Begomovirus

Begomovirus is a genus of viruses, in the family Geminiviridae. They are plant viruses that as a group have a very wide host range, infecting dicotyledonous plants. Worldwide they are responsible for a considerable amount of economic damage to many important crops such as tomatoes, beans, squash, cassava and cotton. There are 445 species in this genus.

Morphology
Virus particles are non-enveloped. The nucleocapsid is 38 nanometers (nm) long and 15–22 nm in diameter. While particles have basic icosahedral symmetry, they consist of two incomplete icosahedra—missing one vertex—joined together. There are 22 capsomeres per nucleocapsid.

Genome
Single stranded closed circular DNA. Many begomoviruses have a bipartite genome: this means that the genome is segmented into two segments (referred to as DNA A and DNA B) that are packaged into separate particles. Both segments are generally required for successful symptomatic infection in a host cell but DNA B is dependent for its replication upon DNA A, which can in some begomoviruses apparently cause normal infections on its own. The DNA A segment typically encodes five to six proteins including replication protein Rep, coat protein and transport and/or regulatory proteins. This component is homologous to the genomes of all other geminiviruses. The proteins encoded on it are required for replication (Rep), control of gene expression, overcoming host defenses, encapsidation (coat protein) and insect transmission. The DNA B segment encodes two different movement proteins. These proteins have functions in intra- and intercellular movement in host plants.

The A and B components share little sequence identity with the exception of a ~200 nucleotide sequence with typically >85% identity known as the common region. This region includes an absolutely conserved (among geminiviruses) hairpin structure and repeated sequences (known as 'iterons') that are the recognition sequences for binding of the replication protein (Rep). Within this loop there is a nonanucleotide sequence (TAATATTAC) that acts as the origin (ori) of virion strand DNA replication.

Component exchange (pseudorecombination) occurs in this genus. The usual mechanism of pseudorecombination is by a process known as 'regulon grafting': the A component donates its common region by recombination to the B component being captured. This results in a new dependent interaction between two components.

The proteins in this genus may lie either on the sense strand (positive orientation) or its complement (negative orientation).

Genes

 * Segment A
 * V1 (R1)—positive orientation: Coat protein—29.7 kilodaltons (kDa)
 * V2—positive orientation: Movement protein (precoat ORF)—12.8 kDa
 * C1 (L1)—negative orientation: Replication initiation protein (Rep)—40.2 kDa
 * C2: (L2)—negative orientation: Transcription activator protein (TrAP)—19.6 kDa
 * C3: (L3)—negative orientation: Replication enhancer—15.6 kDa
 * C4:—negative orientation: May determine symptom expression—12.0 kDa
 * Segment B
 * V1 (R1)—positive orientation: Nuclear shuttle protein—33.1 kDa
 * C1 (L1)—negative orientation: Movement protein—29.6 kDa

Virology
Smaller than unit length virus components—deletion mutants—are common in infections. These are known as defective interfering (di) DNAs due to their capacity to interfere with virus infection. They reduce virus DNA levels and symptom severity.

Phylogenetics
The two components of the genome have very distinct molecular evolutionary histories and likely to be under very different evolutionary pressures. The DNA B genome originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and has subsequently evolved to become an essential genome component.

More than 133 begomovirus species having monopartite genomes are known: all originate from the Old World. No monopartite begomoviruses native to the New World have yet been identified.

Phylogenetic analysis is based on the A component. B components may be exchanged between species and may result in new species.

Analysis of the genus reveals a number of clades. The main division is between the Old and New World strains. The Old World strains can be divided into African, Indian, Japanese and other Asian clades with a small number of strains grouping outside these. The New World strains divide into Central and Southern America strains.

Along with these main groupings are a number of smaller clades. One group infecting a range of legumes originating from India and Southeast Asia (informally 'Legumovirus') and a set of viruses isolated from Ipomoea species originating from America, Asia and Europe (informally 'Sweepovirus') appear to be basal to all the other species. Two species isolated from Corchorus from Vietnam (informally 'Corchovirus') somewhat unexpectedly group with the New World species.

