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International audience; Alphasatellites (family Alphasatellitidae) are circular, single-stranded DNA molecules (similar to 1-1.4 kb) that encode a replication-associated protein and have commonly been associated with some members of the families Geminiviridae, Nanoviridae, and Metaxyviridae (recently established). Here, we provide a taxonomy update for the family Alphasatellitidae following the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021. The taxonomic update includes the establishment of the new subfamily Petromoalphasatellitinae. This new subfamily includes three new genera as well as the genus Babusatellite, which previously belonged to the subfamily Nanoalphasatellitinae. Additionally, three new genera and 14 new species have been established in the subfamily Geminialphasatellitinae, as well as five new species in the subfamily Nanoalphasatellitinae.

Several species in the genus Datura (family Solanaceae) are hosts for begomoviruses (family Geminiviridae), both in the New World and the Old World. Here, we report the genome characterization of two isolates of a novel Old World monopartite begomovirus infecting Datura innoxia in Sudan, which we propose to be named "datura leaf curl virus" (DaLCV). Pairwise sequence comparisons and phylogenetic analysis showed that DaLCV isolates are related to begomoviruses causing tomato yellow leaf curl disease, a global menace for tomato crops. Thus, the novel begomovirus could pose an additional threat to tomato cultivation in Africa.

The common bean is a host for a large number of begomoviruses (genus Begomovirus, family Geminiviridae) in the New World. Based on the current taxonomic criteria established for the genus Begomovirus, two new members of this genus infecting common bean (Phaseolus vulgaris) in Cuba are herein reported. The cloned bipartite genomes, composed of DNA-A and DNA-B, showed the typical organization of the New World begomoviruses. We propose the names common bean severe mosaic virus and common bean mottle virus for the new begomovirus species.

Wild plants of the family Convolvulaceae are hosts for a few New World begomoviruses (genus Begomovirus, family Geminiviridae). In this work, we report the complete genome sequence of a new begomovirus infecting the wild convolvulaceous plant Jacquemontia tamnifolia in Venezuela. The cloned bipartite genome showed the organization of typical New World begomoviruses and was found to be phylogenetically related to those of begomoviruses from Venezuela and other Caribbean countries. Several recombination events have been shown to have occurred involving genome fragment exchange with related begomoviruses infecting crops such as tomato and cucurbits and wild plants, including Jacquemontia sp. We propose the name jacquemontia yellow vein virus (JacYVV) for this new begomovirus.

The complete genome of a bipartite begomovirus (genus Begomovirus, family Geminiviridae) infecting Jacquemontia sp. (Convolvulaceae) in Venezuela has been cloned and sequenced. Sequence comparison and phylogenetic analysis have shown that it represents an isolate of a novel species with closest relatives being two New World bipartite begomoviruses that infect Convolvulaceae, Jacquemontia mosaic Yucatan virus and Merremia mosaic virus. The DNA-As of these begomoviruses, however, share only 77.0-78.4 % nucleotide sequence identity with the DNA-A of the isolate described here, for which a recombinant origin is suggested. Based on the symptoms observed in the field, the name Jacquemontia yellow mosaic virus (JacYMV) is proposed for this novel bipartite begomovirus.

A novel bipartite legumovirus (genus Begomovirus, family Geminiviridae), that naturally infects the wild leguminous plant Desmodium sp. in Uganda, was molecularly characterized and named Desmodium mottle virus. The highest nucleotide identities for DNA-A, obtained from two field-collected samples, were 79.9% and 80.1% with the legumovirus, soybean mild mottle virus. DNA-B had the highest nucleotide identities (65.4% and 66.4%) with a typical non-legumovirus Old World begomovirus, African cassava mosaic virus. This is the first report of a legumovirus in East Africa and extends the known diversity of begomoviruses found infecting wild plants in this continent.

The complete sequences of isolates of two new bipartite begomoviruses (genus Begomovirus, family Geminiviridae) found infecting weeds in Venezuela are provided. The names proposed for these new begomoviruses are "Datura leaf distortion virus" (DLDV), isolated from a Datura stramonium L. (family Solanaceae) plant, and "Dalechampia chlorotic mosaic virus" (DCMV), isolated from infected Dalechampia sp. (family Euphorbiaceae) and Boerhavia diffusa L. (family Nyctaginaceae) plants. Phylogenetic analysis showed that these new begomoviruses segregated in two distinct clades of New World begomoviruses. To our knowledge, this is the first record of a begomovirus infecting Dalechampia sp. plants. Also, this is the first report of a begomovirus infecting Boerhavia spp. and Datura spp. in Venezuela.

Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that cause serious infections in crop plants and are often also associated with non-cultivated plants. Here, we report the detection of two new begomoviruses in Pavonia sp. (Malvaceae). Sequence comparisons and phylogenetic analysis showed that these novel viruses are related to New World begomoviruses. The nucleotide sequences of the DNA-A of both viruses had the highest similarity to abutilon mosaic Bolivia virus (AbMBoV). Based on symptoms observed in the field and considering the host, we propose the names pavonia mosaic virus (PavMV) and pavonia yellow mosaic virus (PavYMV) for these two new begomoviruses.

Wild malvaceous plants are hosts for a large number of begomoviruses (genus Begomovirus, family Geminiviridae) in both the Old World and the New World. Here, we report the complete genome sequences of two new begomoviruses from Melochia sp. plants from Brazil. The cloned bipartite genomes, composed of DNA-A and DNA-B, showed the typical organization of the New World begomoviruses but they were distantly related to the genomes of other begomoviruses. We propose the names Melochia mosaic virus and Melochia yellow mosaic virus for these begomoviruses.

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

The complete genome sequence of two isolates of the bipartite begomovirus (genus Begomovirus, family Geminiviridae) Sida golden mosaic Florida virus (SiGMFV) is presented. We propose that both isolates, found infecting Malvastrum coromandelianum (family Malvaceae) in Cuba, belong to a new strain of SiGMFV. Phylogenetic analysis showed that SiGMFV DNA-A is located in a monophyletic cluster that includes begomoviruses infecting malvaceous weeds from the Caribbean.

The complete genome sequences of isolates of two new bipartite begomoviruses (genus Begomovirus, family Geminiviridae) found infecting common bean in Venezuela are provided. The names proposed for each of these viruses are "bean yellow chlorosis virus" (BYCV) and "bean white chlorosis mosaic virus" (BWCMV). Phylogenetic analysis showed that they segregated in two distinct clades of New World begomoviruses. This is the first report of begomoviruses infecting common bean in Venezuela.

As a result of surveys conducted during the last few years to search for wild reservoirs of begomoviruses in Cuba, we detected a novel bipartite begomovirus, sida yellow mottle virus (SiYMoV), infecting Sida rhombifolia plants. The complete genome sequence was obtained, showing that DNA-A was 2622 nucleotides (nt) in length and that it was most closely related (87.6% nucleotide identity) to DNA-A of an isolate of sida golden mosaic virus (SiGMV) that infects snap beans (Phaseolus vulgaris) in Florida. The DNA-B sequence was 2600 nt in length and shared the highest nucleotide identity (75.1%) with corchorus yellow spot virus (CoYSV). Phylogenetic relationship analysis showed that both DNA components of SiYMoV were grouped in the Abutilon clade, along with begomoviruses from Florida and the Caribbean islands. We also present here the complete nucleotide sequence of a novel strain of sida yellow vein virus found infecting Malvastrum coromandelianum and an isolate of euphorbia mosaic virus that was found for the first time infecting Euphorbia heterophylla in Cuba.

Rhynchosia minima is a host for several begomoviruses, both in the Old World and the New World. In Cuba, a whitefly-transmitted disease causing yellow mosaic symptoms, suggested to be of viral origin, was described more than 30 years ago in R. minima, but no information about the nature of the viruses infecting this weed in this country is available to date. Here, we report the detection of isolates of two novel begomovirus species infecting R. minima in Cuba, which we proposed be named Rhynchosia golden mosaic Havana virus (RhGMHaV) and Rhynchosia rugose golden mosaic virus (RhRGMV). The highest nucleotide sequence identities of RhGMHaV and RhRGMV DNA-A were with isolates of Rhynchosia golden mosaic virus (78.7%) and Sida golden mosaic virus (87.5%), respectively. Phylogenetic analysis demonstrated that these novel viruses belong to two different lineages of New World begomoviruses.

A novel bipartite legumovirus (genus Begomovirus, family Geminiviridae), that naturally infects the wild leguminous plant Desmodium sp. in Uganda, was molecularly characterized and named Desmodium mottle virus. The highest nucleotide identities for DNA-A, obtained from two field-collected samples, were 79.9% and 80.1% with the legumovirus, soybean mild mottle virus. DNA-B had the highest nucleotide identities (65.4% and 66.4%) with a typical non-legumovirus Old World begomovirus, African cassava mosaic virus. This is the first report of a legumovirus in East Africa and extends the known diversity of begomoviruses found infecting wild plants in this continent.