Viral metagenomics reveals sweet potato virus diversity in the Eastern and Western Cape provinces of South Africa

Limited studies have been undertaken with regard to virus complexes contributing to the aetiology of sweet potato virus disease (SPVD) in South Africa (SA). In this study, a metagenomic approach was adopted to reveal the genetic diversity of viruses infecting sweet potato. In order to undertake a comprehensive analysis of viral sequences, total RNA was isolated from 17 asymptomatic and symptomatic sweet potato plants that were collected from the Eastern (EC) and Western Cape (WC) provinces of SA. DNase-treated total RNA was depleted of ribosomal RNA (rRNA) and deep-sequenced using the Illumina MiSeq platform. Genomic DNA, isolated from the same plants, underwent rolling circle amplification (RCA) and deep sequencing. Sequence reads were analysed with the CLC Bio Genomics Workbench. Both de novo and reference-guided assemblies were performed resulting in four near full-length RNA virus genomes. BLAST searches using de novo assembled sequences against published virus genomes confirmed the presence of previously detected begomoviruses in the Western Cape (WC) province, namely Sweet potato mosaic virus (SPMaV) and Sweet potato leaf curl Sao Paulo virus (SPLCSPV). The begomoviruses were detected in mixed infections with two major disease-causing RNA viruses, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV). The sequence data further demonstrated mixed infections of RNA and DNA viruses from 11 of the 17 sequenced samples. Metagenomics is a reliable diagnostic tool for virus diversity detection, in particular virus-complexes and synergies affecting disease aetiology

First Report of Sweet potato badnavirus A and Sweet potato badnavirus B in South Africa

Sweet potato is an important root crop, having significant nutritional and economic value in sub-Saharan countries such as South Africa. Sweet potato badnaviruses were first discovered in Peru using small RNA deep sequencing (Kreuze et al. 2009) and were later detected in Tanzania (Mbanzibwa et al. 2014), Honduras, and Guatemala (Kashif et al. 2012). Badnaviruses are pararetroviruses (family Caulimoviridae) with circular double-stranded DNA genomes (dsDNA) that range between 7.2 and 8.5 kb in size (Bhat et al. 2016). In this study we report the detection of sweet potato badnaviruses in plants collected during a survey in the Eastern and Western Cape provinces of South Africa. Symptomatic plants exhibited leaf curling, chlorotic spots, and chlorotic spots with purple rings. Small RNAs (sRNA) were isolated from five symptomatic and two asymptomatic plants using the Ambion mirVana miRNA RNA Isolation Kit (Ambion, Naugatuck, CT). The sRNA samples were prepared for sequencing using the Illumina TruSeq Small RNA Sample Preparation Kit (Illumina, San Diego, CA). The seven libraries were independently sequenced on the Illumina MiSeq platform (Illumina). Each of the seven libraries underwent quality trimming and downstream analysis. Over 6.9 million sequence reads from the seven libraries remained after quality control analysis. Sequence reads were assembled into contiguous (contigs) sequences using Velvet (Zerbino and Birney 2008). BLASTn and BLASTx searches against viral sequences revealed the presence of sweet potato badnavirus A (SPBVA) and sweet potato badnavirus B (SPBVB) in all seven libraries. The total number of SPBVA specific reads was 12,050, whereas 16,279 reads were identified as SPBVB. Both badnaviruses were detected in the symptomatic and asymptomatic samples as coinfections. The identity of the badnaviruses was confirmed by conventional Sanger sequencing of amplified polymerase chain reaction products. Virus-specific primers targeting the polyprotein gene of SPBVA and the ORF3b gene of SPBVB were designed using the CLC Bio Genomics Workbench (version 7.5.1) (CLC bio, Aarhus, Denmark). Amplification was achieved using the following primers: SPBVA-F (5′-TCCCACCTAAGGCTCAAGAA-3′), SPBVA-R (5′-GCAAACTGTTGCCCCTGTAT-3′), SPBVB-F (5′-TGGGTGCAATTTCATCAGAA-3′), and SPBVB-R (5′-GTGCATTTACCAGCCCAAAT-3′). The expected amplicons of 593 and 679 bp for SPBVA and SPBVB, respectively, were amplified and sent to Inqaba Biotechnical Industries for direct Sanger sequencing. The SPBVA sequence shared 100% nucleotide (nt) identity with the SPBVA isolate from China (GenBank accession no. KT448733), and the SPBVB sequence shared 99% nt identity with the Spanish isolate (GenBank accession no. KU511272). The sequences were submitted to GenBank under the accession numbers KY829453 and KY829454, for SPBVA and SPBVB, respectively. To our knowledge, this is the first report of sweet potato badnaviruses in South Africa. Future studies are necessary to determine what role badnaviruses play in the etiology of sweet potato disease, because they are known to trigger infections and cause emerging diseases

