporary G2P[4] variants to be distinguished. Altogether, these findings suggest that major changes in the genomic composition of recent G2P[4] RVAs occurred in the early 2000s, leading to the appearance of a novel variant of the DS-1-like genotype constellation. Whether the modifications observed in the neutralizing antigens and in the genome composition of modern G2P[4] RVAs may affect the long-term effectiveness of the vaccination programmes remains to be explored.

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Gene Losses and Variations in Chloroplast Genome of Parasitic Plant Macrosolen and Phylogenetic Relationships within Santalales

International Journal of Molecular Sciences ◽

10.3390/ijms20225812 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5812

Author(s):

Liping Nie ◽

Yingxian Cui ◽

Liwei Wu ◽

Jianguo Zhou ◽

Zhichao Xu ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Folk Medicine ◽

Genome Sequences ◽

Illumina Hiseq ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

Genome Analyses ◽

Simple Sequence

Macrosolen plants are parasitic shrubs, several of which are important medicinal plants, that are used as folk medicine in some provinces of China. However, reports on Macrosolen are limited. In this study, the complete chloroplast genome sequences of Macrosolen cochinchinensis, Macrosolen tricolor and Macrosolen bibracteolatus are reported. The chloroplast genomes were sequenced by Illumina HiSeq X. The length of the chloroplast genomes ranged from 129,570 bp (M. cochinchinensis) to 126,621 bp (M. tricolor), with a total of 113 genes, including 35 tRNA, eight rRNA, 68 protein-coding genes, and two pseudogenes (ycf1 and rpl2). The simple sequence repeats are mainly comprised of A/T mononucleotide repeats. Comparative genome analyses of the three species detected the most divergent regions in the non-coding spacers. Phylogenetic analyses using maximum parsimony and maximum likelihood strongly supported the idea that Loranthaceae and Viscaceae are monophyletic clades. The data obtained in this study are beneficial for further investigations of Macrosolen in respect to evolution and molecular identification.

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Presence of broadly reactive and group-specific neutralizing epitopes on newly described isolates of Crimean-Congo hemorrhagic fever virus

Journal of General Virology ◽

10.1099/vir.0.81175-0 ◽

2005 ◽

Vol 86 (12) ◽

pp. 3327-3336 ◽

Cited By ~ 29

Author(s):

Asim A. Ahmed ◽

Jeanne M. McFalls ◽

Christian Hoffmann ◽

Claire Marie Filone ◽

Shaun M. Stewart ◽

...

Keyword(s):

South Africa ◽

Vaccine Development ◽

Phylogenetic Analyses ◽

Hemorrhagic Fever ◽

Human Case ◽

Fever Virus ◽

Infected Tick ◽

Crimean Congo Hemorrhagic Fever ◽

Hemorrhagic Fever Virus ◽

Neutralizing Epitopes

Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the genus Nairovirus of the family Bunyaviridae, causes severe disease in humans with high rates of mortality. The virus has a tripartite genome composed of a small (S), a medium (M) and a large (L) RNA segment; the M segment encodes the two viral glycoproteins, GN and GC. Whilst relatively few full-length M segment sequences are available, it is apparent that both GN and GC may exhibit significant sequence diversity. It is unknown whether considerable antigenic differences exist between divergent CCHFV strains, or whether there are conserved neutralizing epitopes. The M segments derived from viral isolates of a human case of CCHF in South Africa (SPU 41/84), an infected tick (Hyalomma marginatum) in South Africa (SPU 128/81), a human case in Congo (UG 3010), an infected individual in Uzbekistan (U2-2-002) and an infected tick (Hyalomma asiaticum) in China (Hy13) were sequenced fully, and the glycoproteins were expressed. These novel sequences showed high variability in the N-terminal region of GN and more modest differences in the remainder of GN and in GC. Phylogenetic analyses placed these newly identified strains in three of the four previously described M segment groups. Studies with a panel of mAbs specific to GN and GC indicated that there were significant antigenic differences between the M segment groups, although several neutralizing epitopes in both GN and GC were conserved among all strains examined. Thus, the genetic diversity exhibited by CCHFV strains results in significant antigenic differences that will need to be taken into consideration for vaccine development.

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La Traviata Affair

10.1525/california/9780520299887.001.0001 ◽

2018 ◽

Author(s):

Hilde Roos

Keyword(s):

South Africa ◽

Racial Boundaries ◽

Cultural Organization ◽

Colored People ◽

Art Forms ◽

Group A ◽

La Traviata ◽

Apartheid Regime ◽

Opera Production ◽

The Way

Opera, race, and politics during apartheid South Africa form the foundation of this historiographic work on the Eoan Group, a so-called colored cultural organization that performed opera in the Cape. The La Traviata Affair: Opera in the Time of Apartheid charts Eoan’s opera activities from its inception in 1933 until the cessation of its work by 1980. By accepting funding from the apartheid government and adhering to apartheid conditions, the group, in time, became politically compromised, resulting in the rejection of the group by their own community and the cessation of opera production. However, their unquestioned acceptance of and commitment to the art of opera lead to the most extraordinary of performance trajectories. During apartheid, the Eoan Group provided a space for colored people to perform Western classical art forms in an environment that potentially transgressed racial boundaries and challenged perceptions of racial exclusivity in the genre of opera. This highly significant endeavor and the way it was thwarted at the hands of the apartheid regime is the story that unfolds in this book.

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