Transmission
The virus is obligately transmitted by an insect vector, which can be the whitefly Bemisia tabaci or can be other whiteflies. This vector allows rapid and efficient propagation of the virus because it is an indiscriminate feeder. The vector transmits in a persistent, circulative, non-propagative manner.

This USDA document describes a 5-year plan starting in 1992 to mitigate whiteflies.

Diseases
Several begomoviruses cause severe diseases all over the world. Those begomovirus species infecting tomato such as Tomato yellow leaf curl virus (TYLCV) and Tomato yellow mosaic virus (ToYMV), first identified in the late 1980s, cause significant economic losses worldwide. In countries where these viruses have become widespread such as Trinidad, the Dominican Republic, Mexico and much of Central America, Israel, as well as across Southeast Asia including Thailand, Cambodia, Indonesia, and India, these diseases in tomato and other crops including pepper, and eggplant, can cause an estimated yield loss of 50–60%. Begomoviruses infecting pepper (Capsicum spp.) such as Pepper leaf curl virus and Chilli leaf curl virus also cause significant losses worldwide. Disease is typically manifested in the infected plant as chlorosis, leaf distortion, flower bud absicion and crinkling and stunting. In countries where these viruses have become widespread across Southeast Asia including Thailand, Cambodia, Indonesia, Sri Lanka, and India, these diseases in pepper and other crops including tomato, cucumber, pumpkin, melon, and eggplant, can cause an estimated yield loss of 40–70%. Bean golden yellow mosaic virus (BGYMV) causes a serious disease in bean species within Central America, the Caribbean and southern Florida.

