Black pepper (Piper nigrum L.) is one of the most ancient spice crops in the world. Hainan Province is the largest black pepper‐producing region in China. Viral disease is one of the main factors affecting black pepper. However, there are rarely studies on black pepper viral disease in China. We performed a survey in five major black pepper‐growing counties (Qionghai, Wenchang, Wanning, Haikou and Ding'an) of Hainan Province and collected 589 samples, with virus‐like symptoms from 2014 to 2019. Various viruses were identified including cucumber mosaic virus (CMV), piper yellow mottle virus (PYMoV), Piper DNA virus 1 (PDV‐1) and Piper DNA virus 2 (PDV‐2) using small RNA deep sequencing. The RT‐PCR screening of field samples indicated three types of infection: CMV alone (5.56%), PYMoV + PDV‐1 + PDV‐2 (25.00%) and PYMoV + CMV +PDV‐1 + PDV‐2 (69.44%). The data suggested that PYMoV might be the main pathogen causing virus diseases of black pepper. Two complete genome sequences of PYMoV were obtained. Phylogenetic analysis showed that PYMoV isolates from China were placed in a branch distinct from PYMoV isolates from India. To our knowledge, this is the first report of PYMoV, PDV‐1 and PDV‐2 naturally infecting black pepper, and the first genome sequence of PYMoV in China.

The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing was performed using chieh-qua leaf samples with typical viral symptoms. The virome of chieh-qua comprises four known viruses (melon yellow spot virus (MYSV), cucurbit chlorotic yellows virus (CCYV), papaya ringspot virus (PRSV) and watermelon silver mottle virus (WSMoV) and two novel viruses: cucurbit chlorotic virus (CuCV) in the genus Crinivirus and chieh-qua endornavirus (CqEV) in the genus Alphaendornavirus. The complete genomes of the two novel viruses in chieh-qua and three other isolates of CuCV in pumpkin, watermelon and cucumber were determined and the recombination signals of pumpkin and watermelon isolates of CuCV were detected. A reverse transcriptase PCR indicated that the dominant viruses of chieh-qua in Hainan are MYSV (66.67%) and CCYV (55.56%), followed by CuCV (27.41%), WSMoV (7.41%), cucumber mosaic virus (8.15%), zucchini yellow mosaic virus (6.67%), PRSV (6.67%) and CqEV (35.56%). Our findings support diagnostic and prevalence studies of viruses infecting chieh-qua in China, enabling sustainable control strategies for cucurbit viruses worldwide.