Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

Nakamura, Shota; Yang, Cheng-Song; Sakon, Naomi; Ueda, Mayo; Tougan, Takahiro; Yamashita, Akifumi; Goto, Naohisa; Takahashi, Kazuo; Yasunaga, Teruo; Ikuta, Kazuyoshi; Mizutani, Tetsuya; Okamoto, Yoshiko; Tagami, Michihira; Morita, Ryoji; Maeda, Norihiro; Kawai, Jun; Hayashizaki, Yoshihide; Nagai, Yoshiyuki; Horii, Toshihiro; Iida, Tetsuya; Nakaya, Takaaki

In addition to these human viruses, several plant virus-derived sequences were also detected in the fecal samples (Table 1 ). In particular, pepper mild mottle virus (PMMV) was found in two specimens (#N1 and #N5) and was confirmed with RT-PCR (data not shown). The total number of PMMV reads outnumbered the norovirus reads in sample #N5 (Table 1 ). In addition, Kyuri green mottle mosaic virus (KGMMV) was also abundantly detected in sample #N3 (813 KGMMV-specific reads in a total 25,500 reads). KGMMV was also detected after ultracentrifugation (data not shown), suggesting that KGMMV viral particles were present in the human gut. Previously, PMMV was detected at 10 9 virions per gram of dry weight fecal matter, and was detected in 12 (66.7%) of the 18 fecal samples collected from healthy humans [31] . This previous publication also showed that fecal PMMV was infectious to host plants [31] . Therefore, these plant-derived viruses may retain their infectivity in the feces and may even be present in diarrhea. Almost all of the detected viruses, except for the citrus tristeza virus, a member of the Closterovirus group, belong to the Tobamovirus group (Table 1) . It is currently unknown if there is an interaction between these plus-stranded RNA viruses and norovirus. The most abundantly detected PMMV was also found in healthy humans [31] . Although the previous paper [31] reported that there is a lack of evidence to show that active replication of PMMV occurs in human feces, further investigations regarding plant virus replication in the human gut (epithelial cells) seem necessary.