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A comprehensive survey reveals high viral diversity and novel infections in pea and broad bean crops in Yunnan Province, China
Journal article   Open access   Peer reviewed

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

Wenhui Li, Shuting Yu, Changfang Long, Guanlin Tan, Steve Wylie, Hong Cai, Xiaojiao Chen, Pingxiu Lan and Fan Li
Journal of Integrative Agriculture, In Press, Journal Pre-proof
2026
DOI: https://doi.org/10.1016/j.jia.2026.02.018
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Open Access CC BY-NC-ND V4.0

Abstract

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

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