A comprehensive survey reveals high viral diversity and novel infections in pea and broad bean crops in Yunnan Province, China

doi:10.1016/j.jia.2026.02.018

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Wenhui Li^1*, Shuting Yu^1*, Changfang Long^1*, Guanlin Tan², Steve Wylie³, Hong Cai¹, Xiaojiao Chen¹, Pingxiu Lan¹^#, Fan Li¹^#

¹ State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China

² Modern Education Technology Center, Yunnan Agricultural University, Kunming 650201, China

³ Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia

Highlights

l A total of 18 viruses were detected in pea and 17 in broad bean in Yunnan Province, China. Virus co-infections are common in both crops, and their distribution exhibits significant regional variation.

l A novel enamovirus, designated pea enamovirus (PEnV‑3) and provisionally named Enamovirus pisi, has been identified and characterized from both pea and broad bean, representing the first report of this virus species.

l Brassica yellows virus (BrYV), tomato yellow mottle-associated virus (TYMaV), Bidens mottle virus (BiMoV) and Vicia cryptic virus (VCV) are reported for the first time infecting pea. Additionally, BrYV and TYMaV represent the first documented infections of broad bean by these viruses.

Abstract
References

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摘要

[目的]豌豆（Pisum sativum）和蚕豆（Vicia faba）是全球重要的豆类作物，其生产常受病毒病害威胁。云南省常年温和的气候和连作制度为病毒病的发生与传播提供了有利条件。[方法]2020—2022年，对云南省昆明市、玉溪市、保山市、楚雄州、大理市、红河州6个地区的豌豆、蚕豆主要种植区进行病毒病调查，并将采集到的261份豌豆和164份蚕豆典型症状样品进行高通量测序及RT-PCR检测。[结果]结果共鉴定出17种（包括一种新病毒）病毒共同侵染两种作物，且在豌豆中还单独发现芜菁黄化病毒（Turnip yellows virus，TuYV）的侵染。新病毒（暂时命名为PEnV-3）受基因组序列和系统发育分析结果的支持，我们建议命名为Enamovirus pisi。病毒分布分析显示，豌豆耳突花叶病毒1号（pea enation mosaic virus 1，PEMV-1）和菜豆黄花叶病毒（Bean yellow mosaic virus，BYMV）分别为豌豆和蚕豆中的优势病毒，检出率分别为54.02%和81.10%。病毒复合侵染现象普遍，豌豆与蚕豆上分别发现148和97种复合侵染类型。病毒分布在六个采样区域间差异显著。PEMV-1、豌豆种传花叶病毒（pea seed-borne mosaic virusl，PSbMV）、BYMV、芸薹黄化病毒（Brassica yellows virus，BrYV）和鹰嘴豆褪绿丛矮病毒（chickpea chlorotic stunt virus，CpCSV）分布最广，在所有区域均有出现。相比之下，野豌豆隐潜病毒（Vicia cryptic virus，VCV）仅在大理的豌豆样本中检出，而PEnV-3和三叶草黄脉病毒（clover yellow vein virus，ClYVV）则为昆明豌豆样本所特有。蚕豆中BYMV和PSbMV在五个区域被检测到，而PEnV-3同样仅限于昆明。病毒多样性以昆明豌豆（15种）和大理蚕豆（15种）最高，红河地区最低（豌豆9种，蚕豆仅BrYV）。本研究首次报道BrYV、番茄黄斑伴随病毒（tomato yellow mottle-associated virus，TYMaV）、鬼针草斑驳病毒（Bidens mottle virus，BiMoV）和VCV侵染豌豆，在国内首次报道TuYV侵染豌豆，并在云南首次鉴定出ClYVV侵染豌豆。同时，首次报道BrYV和TYMaV侵染蚕豆，在国内首次报道BiMoV侵染蚕豆，并于云南首次检出VCV和ClYVV侵染蚕豆。[结论与创新性]综上，云南省豌豆与蚕豆田间病毒多样性丰富，复合侵染普遍，分布具有明显的地理差异。研究首次报道PEnV-3新病毒并更新多种病毒发生记录，为云南省豆类病毒病害的监测与防控提供重要依据，同时也揭示了该地区作为病毒多样性热点的独特性，为病毒生态与进化研究提供新视角。