Species

 * Abutilon golden mosaic virus
 * Abutilon mosaic Bolivia virus
 * Abutilon mosaic Brazil virus
 * Abutilon mosaic virus
 * African cassava mosaic Burkina Faso virus
 * African cassava mosaic virus
 * Ageratum enation virus
 * Ageratum leaf curl Sichuan virus
 * Ageratum leaf curl virus
 * Ageratum yellow vein Hualian virus
 * Ageratum yellow vein Sri Lanka virus
 * Ageratum yellow vein virus
 * Allamanda leaf curl virus
 * Allamanda leaf mottle distortion virus
 * Alternanthera yellow vein virus
 * Andrographis yellow vein leaf curl virus
 * Asystasia mosaic Madagascar virus
 * Bean bushy stunt virus
 * Bean calico mosaic virus
 * Bean chlorosis virus
 * Bean dwarf mosaic virus
 * Bean golden mosaic virus
 * Bean golden yellow mosaic virus
 * Bean latent virus
 * Bean leaf crumple virus
 * Bean white chlorosis mosaic virus
 * Bean yellow mosaic Mexico virus
 * Bhendi yellow vein Bhubhaneswar virus
 * Bhendi yellow vein Haryana virus
 * Bhendi yellow vein mosaic Delhi virus
 * Bhendi yellow vein mosaic virus
 * Bitter gourd yellow mosaic virus
 * Blainvillea yellow spot virus
 * Blechum interveinal chlorosis virus
 * Blechum yellow vein virus
 * Boerhavia yellow spot virus
 * Cabbage leaf curl Jamaica virus
 * Cabbage leaf curl virus
 * Capraria yellow spot virus
 * Cassava mosaic Madagascar virus
 * Catharanthus yellow mosaic virus
 * Centrosema yellow spot virus
 * Chayote yellow mosaic virus
 * Chenopodium leaf curl virus
 * Chilli leaf curl Ahmedabad virus
 * Chilli leaf curl Bhavanisagar virus
 * Chilli leaf curl Gonda virus
 * Chilli leaf curl India virus
 * Chilli leaf curl Kanpur virus
 * Chilli leaf curl Sri Lanka virus
 * Chilli leaf curl Vellanad virus
 * Chilli leaf curl virus
 * Chino del tomate Amazonas virus
 * Chino del tomate virus
 * Cleome golden mosaic virus
 * Cleome leaf crumple virus
 * Clerodendron golden mosaic virus
 * Clerodendron yellow mosaic virus
 * Clerodendrum golden mosaic China virus
 * Clerodendrum golden mosaic Jiangsu virus
 * Cnidoscolus mosaic leaf deformation virus
 * Coccinia mosaic Tamil Nadu virus
 * Common bean mottle virus
 * Common bean severe mosaic virus
 * Corchorus golden mosaic virus
 * Corchorus yellow spot virus
 * Corchorus yellow vein Cuba virus
 * Corchorus yellow vein mosaic virus
 * Corchorus yellow vein virus
 * Cotton chlorotic spot virus
 * Cotton leaf crumple virus
 * Cotton leaf curl Alabad virus
 * Cotton leaf curl Bangalore virus
 * Cotton leaf curl Barasat virus
 * Cotton leaf curl Gezira virus
 * Cotton leaf curl Kokhran virus
 * Cotton leaf curl Multan virus
 * Cotton yellow mosaic virus
 * Cowpea bright yellow mosaic virus
 * Cowpea golden mosaic virus
 * Crassocephalum yellow vein virus
 * Croton golden mosaic virus
 * Croton yellow vein mosaic virus
 * Cucumber chlorotic leaf virus
 * Cucurbit leaf crumple virus
 * Dalechampia chlorotic mosaic virus
 * Datura leaf curl virus
 * Datura leaf distortion virus
 * Deinbollia mosaic virus
 * Desmodium leaf distortion virus
 * Desmodium mottle virus
 * Dicliptera yellow mottle Cuba virus
 * Dicliptera yellow mottle virus
 * Dolichos yellow mosaic virus
 * Duranta leaf curl virus
 * East African cassava mosaic Cameroon virus
 * East African cassava mosaic Kenya virus
 * East African cassava mosaic Malawi virus
 * East African cassava mosaic virus
 * East African cassava mosaic Zanzibar virus
 * Eclipta yellow vein virus
 * Emilia yellow vein Fujian virus
 * Emilia yellow vein Thailand virus
 * Emilia yellow vein virus
 * Erectites yellow mosaic virus
 * Eupatorium yellow vein mosaic virus
 * Eupatorium yellow vein virus
 * Euphorbia leaf curl Guangxi virus
 * Euphorbia leaf curl virus
 * Euphorbia mosaic Peru virus
 * Euphorbia mosaic virus
 * Euphorbia yellow leaf curl virus
