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In this report, we present the first description of nine complete genome sequences of a new strain of chayote yellow mosaic virus (ChaYMV, genus Begomovirus, family Geminiviridae), provisionally named Côte d'Ivoire (ChaYMV-CI), isolated from bitter melon (Momordica charantia) leaf samples showing yellow mosaic symptoms collected in the region of Abidjan in Côte d'Ivoire in 2013 and 2019. The nucleotide sequences of ChaYMV-CI DNA-A-like genome share the highest nucleotide sequence identities (91.8–92.5%) with those of ChaYMV isolates from Benin and Cameroon. Phylogenetic analysis confirmed the segregation of ChaYMV isolates into two distinct clades and their affiliation to Old World monopartite begomoviruses. The discovery of a new strain of ChaYMV in West Africa, at the limit of the taxonomic demarcation threshold for begomoviruses (91%), call for further investigations into the molecular diversity, geographical distribution and host range of ChaYMV in Western Africa. [ABSTRACT FROM AUTHOR]

In this report, we present the first description of the complete genome sequences of a new monopartite begomovirus isolated from tomato with symptoms of interveinal yellowing of leaves collected in the region of Worodougou in the northwest of Côte d'Ivoire and provisionally named "tomato interveinal yellowing virus" (ToIYV). The DNA-A-like nucleotide sequences of ToIYV share the highest nucleotide sequence identity (83%) with tobacco leaf curl Zimbabwe virus (ToLCZWV). Phylogenetic analysis confirmed that ToIYV is related to Old World monopartite begomoviruses. The discovery of a member of a new virus species on diseased tomato plants confirms the high genetic diversity in monopartite begomoviruses in West Africa and stresses the importance of maintaining epidemiological crop surveillance. [ABSTRACT FROM AUTHOR]

Nine complete nucleotide sequences of geminialphasatellites (subfamily Geminialphasatellitinae, family Alphasatellitidae) recovered from the wild Poaceae Sorghum arundinaceum collected in Reunion are described and analyzed. While the helper geminivirus was identified as an isolate of maize streak virus (genus Mastrevirus, family Geminiviridae), the geminialphasatellite genomes were most closely related to, and shared ~63% identity with, clecrusatellites. Even though the geminialphasatellite molecules lack an adenine rich-region, they have the typical size of geminialphasatellites, encode a replication-associated protein in the virion sense, and have probable stem-loop structures at their virion-strand origins of replication. According to the proposed geminialphasatellite species and genus demarcation thresholds (88% and 70% nucleotide identity, respectively), the genomes identified here represent a new species (within a new genus) for which we propose the name "Sorghum mastrevirus-associated alphasatellite" (genus "Sorgasalphasatellite"). [ABSTRACT FROM AUTHOR]

Using high-throughput sequencing of small interfering RNAs (siRNAs), virion-associated nucleic acid (VANA), and double stranded RNAs (dsRNAs), we have determined the complete genome sequences of Comorian isolates of two ipomoviruses, cassava brown streak virus (CBSV) and a divergent isolate of Ugandan cassava brown streak virus (UCBSV-KM) representing a new strain of this virus. While the large ORF of CBSV shares the highest nucleotide sequence identity (95.9%) with a Tanzanian isolate of CBSV, the large UCBSV-KM ORF shares the highest nucleotide sequence identity (77.5%) with a Malawian isolate of UCBSV. This low value is near the species demarcation threshold for the family Potyviridae (<76%). Phylogenetic analysis confirms that UCBSV-KM represents a new lineage that is genetically distinct from the currently described UCBSV strains. [ABSTRACT FROM AUTHOR]

This is the first description of the complete genome sequence of a new monopartite begomovirus isolated from tomato with symptoms of tomato (yellow) leaf curl disease collected in northwestern Namibia, which we provisionally name "tomato leaf curl Kunene virus". The DNA-A-like nucleotide sequence shares the highest nucleotide sequence identity (82.8%) with tobacco leaf curl Zimbabwe virus (ToLCZWV). Phylogenetic analysis confirmed its affiliation with Old World monopartite begomoviruses. The discovery of a new begomovirus in a vegetable plant in Namibia highlights the importance of maintaining epidemiological surveillance in southern Africa. [ABSTRACT FROM AUTHOR]

This is the first description of the complete genome sequence of a new monopartite begomovirus isolated from tomato with symptoms of tomato (yellow) leaf curl disease collected in the Seychelles. The DNA-A-like nucleotide sequences share the highest nucleotide sequence identity (84%) with tomato leaf curl Anjouan virus (ToLCAnjV) from the Comoros islands. Phylogenetic analysis confirmed its recombinant nature and its relationship to Old World monopartite and bipartite begomoviruses. This discovery of a new member of a species confirms the high genetic diversity of begomoviruses in the south-western Indian Ocean islands. [ABSTRACT FROM AUTHOR]