Diversities, affinities and diasporas: a southern lens and methodology for understanding multilingualisms

We frame multilingualisms through a growing interest in a linguistics and sociology of the ‘south’ and acknowledge earlier contributions of linguists in Africa, the Américas and Asia who have engaged with human mobility, linguistic contact and consequential ecologies that alter over time and space. Recently, conversations of multilingualism have drifted in two directions. Southern conversations have become intertwined with ‘decolonial theory’, and with ‘southern’ theory, thinking and epistemologies. In these, ‘southern’ is regarded as a metaphor for marginality, coloniality and entanglements of the geopolitical north and south. Northern debates that receive traction appear to focus on recent ‘re-awakenings’ in Europe and North America that mis-remember southern experiences of linguistic diversity. We provide a contextual backdrop for articles in this issue that illustrate intelligences of multilingualisms and the linguistic citizenship of southern people. In these, southern multilingualisms are revealed as phenomena, rather than as a phenomenon defined usually in English. The intention is to suggest a third direction of mutual advantage in rethinking the social imaginary in relation to communality, entanglements and interconnectivities of both South and North

Framing rights and responsibilities: accounts of women with a history of AIDS activism

<p>Abstract</p> <p>Background</p> <p>In South Africa, policy with respect to HIV/AIDS has had a strong rights-based framing in line with international trends and in keeping with the constitutional overhaul in the post-Apartheid era. There have also been considerable advances since 1994 towards legal enshrinement of sexual and reproductive health rights and in the provision of related services. Since HIV in this setting has heavily affected women of reproductive age, there has been discussion about the particular needs of this subgroup, especially in the context of service integration. This paper is concerned with the way in which HIV positive women conceptualise these rights and whether they wish and are able to actualise them in their daily lives.</p> <p>Methods</p> <p>In 2003 a group of women involved with the Treatment Action Campaign and Medicines Sans Frontières participated in an initiative to ‘map’ their bodies as affected by the virus. A book containing the maps and narratives was published and used as a political tool to pressure the government of the day to roll out antiretroviral therapy (ART) to the population. In 2008, the authors coordinated an initiative that involved conducting follow-up in-depth interviews in which five of these women reflected on those body maps and on how their lives had changed in the intervening five years since gaining the right to treatment through the public sector.</p> <p>Results</p> <p>Drawing upon this qualitative data and published sources, these new accounts are analysed in order to reflect the perspectives of these women living with chronic HIV with respect to their sexual relations and fertility desires. The paper reveals difficulties faced by these women in negotiating sexual relationships and disclosure of their HIV positive status. It focuses on how they perceive relative responsibilities in terms of taking preventative measures in sexual encounters. Women adopt tactics within a context characterised by various inequalities in order to ‘make do’, such as by remaining silent about their status. Concerns about childbearing can be addressed by information and support from a health care worker.</p> <p>Conclusions</p> <p>Women’s experience of HIV as a chronic illness and the need to adhere to ART, is linked to the way in which the language of responsibility can come to counter-balance a language of rights in treatment programmes.</p