 * Euphorbia yellow mosaic virus
 * French bean leaf curl virus
 * Hedyotis uncinella yellow mosaic virus
 * Hemidesmus yellow mosaic virus
 * Hibiscus golden mosaic virus
 * Hibiscus yellow vein leaf curl virus
 * Hollyhock leaf curl virus
 * Hollyhock yellow vein mosaic virus
 * Hollyhock yellow vein virus
 * Honeysuckle yellow vein virus
 * Horsegram yellow mosaic virus
 * Hybanthus yellow mosaic virus
 * Indian cassava mosaic virus
 * Jacquemontia mosaic Yucatan virus
 * Jacquemontia yellow mosaic virus
 * Jacquemontia yellow vein virus
 * Jatropha leaf curl Gujarat virus
 * Jatropha leaf curl virus
 * Jatropha leaf yellow mosaic virus
 * Jatropha mosaic India virus
 * Jatropha mosaic Nigeria virus
 * Jatropha mosaic virus
 * Jatropha yellow mosaic virus
 * Kudzu mosaic virus
 * Leonurus mosaic virus
 * Lindernia anagallis yellow vein virus
 * Lisianthus enation leaf curl virus
 * Ludwigia yellow vein Vietnam virus
 * Ludwigia yellow vein virus
 * Luffa yellow mosaic virus
 * Lycianthes yellow mosaic virus
 * Macroptilium bright mosaic virus
 * Macroptilium common mosaic virus
 * Macroptilium golden mosaic virus
 * Macroptilium mosaic Puerto Rico virus
 * Macroptilium yellow mosaic Florida virus
 * Macroptilium yellow mosaic virus
 * Macroptilium yellow spot virus
 * Macroptilium yellow vein virus
 * Malvastrum bright yellow mosaic virus
 * Malvastrum leaf curl Philippines virus
 * Malvastrum leaf curl virus
 * Malvastrum yellow mosaic Helshire virus
 * Malvastrum yellow mosaic Jamaica virus
 * Malvastrum yellow mosaic virus
 * Malvastrum yellow vein Cambodia virus
 * Malvastrum yellow vein Honghe virus
 * Malvastrum yellow vein Lahore virus
 * Malvastrum yellow vein virus
 * Malvastrum yellow vein Yunnan virus
 * Melochia mosaic virus
 * Melochia yellow mosaic virus
 * Melon chlorotic leaf curl virus
 * Melon chlorotic mosaic virus
 * Melon yellow mosaic virus
 * Merremia mosaic Puerto Rico virus
 * Merremia mosaic virus
 * Mesta yellow vein mosaic Bahraich virus
 * Mimosa yellow leaf curl virus
 * Mirabilis leaf curl virus
 * Mungbean yellow mosaic India virus
 * Mungbean yellow mosaic virus
 * Ocimum golden mosaic virus
 * Ocimum mosaic virus
 * Ocimum yellow vein virus
 * Okra enation leaf curl virus
 * Okra leaf curl Oman virus
 * Okra mottle virus
 * Okra yellow crinkle virus
 * Okra yellow mosaic Mexico virus
 * Oxalis yellow vein virus
 * Papaya leaf crumple virus
 * Papaya leaf curl China virus
 * Papaya leaf curl Guandong virus
 * Papaya leaf curl virus
 * Papaya severe leaf curl virus 1
 * Papaya severe leaf curl virus 2
 * Papaya yellow leaf curl virus
 * Passionfruit leaf curl virus
 * Passionfruit leaf distortion virus
 * Passionfruit severe leaf distortion virus
 * Pavonia mosaic virus
 * Pavonia yellow mosaic virus
 * Pea leaf distortion virus
 * Pedilanthus leaf curl virus
 * Pepper blistering leaf virus
 * Pepper golden mosaic virus
 * Pepper huasteco yellow vein virus
 * Pepper leaf curl Bangladesh virus
 * Pepper leaf curl Lahore virus
 * Pepper leaf curl virus
 * Pepper leaf curl Yunnan virus
 * Pepper leafroll virus
 * Pepper yellow leaf curl Aceh virus
 * Pepper yellow leaf curl Indonesia virus
 * Pepper yellow leaf curl Indonesia virus 2
 * Pepper yellow leaf curl Thailand virus
 * Pepper yellow leaf curl virus
 * Pepper yellow vein Mali virus
 * Polygala garcinii virus
 * Potato yellow mosaic Panama virus
 * Potato yellow mosaic virus
 * Pouzolzia golden mosaic virus
 * Pouzolzia mosaic Guangdong virus
 * Pouzolzia yellow mosaic virus
 * Premna leaf curl virus
 * Pumpkin yellow mosaic virus
 * Ramie mosaic Yunnan virus
 * Rhynchosia golden mosaic Havana virus
 * Rhynchosia golden mosaic Sinaloa virus
 * Rhynchosia golden mosaic virus
 * Rhynchosia mild mosaic virus
