Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania

Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in data-bases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.Peer reviewe

Conserved domains in the polyprotein encoded by PvEV-1 and PvEV-2 from Nicaragua.

<p>Numbers indicate the residues defining the conserved domains. Hel-1, helicase; CPS, putative capsular polysaccharide synthase; UGT, UDP-glycosyltransferase; RdRp, RNA-dependant RNA polymerase; and MTR, methyltransferase.</p

Viruses detected in the pools of common bean samples from Nicaragua (NI) and Tanzania (TZ) by VirusDetect.

<p>Viruses detected in the pools of common bean samples from Nicaragua (NI) and Tanzania (TZ) by VirusDetect.</p

Detection of PvEV-1 by RT-PCR in common beans in Tanzania.

<p>In the list below, landraces are marked with asterisk (*). Other samples represent improved varieties (origin of samples shown in parenthesis). Lane labelled ‘M’ represents a O'GeneRuler 1 kb Plus DNA ladder. The expected size of PCR products was 374 bp. Lanes 1, ‘Njugu’* (Southern Highlands zone); 2, ‘pooled RNA’ (Southern Highlands zone); 3, ‘pooled RNA’ (Eastern zone); 4, ‘pooled RNA’ (Northern zone); 5, ‘Rosekoko’/’Lyamungu 85’ (Eastern zone); 6, ‘Salundi’ (Southern Highlands zone); 7, ‘E 36’ (Southern Highlands zone); 8, ‘Msafiri’* (Southern Highlands zone); 9, ‘Msafiri’* (Eastern zone); and 10, ‘Mshindi’ (Eastern zone).</p

Symptoms observed in common bean plants in La Compañia, Nicaragua.

<p>(a), Stunting of the plant, malformation and blistering of leaves. (b), Mild epinasty and vein reversion. (c), Green-yellow chlorosis. (d), Green-yellow mosaic.</p

Identification of PvEV-2 in the sample pool HXH8 from the Southern Highland zone of Tanzania based on small-RNA deep sequencing.

<p>(a), Viral contigs (red bars) mapped to the sequence of PvEV-2-Okada (AB719398) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178242#pone.0178242.ref025" target="_blank">25</a>] using VirusDetect [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178242#pone.0178242.ref051" target="_blank">51</a>]. Each nucleotide in the contigs was covered by siRNA reads at least 5 times. (b) The 21- to 24-nt reads mapped to the sequence of PvEV-2. The <i>x</i> axis and the scale below the figure depict the viral genome and nucleotide positions, respectively. The <i>y</i> axis indicates the number of siRNA reads derived from the coding strand (blue bars above the <i>x</i> axis) and complementary strand (red bars below the <i>x</i> axis).</p

Enhanced infection prophylaxis reduces mortality in severely immunosuppressed HIV-infected adults and older children initiating antiretroviral therapy in Kenya, Malawi, Uganda and Zimbabwe: the REALITY trial

Meeting abstract FRAB0101LB from 21st International AIDS Conference 18–22 July 2016, Durban, South Africa. Introduction: Mortality from infections is high in the first 6 months of antiretroviral therapy (ART) among HIV‐infected adults and children with advanced disease in sub‐Saharan Africa. Whether an enhanced package of infection prophylaxis at ART initiation would reduce mortality is unknown. Methods: The REALITY 2×2×2 factorial open‐label trial (ISRCTN43622374) randomized ART‐naïve HIV‐infected adults and children >5 years with CD4 <100 cells/mm3. This randomization compared initiating ART with enhanced prophylaxis (continuous cotrimoxazole plus 12 weeks isoniazid/pyridoxine (anti‐tuberculosis) and fluconazole (anti‐cryptococcal/candida), 5 days azithromycin (anti‐bacterial/protozoal) and single‐dose albendazole (anti‐helminth)), versus standard‐of‐care cotrimoxazole. Isoniazid/pyridoxine/cotrimoxazole was formulated as a scored fixed‐dose combination. Two other randomizations investigated 12‐week adjunctive raltegravir or supplementary food. The primary endpoint was 24‐week mortality. Results: 1805 eligible adults (n = 1733; 96.0%) and children/adolescents (n = 72; 4.0%) (median 36 years; 53.2% male) were randomized to enhanced (n = 906) or standard prophylaxis (n = 899) and followed for 48 weeks (3.8% loss‐to‐follow‐up). Median baseline CD4 was 36 cells/mm3 (IQR: 16–62) but 47.3% were WHO Stage 1/2. 80 (8.9%) enhanced versus 108(12.2%) standard prophylaxis died before 24 weeks (adjusted hazard ratio (aHR) = 0.73 (95% CI: 0.54–0.97) p = 0.03; Figure 1) and 98(11.0%) versus 127(14.4%) respectively died before 48 weeks (aHR = 0.75 (0.58–0.98) p = 0.04), with no evidence of interaction with the two other randomizations (p > 0.8). Enhanced prophylaxis significantly reduced incidence of tuberculosis (p = 0.02), cryptococcal disease (p = 0.01), oral/oesophageal candidiasis (p = 0.02), deaths of unknown cause (p = 0.02) and (marginally) hospitalisations (p = 0.06) but not presumed severe bacterial infections (p = 0.38). Serious and grade 4 adverse events were marginally less common with enhanced prophylaxis (p = 0.06). CD4 increases and VL suppression were similar between groups (p > 0.2). Conclusions: Enhanced infection prophylaxis at ART initiation reduces early mortality by 25% among HIV‐infected adults and children with advanced disease. The pill burden did not adversely affect VL suppression. Policy makers should consider adopting and implementing this low‐cost broad infection prevention package which could save 3.3 lives for every 100 individuals treated