Abstract

Pea (Pisum sativum) and broad bean (Vicia faba) are important legume crops grown worldwide. Viral diseases pose a significant threat to these crops in China, particularly in Yunnan Province, where the year-round mild climate and continuous cropping systems create favorable conditions for virus infection and spread. From 2020 to 2022, a survey of viral diseases was conducted in pea and broad bean fields across six major regions of Yunnan Province, namely Kunming, Yuxi, Baoshan, Chuxiong, Dali, and Honghe. High-throughput sequencing (HTS) combined with RT-PCR was used to detect and identify viruses in 261 pea and 164 broad bean samples. Seventeen distinct viruses, including a new species, were identified in both pea and broad bean samples, whereas turnip yellows virus (TuYV) was detected only in pea samples. A novel virus, tentatively designated pea enamovirus 3 (PEnV-3), was identified based on the complete genome sequence of isolate YWD and phylogenetic analyses. Accordingly, we propose the species name Enamovirus pisi. Pea enation mosaic virus 1 (PEMV-1) and bean yellow mosaic virus (BYMV) were the most prevalent viruses detected in pea and broad bean crops, with detection rates of 54.02% and 81.10%, respectively. Co-infections with multiple viruses were common in both pea and broad bean samples, with 148 and 97 co-infected samples identified, respectively. The geographic distribution of the viruses varied considerably across the six sampling regions. PEMV-1, pea seed-borne mosaic virus (PSbMV), BYMV, Brassica yellows virus (BrYV), and chickpea chlorotic stunt virus (CpCSV) were the most widespread, occurring in all regions. In contrast, Vicia cryptic virus (VCV) was found only in pea samples from Dali, while PEnV-3 and clover yellow vein virus (ClYVV) were unique to pea samples from Kunming. In broad bean samples, BYMV and PSbMV were also the most prevalent, detected in five regions, whereas PEnV-3 was again confined to samples from Kunming. Regarding virus detection across crops and regions, Kunming exhibited the highest viral diversity in pea crops, with 15 different viruses identified, whereas Honghe had the lowest (9 viruses). Dali displayed the greatest viral diversity in broad bean crops (15 viruses), while Honghe showed the least, with BrYV as the sole virus detected. This study reveals several novel virus-host associations and previously unreported occurrences of viruses in specific region. To our knowledge, this study represents the first report of pea infection by BrYV, tomato yellow mottle-associated virus (TYMaV), Bidens mottle virus (BiMoV) and VCV. Additionally, its also documents the first report of TuYV in pea in China, as well as the first identification of ClYVV in pea in Yunnan Province. Similarly, infections of broad beans by BrYV and TYMaV are reported here for the first time. Furthermore, this study presents the first detection of BiMoV in China, and the first detections of VCV and ClYVV in Yunnan Province.

Keywords: pea broad bean high-throughput sequencing virus diversity occurrence and distribution

Online: 10 February 2026

Fund:

This research was funded by the National Key R&D Program of China (2022YFD1400700, 2022YFD1401200).

About author: Wenhui Li, E-mail: 13834612359@163.com; Shuting Yu, E-mail: 1530418085@qq.com; Changfang Long, E-mail: 1632646270@qq.com; #Correspondence Pingxiu Lan, E-mail: lanpx22@126.com; Fan Li, E-mail: fanli@ynau.edu.cn *These authors contributed equally to this study

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Cite this article:

Wenhui Li, Shuting Yu, Changfang Long, Guanlin Tan, Steve Wylie, Hong Cai, Xiaojiao Chen, Pingxiu Lan, Fan Li. 2026. A comprehensive survey reveals high viral diversity and novel infections in pea and broad bean crops in Yunnan Province, China. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.02.018

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