Yield losses induced by a complex of begomoviruses are observed across all major tomato-producing areas in Brazil. Tomato severe rugose virus (ToSRV) is the most widespread begomovirus in the country. Conversely, tomato common mosaic virus (ToCmMV) displays a more restricted geographical distribution to areas associated with the Atlantic Rain Forest (ARF) biome, encompassing the States of Espírito Santo–ES, Minas Gerais–MG, and Rio de Janeiro–RJ. Here, we characterized 277 tomato-infecting isolates collected in fields located within the ARF biome from 2006 to 2018. ToSRV displayed the highest prevalence (n = 157), followed by ToCmMV (n = 95) and tomato interveinal chlorosis virus (n = 14). Four other begomoviruses were also detected, but with very low incidences. ToCmMV was the predominant begomovirus in the ARF biome up to 2014–2015 with very low ToSRV incidence. Subsequently, ToSRV became the most prevalent species in ES and RJ, but ToCmMV was still predominating in the “Zona da Mata” meso-region in MG. Due to the remarkable endemic distribution of ToCmMV, we carried out phylogeographical studies of this virus using information from all 28 available isolates with complete DNA–A sequences. The closest common ancestor of ToCmMV was more likely originated around Coimbra–MG area ≈ 25 years before the formal report of this viral species. So far, all surveys indicated tomatoes as the only natural hosts of ToCmMV with outbreaks occurring mainly (but not exclusively) in highland areas. ToSRV shows a more widespread incidence across both highland and lowland areas of the ARF biome.

在巴西的所有主要番茄产区都观察到了由 Begomovirus 复合体引起的产量损失。番茄严重皱纹病毒 (ToSRV) 是该国最普遍的 begomovirus。相反，番茄普通花叶病毒 (ToCmMV) 在与大西洋雨林 (ARF) 生物群落相关的地区显示出更有限的地理分布，包括圣埃斯皮里图-ES、米纳斯吉拉斯-MG 和里约热内卢-RJ。在这里，我们表征了 2006 年至 2018 年在 ARF 生物群落内的田间收集的 277 株番茄感染分离株。ToSRV 的流行率最高（n  = 157），其次是 ToCmMV（n  = 95）和番茄叶脉间萎黄病病毒（n = 14）。还检测到其他四种贝戈莫病毒，但发生率非常低。直到 2014-2015 年，ToCmMV 是 ARF 生物群落中的主要 begomovirus，ToSRV 发生率非常低。随后，ToSRV 成为 ES 和 RJ 中最流行的物种，但 ToCmMV 在 MG 的“Zona da Mata”中区仍占主导地位。由于 ToCmMV 的显着地方性分布，我们使用来自具有完整 DNA-A 序列的所有 28 个可用分离株的信息对该病毒进行了系统地理学研究。ToCmMV 的最接近的共同祖先更有可能起源于 Coimbra-MG 区域 ≈ 25 年前该病毒物种的正式报告。到目前为止，所有调查都表明西红柿是 ToCmMV 的唯一自然宿主，主要（但不完全）发生在高原地区。