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An extensive survey was carried out in the Dominican Republic in order to monitor the prevalence of the three most widespread BSV species: Banana streak OL virus (BSOLV), Banana streak GF virus (BGFV) and Banana streak IM virus (BSIMV), in Macho x Hembra (MxH) and FHIA-21 plantains and in Cavendish dessert banana throughout all banana-producing areas. This survey led to the first detection of BSVs in the Dominican Republic. BSGFV was the most prevalent of the three targeted BSV species in both FHIA-21 and MxH varieties. Prevalence of BSGFV and BSOLV were substantially higher in FHIA-21 than in MxH. Molecular analysis of the eBSV pattern of sampled FHIA-21 and MxH plants showed that both varieties harbor infectious alleles OL1 (eBSOLV) and GF7 (eBSGFV) and are devoid of eBSIMV. Very low prevalence was recorded for both BSOLV and BSGFV in Cavendish banana, which is devoid of infectious eBSVs. BSIMV was not detected at all. Our results point to a marginal role of insect-borne transmission in the epidemiology of BSVs in the Dominican Republic.

Banana streak virus (BSV) belongs to the members of the genus Badnavirus, family Caulimoviridae. At present, BSV contains nine species in the International Committee on Taxonomy of Viruses (ICTV) classification report (2018b release). Previous study indicated that the viral particles of Banana streak virus Acuminata Yunnan (BSV-Acum) were purified from banana (Cavendish Musa AAA group) leaves in Yunnan Province, China, and its complete genome was obtained. To further determine whether this sample infecting with Banana streak GF virus (BSGFV), the polymerase chain reaction (PCR) cloning and complete genome analysis of the Banana streak GF virus Yunnan isolate (BSGFV-YN) isolate were carried out in this study. The result showed that BSGFV-YN infecting Cavendish Musa AAA group was co-infecting this sample. Its genome contains a total of 7,325 bp in length with 42% GC content. This complete genome sequence was deposited in GenBank under accession number MN296502. Sequence analysis showed that the complete genome of BSGFV-YN was 98.14% sequence similarity to BSGFV Goldfinger, while it was 49.10–57.09% to other BSV species. Two phylogenetic trees based on the complete genome and ORFIII polyprotein indicated that BSGFV-YN and other BSV species clustered into a group, while it was the highest homology with BSGFV Goldfinger. Although BSGFV-YN and BSGFV Goldfinger were highly homologous, their cultivating bananas are different. The former cultivating banana was from Cavendish Musa AAA group, while the latter cultivating banana was from Goldfinger Musa AAAB group. Compared with BSGFV Goldfinger, the genome of BSGFV-YN has an extra multiple repetitive sequences in the intergenetic region between ORFIII and ORFI, suggesting that this region might be related to host selection. In summary, a BSGFV-YN distant from BSV-Acum was identified from the same sample, and its complete genome sequence was determined and analyzed. The study extends the polymorphism of BSVs in China and provides scientific clue for the evolutionary relationship with host selection of badnaviruses.

Banana streak viruses (BSV) belong to the genus Badnavirus of the family Caulimoviridae. They cause banana streak disease on banana and plantains worldwide. The recent detection of BSV in Cuba has prompted a nationwide research effort focused on the occurrence, prevalence and diversity of BSV species on dessert type banana on the island. Indexing by multiplex immunocapture-PCR (M-IC-PCR) performed on samples collected throughout the country showed that the overall prevalence of Banana streak OL virus, Banana streak GF virus and Banana streak IM virus is low in Musa acuminata genotypes in Cuba. However, the prevalence of BSV species Mysore (BSMYV) was surprisingly high in samples of cv Yangambi km5 collected from distinct and distant locations. The presence in Cuba of an as yet unreported BSV species was also investigated, showing that Banana steak VN virus is also present in Musa acuminata genotypes.

