Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing

Abstract

The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.

Analyses of orthotospovirus populations and dispersion under different environmental conditions in Brazil and in the Dominican Republic

“…TCSV was also found infecting tobacco plants for the first time in the province of Santiago. Taken together, these findings clearly demonstrate that TCSV was introduced in the Dominican Republic, probably around five years ago (Almeida et al 2014;Martínez et al 2018) and was able to infect several crops and spread to different vegetablegrowing areas in the country. The transmission efficiency of TSWV and TCSV by the main thrips species present on the Island will likely determine which orthotospovirus will prevail.…”

“…The acquisition by TCSV of the M RNA region from GRSV could have influenced the recent spread of TCSV to North and Central America and to the Caribbean basin, including the Dominican Republic (Almeida et al 2014;Webster et al 2015;Londoño et al 2012;Martínez et al 2018), but that hypothesis remains to be proven.…”

“…In the Dominican Republic, TSWV was reported for the first time in 2009, simultaneously with the identification of F. occidentalis on the Island. Recently, with the introduction of new virus species, vegetable production has been threatened by orthotospovirus such as TCSV (Martínez et al 2013;Almeida et al 2014;Martínez et al 2018).…”

Tomato Chlorotic Spot Virus (TCSV) Putatively Incorporated a Genomic Segment of Groundnut Ringspot Virus (GRSV) Upon a Reassortment Event

“…In any case, it may have increased the virus adaptation to both plant and invertebrate hosts since the parental genotypes of TCSV have not been reported so far. It is worthy to notice that in recent years, TCSV have significantly increased its spread to other regions of the Americas [ 27 , 28 , 29 , 30 , 31 , 32 ] as a possible biological advantage of these recurrent interspecific reassortment events.…”

Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

“…Evidence increasingly supports a role for HBV genotype in influencing disease progression, including risk of developing chronic infection, e-antigen seroconversion, transmission mode and the development of hepatocellular carcinoma [ 7, 8 ]. Studies often refer to ‘wild-type’ virus [ 8, 9 ], but wild-type for one genotype may not reflect consensus for other genotypes [ 10, 11 ]. Understanding the diverse range of HBV strains circulating globally, and their associations with disease, will allow us to move towards a more specific and precise approach to analysis.…”