 * Rhynchosia rugose golden mosaic virus
 * Rhynchosia yellow mosaic India virus
 * Rhynchosia yellow mosaic virus
 * Rose leaf curl virus
 * Sauropus leaf curl virus
 * Senecio yellow mosaic virus
 * Senna leaf curl virus
 * Sida angular mosaic virus
 * Sida bright yellow mosaic virus
 * Sida chlorotic leaf virus
 * Sida chlorotic mottle virus
 * Sida chlorotic vein virus
 * Sida ciliaris golden mosaic virus
 * Sida common mosaic virus
 * Sida golden mosaic Braco virus
 * Sida golden mosaic Brazil virus
 * Sida golden mosaic Buckup virus
 * Sida golden mosaic Costa Rica virus
 * Sida golden mosaic Florida virus
 * Sida golden mosaic Lara virus
 * Sida golden mosaic virus
 * Sida golden mottle virus
 * Sida golden yellow spot virus
 * Sida golden yellow vein virus
 * Sida interveinal bright yellow virus
 * Sida leaf curl virus
 * Sida micrantha mosaic virus
 * Sida mosaic Alagoas virus
 * Sida mosaic Bolivia virus 1
 * Sida mosaic Bolivia virus 2
 * Sida mosaic Sinaloa virus
 * Sida mottle Alagoas virus
 * Sida mottle virus
 * Sida yellow blotch virus
 * Sida yellow golden mosaic virus
 * Sida yellow leaf curl virus
 * Sida yellow mosaic Alagoas virus
 * Sida yellow mosaic China virus
 * Sida yellow mosaic virus
 * Sida yellow mosaic Yucatan virus
 * Sida yellow mottle virus
 * Sida yellow net virus
 * Sida yellow vein Vietnam virus
 * Sida yellow vein virus
 * Sidastrum golden leaf spot virus
 * Siegesbeckia yellow vein Guangxi virus
 * Siegesbeckia yellow vein virus
 * Solanum mosaic Bolivia virus
 * South African cassava mosaic virus
 * Soybean blistering mosaic virus
 * Soybean chlorotic blotch virus
 * Soybean mild mottle virus
 * Spilanthes yellow vein virus
 * Spinach yellow vein virus
 * Squash leaf curl China virus
 * Squash leaf curl Philippines virus
 * Squash leaf curl virus
 * Squash leaf curl Yunnan virus
 * Squash mild leaf curl virus
 * Sri Lankan cassava mosaic virus
 * Stachytarpheta leaf curl virus
 * Sunn hemp leaf distortion virus
 * Sweet potato golden vein Korea virus
 * Sweet potato leaf curl Canary virus
 * Sweet potato leaf curl China virus
 * Sweet potato leaf curl Georgia virus
 * Sweet potato leaf curl Guangxi virus
 * Sweet potato leaf curl Henan virus
 * Sweet potato leaf curl Hubei virus
 * Sweet potato leaf curl Sao Paulo virus
 * Sweet potato leaf curl Shandong virus
 * Sweet potato leaf curl Sichuan virus 1
 * Sweet potato leaf curl Sichuan virus 2
 * Sweet potato leaf curl South Carolina virus
 * Sweet potato leaf curl virus
 * Sweet potato mosaic virus
 * Synedrella yellow vein clearing virus
 * Telfairia golden mosaic virus
 * Tobacco curly shoot virus
 * Tobacco leaf curl Comoros virus
 * Tobacco leaf curl Cuba virus
 * Tobacco leaf curl Dominican Republic virus
 * Tobacco leaf curl Pusa virus
 * Tobacco leaf curl Thailand virus
 * Tobacco leaf curl Yunnan virus
 * Tobacco leaf curl Zimbabwe virus
 * Tobacco leaf rugose virus
 * Tobacco mottle leaf curl virus
 * Tobacco yellow crinkle virus
 * Tomato bright yellow mosaic virus
 * Tomato bright yellow mottle virus
 * Tomato chino La Paz virus
 * Tomato chlorotic leaf curl virus
 * Tomato chlorotic leaf distortion virus
 * Tomato chlorotic mottle Guyane virus
 * Tomato chlorotic mottle virus
 * Tomato common mosaic virus
 * Tomato curly stunt virus
 * Tomato dwarf leaf virus
 * Tomato enation leaf curl virus
 * Tomato golden leaf distortion virus
 * Tomato golden leaf spot virus
 * Tomato golden mosaic virus
 * Tomato golden mottle virus
 * Tomato golden vein virus
 * Tomato interveinal chlorosis virus
 * Tomato latent virus
 * Tomato leaf curl Anjouan virus
 * Tomato leaf curl Arusha virus
 * Tomato leaf curl Bangalore virus
 * Tomato leaf curl Bangladesh virus
 * Tomato leaf curl Burkina Faso virus
 * Tomato leaf curl Cebu virus