Banana plants are hosts to a large number of Banana streak virus (BSV) species. However, diagnostic methods for BSV are inadequate because of the considerable genetic and serological diversity among BSV isolates and the presence of integrated BSV sequences in some banana cultivars which leads to false positives. In this study, a sequence-nonspecific, rolling-circle amplification (RCA) technique was developed and shown to overcome these limitations for the detection and subsequent characterization of BSV isolates infecting banana. This technique was shown to discriminate between integrated and episomal BSV DNA, specifically detecting the latter in several banana cultivars known to contain episomal or integrated sequences of Banana streak Mysore virus (BSMyV), Banana streak OL virus (BSOLV), and Banana streak GF virus (BSGFV). Using RCA, the presence of BSMyV and BSOLV was confirmed in Australia, while BSOLV, BSGFV, Banana streak Uganda I virus (BSUgIV), Banana streak Uganda L virus (BSUgLV), and Banana streak Uganda M virus (BSUgMV) were detected in Uganda. This is the first confirmed report of episomally-derived BSUglV, BSUgLV, and BSUgMV in Uganda. As well as its ability to detect BSV, RCA was shown to detect two other pararetroviruses, Sugarcane bacilliform virus in sugarcane and Cauliflower mosaic virus in turnip.

Viruses are considered as major constraints to the exchange of germplasm, genetic improvement and breeding of banana and plantain (Musa spp) through the world. To date, six viruses are recognized to affect Musa spp: Banana bunchy top virus (BBTV), Banana streak viruses (BSV), Cucumber mosaic virus (CMV), Banana bract mosaic virus (BBrMV), Banana mild mosaic virus (BanMMV), Banana virus x (BVX). BBTV, the most devastating virus of banana, is currently spread in 14 countries of Africa including the Democratic Republic of Congo (DRC), where the virus was observed for the first time in 1950 in Yangambi, Kisangani region. The situation of others banana viruses remains unknown however, some of these viruses were observed in DRC bordering countries. The main aim of this work was to elucidate the epidemiological situation, the genetic variability and the origin of banana viruses in Democratic Republic of Congo. Epidemiological surveys were conducted in southwestern part of DRC, with a special emphasis on Bas Congo province, in order to search major banana viruses. Up to 666 samples were collected from at least 122 locations and analysed using PCR based method. BBTV is a multi component virus, which possesses six DNA components named DNA-R, M, N, C, U3, S. To understand the BBTV epidemiology, 52 complete sequences of DNA-R and 30 full sequences of DNA-R, U3, M, N, C, S were study. Phylogenetic analysis was carried out by isolates nucleotides sequences comparison, for all viruses detected (BBTV, BSV, CMV). Result show that BBTV is the most widespread banana virus in DRC. The main factor contributed to the spread of this threat is the human exchange of infected planting material. Data reveals a low genetic variability of BBTV isolates, which are grouped in South Pacific group. Theses BBTV isolates are close between them and with those of other sub-Saharian Africa countries. The earliest report of BBTV in Africa relates to an isolate described in Egypt in 1901. Since the earliest BBTV report in sub-Saharian Africa was in Democratic Republic of Congo in 1950, it is likely that Banana bunchy top virus spread from DRC to other SSA countries rather than from Egypt and that at least two Banana bunchy top virus introductions occurred in Africa from Java and Taiwan respectively. However, at a global scale, molecular analyses support infrequent Banana bunchy top virus dispersal events among continents. Democratic Republic of Congo seems to be the primary center of Banana bunchy top virus spread in Africa. Haplotypes analysis based on the coding region m-Rep protein showed 39 haplotypes (H1 to H39) (haplotype diversity value of 0.944±0.013). The most frequent haplotypes were H17, H9, H7 and H24 representing 31.6, 21.1, 21.1 and 27% of the BBTV isolates, respectively. Symptoms of banana streak disease including yellow streak, splitting of pseudo-stem, death of cigar leaf, were associated to the presence of Banana streak virus species (frequency = 20 %). The most widespread was Banana streak GF virus (BSGFV) (frequency = 68%) and Banana streak OL virus (BSOLV)(frequency = 25.5%). Musa acuminata cultivars are infected although no banana streak disease epidemic was reported any more, since the study revealed the transmission of BSV species from plantain (B genome) to banana (A genome). The frequency of mealybugs was about 9.3%, suggesting transmission of the disease. The sequenced isolate of BSGFV and BSOLV gather in the clade I, recognized to gathering the BSV species with endogenous counterpart. Cucumber mosaic virus was detected (frequency = 