This is the first description of the complete genome sequence of a new bipartite begomovirus isolated from tomato ( Solanum lycopersicum) in French Guiana, for which we propose the tentative name 'tomato chlorotic mottle Guyane virus' (ToCMoGFV). DNA-A and -B nucleotide sequences of ToCMoGFV are only distantly related to known New World begomoviruses. They share the highest nucleotide sequence identity of 80 % with the Brazilian isolates of macroptilium yellow spot virus (MacYSV) and 73 % with soybean chlorotic spot virus (SBCSV). Phylogenetic analysis demonstrated that this novel virus belongs to a new lineage of New World bipartite begomoviruses. The discovery of this new virus confirms the high genetic diversity of begomoviruses in Latin America. [ABSTRACT FROM AUTHOR]

Two complete nucleotide sequences of an alphasatellite isolated from a cassava plant with mosaic disease symptoms in Madagascar are described and analyzed. While the helper begomovirus was identified as an isolate of East African cassava mosaic Kenya virus (EACMKV), its associated alphasatellite was most closely related (80 % nucleotide sequence identity) to cotton leaf curl Gezira alphasatellite. These satellite molecules have typical features of alphasatellites, with a single gene in the virion sense, an A-rich region and a stem-loop structure. According to the proposed species demarcation threshold of alphasatellites (83 % nucleotide identity), they are isolates of a new species for which we propose the name 'Cassava mosaic alphasatellite'. [ABSTRACT FROM AUTHOR]

Cassava mosaic geminiviruses (CMGs) are implicated in cassava mosaic disease (CMD), the main constraint to cassava production in Africa. Here, we report the complete nucleotide sequences of the DNA-A and DNA-B of a newly characterized CMG found infecting cassava in Madagascar, for which we propose the tentative name cassava mosaic Madagascar virus. With the exception of two recombinant regions that resembled a CMG, we determined that the non-recombinant part of the DNA-A component is distantly related to the other CMGs. Whereas the DNA-B component possesses one recombinant region originating from an unidentified virus, the rest of the genome was seen to be closely related to members of the species East African cassava mosaic Zanzibar virus (EACMZV). Phylogenetic analysis based on complete genome sequences demonstrated that DNA-A and DNA-B components are outliers related to the clade of EACMV-like viruses and that DNA-A is related to the monopartite tomato leaf curl begomoviruses described in islands in the south-west Indian Ocean. [ABSTRACT FROM AUTHOR]

Background: Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands. Results: The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG's presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. Conclusions: Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthropic factors in CMGs spread as the principal axes of viral migration correspond with major routes of human movement and commercial trade. Finer-scale temporal analyses of CMGs to precisely scale the relative contributions of human and insect transmission to their movement dynamics will require further extensive sampling in the SWIO region. [ABSTRACT FROM AUTHOR]

Yellow vein disease (YVD) is a major problem in pepper in West Africa. Despite the recent implication of a begomovirus in YVD in Mali and in Burkina Faso, the aetiology of the disease remains unclear. Using symptomatic samples from the main vegetable cultivation regions in Burkina Faso, 10 full-length DNA-A-like begomovirus sequences were obtained, each showing 98% nucleotide identity to pepper yellow vein Mali virus (PepYVMV). The host range was determined after construction of a viral clone for agroinfection. Severe symptoms developed in tomato and Nicotiana benthamiana. By contrast, no symptoms developed in either commercial or local pepper cultivars, demonstrating that the aetiology of YVD is not only associated with the presence of PepYVMV. [ABSTRACT FROM AUTHOR]

Here, we describe for the first time the complete genome sequence of a new bipartite begomovirus in Madagascar isolated from the weed Asystasia gangetica (Acanthaceae), for which we propose the tentative name asystasia mosaic Madagascar virus (AMMGV). DNA-A and -B nucleotide sequences of AMMGV were only distantly related to known begomovirus sequence and shared highest nucleotide sequence identity of 72.9 % (DNA-A) and 66.9 % (DNA-B) with a recently described bipartite begomovirus infecting Asystasia sp. in West Africa. Phylogenetic analysis demonstrated that this novel virus from Madagascar belongs to a new lineage of Old World bipartite begomoviruses. [ABSTRACT FROM AUTHOR]

Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We undertook a temporally-scaled, phylogeographic analysis of all publicly available, full genome sequences of TYLCV, together with 70 new genome sequences from Australia, Iran and Mauritius. This revealed that whereas epidemics in Australia and China likely originated through multiple independent viral introductions from the East-Asian region around Japan and Korea, the New Caledonian epidemic was seeded by a variant from the Western Mediterranean region and the Mauritian epidemic by a variant from the neighbouring island of Reunion. Finally, we show that inter-continental scale movements of TYLCV to East Asia have, at least temporarily, ceased, whereas long-distance movements to the Americas and Australia are probably still ongoing. [ABSTRACT FROM AUTHOR]