 * Tomato leaf curl China virus
 * Tomato leaf curl Comoros virus
 * Tomato leaf curl Diana virus
 * Tomato leaf curl Ghana virus
 * Tomato leaf curl Guangdong virus
 * Tomato leaf curl Guangxi virus
 * Tomato leaf curl Gujarat virus
 * Tomato leaf curl Hainan virus
 * Tomato leaf curl Hanoi virus
 * Tomato leaf curl Hsinchu virus
 * Tomato leaf curl Iran virus
 * Tomato leaf curl Japan virus
 * Tomato leaf curl Java virus
 * Tomato leaf curl Joydebpur virus
 * Tomato leaf curl Karnataka virus
 * Tomato leaf curl Karnataka virus 2
 * Tomato leaf curl Karnataka virus 3
 * Tomato leaf curl Kerala virus
 * Tomato leaf curl Kunene virus
 * Tomato leaf curl Laos virus
 * Tomato leaf curl Liwa virus
 * Tomato leaf curl Madagascar virus
 * Tomato leaf curl Mahe virus
 * Tomato leaf curl Malaysia virus
 * Tomato leaf curl Mali virus
 * Tomato leaf curl Mindanao virus
 * Tomato leaf curl Moheli virus
 * Tomato leaf curl Namakely virus
 * Tomato leaf curl New Delhi virus
 * Tomato leaf curl New Delhi virus 2
 * Tomato leaf curl New Delhi virus 4
 * Tomato leaf curl New Delhi virus 5
 * Tomato leaf curl Nigeria virus
 * Tomato leaf curl Palampur virus
 * Tomato leaf curl Patna virus
 * Tomato leaf curl Philippines virus
 * Tomato leaf curl Pune virus
 * Tomato leaf curl purple vein virus
 * Tomato leaf curl Rajasthan virus
 * Tomato leaf curl Seychelles virus
 * Tomato leaf curl Sinaloa virus
 * Tomato leaf curl Sri Lanka virus
 * Tomato leaf curl Sudan virus
 * Tomato leaf curl Sulawesi virus
 * Tomato leaf curl Taiwan virus
 * Tomato leaf curl Tanzania virus
 * Tomato leaf curl Toliara virus
 * Tomato leaf curl Uganda virus
 * Tomato leaf curl Vietnam virus
 * Tomato leaf curl virus
 * Tomato leaf deformation virus
 * Tomato leaf distortion virus
 * Tomato mild mosaic virus
 * Tomato mild yellow leaf curl Aragua virus
 * Tomato mosaic Havana virus
 * Tomato mosaic severe dwarf virus
 * Tomato mottle leaf curl virus
 * Tomato mottle Taino virus
 * Tomato mottle virus
 * Tomato mottle wrinkle virus
 * Tomato rugose mosaic virus
 * Tomato rugose yellow leaf curl virus
 * Tomato severe leaf curl Kalakada virus
 * Tomato severe leaf curl virus
 * Tomato severe rugose virus
 * Tomato twisted leaf virus
 * Tomato vein clearing leaf deformation virus
 * Tomato wrinkled mosaic virus
 * Tomato yellow leaf curl Axarquia virus
 * Tomato yellow leaf curl China virus
 * Tomato yellow leaf curl Guangdong virus
 * Tomato yellow leaf curl Indonesia virus
 * Tomato yellow leaf curl Kanchanaburi virus
 * Tomato yellow leaf curl Malaga virus
 * Tomato yellow leaf curl Mali virus
 * Tomato yellow leaf curl Sardinia virus
 * Tomato yellow leaf curl Shuangbai virus
 * Tomato yellow leaf curl Thailand virus
 * Tomato yellow leaf curl Vietnam virus
 * Tomato yellow leaf curl virus
 * Tomato yellow leaf curl Yunnan virus
 * Tomato yellow leaf deformation dwarf virus
 * Tomato yellow leaf distortion virus
 * Tomato yellow margin leaf curl virus
 * Tomato yellow mottle virus
 * Tomato yellow spot virus
 * Tomato yellow vein streak virus
 * Triumfetta yellow mosaic virus
 * Velvet bean golden mosaic virus
 * Velvet bean severe mosaic virus
 * Verbena mottle virus
 * Vernonia crinkle virus
 * Vernonia yellow vein Fujian virus
 * Vernonia yellow vein virus
 * Vigna yellow mosaic virus
 * Vinca leaf curl virus
 * Watermelon chlorotic stunt virus
 * West African Asystasia virus 1
 * West African Asystasia virus 2
 * West African Asystasia virus 3
 * Whitefly-associated begomovirus 1
 * Whitefly-associated begomovirus 2
 * Whitefly-associated begomovirus 3
 * Whitefly-associated begomovirus 4
 * Whitefly-associated begomovirus 6
 * Whitefly-associated begomovirus 7
 * Wissadula golden mosaic virus
 * Wissadula yellow mosaic virus