9.3%) mainly on asymptomatic samples collected. Genetic diversity analysis reveals the high similarity between Congolese CMV isolates and with South African isolates. These results suggest the hypothesis of the existence of the Cucumber mosaic virus single strain that dispersed througthout the study area. Banana bract mosaic virus was not detected in the collected samples despite the targeted sampling approach developed. The result suggests that the virus still absent in Bas Congo, Democratic Republic of Congo. Les virus constituent une contrainte majeure à l’amélioration et aux échanges de germplasm du bananier et plantain (Musa spp) dans le monde. Les études récentes rapportent que six virus affectent le bananier et plantain (Musa spp) dont le Banana bunchy top virus (BBTV), le Banana streak virus (BSV), Cucumber mosaic virus (CMV), Banana bract mosaic virus (BBrMV), Banana mild mosaic virus (BanMMV), le Banana virus x (BVX). Le BBTV est considéré comme le virus le plus dévastateur présent dans au moins 14 pays africains y compris la République démocratique du Congo (RDC) où il a été détecté pour la première fois, en 1950, à Yangambi dans la région de Kisangani. La situation des autres virus du bananier demeure inconnue malgré que certains d’entre eux aient été détectés dans les pays limitrophes de la RDC. Le principal objectif de cette thèse a été d’élucider la présence des virus impactant la culture du bananier (Musa spp.) en RDC, leurs origines et leurs diversités génétiques. Les enquêtes épidémiologiques ont été menées en vue de rechercher les principaux virus du bananier. Un accent particulier a été mis sur les zones moins investiguées en RDC, particulièrement la province du Bas Congo, à cause de sa position géographique, pour la recherche des nouveaux virus. Plus de 666 échantillons de feuilles de bananier ont été collectés dans 122 sites et analysés en utilisant la PCR comme base technique. Le BBTV est un virus à génome multipartite composé d’au moins six ADN nommés ADN-R, M, N, C, U3, S. Au total 52 séquences complètes d'ADN-R et 30 séquences complètes de M, N, C, U3, S ont été étudiées en vue de comprendre son épidémiologie. Les analyses phylogénétiques et la comparaison des séquences nucléotidiques ont été réalisées pour tous les virus détectés (BBTV, BSV, CMV). Les résultats indiquent que le BBTV est le virus du bananier le plus répandu en RDC. Le facteur humain constitue le principal moteur de dispersion de ce virus, particulièrement à travers l’échange de matériel de plantation infecté. Les données indiquent une faible variabilité génétique des isolats BBTV et leur regroupement dans le sous-groupe Sud Pacifique. Les isolats congolais de BBTV sont proches entre eux et aussi proches de ceux des autres pays d’Afrique sub-Saharienne (SSA). Les résultats confirment aussi que l’Afrique aurait subi une double introduction du BBTV venant respectivement de Java et de Taiwan. La première introduction du BBTV fut en Egypte en 1901 et la seconde en RDC en 1950. Au niveau moléculaire, les données supportent une distribution sur le continent africain - la RDC semble être un foyer primaire de dispersion en Afrique. L’analyse des haplotypes basée sur la région codante de la protéine m-Rep montre la présence de 39 haplotypes (H1 à H39) avec des valeurs de diversité de 0,944±0,013 dont les plus répandus sont H17, H9, H7 et H24, représentant respectivement 31,6 ; 21,1 ; 21,1 et 27,0 % des isolats BBTV. Les symptômes de banana streak disease incluant les stries jaunes, l’éclatement du pseudo-tronc, le dépérissement de la feuille cigare ont été associés à la présence des espèces Banana streak virus (fréquence de 20 %). Les espèces BSV les plus répandues sont Banana streak GF virus (BSGFV) (fréquence = 68 %) et Banana streak OL virus (BSOLV) (fréquence = 25,5 %). Les bananiers à génome Musa acuminata sont les plus infectés par le BSV, ce qui suggère le développement d’une épidémie BSV suite à la transmission du virus des hybrides interspécifiques (génome B) vers le bananier dessert (génome A). La fréquence de la cochenille a été évaluée à 9,3 %, ce qui renforce l’hypothèse d’une transmission de Banana streak virus. Les isolats de BSGFV et ceux de BSOLV séquencés, se groupent dans le clade I reconnu comme un clade ressemblant les espèces BSV ayant une contrepartie endogène. Cucumber mosaic virus a été détecté (fréquence = 9,3%) principalement sur les échantillons asymptomatiques. L’analyse de la diversité génétique révèle une similarité élevée entre les isolats de la RDC. Ce qui appuie l’hypothèse de l’existence d’une unique souche de CMV qui se disperse à travers le pays. Malgré l’approche de collecte d’échantillons utilisée, Banana bract mosaic virus n’a pas été détecté dans les échantillons collectés. Ces résultats suggèrent que Banana bract mosaic virus demeure absent du Bas Congo, RDC. (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2016