Analysis of Coinfection Pathogens From Foot‐and‐Mouth Disease Virus Persistently Infected Cattle Using Oxford Nanopore Sequencing

The persistent infection caused by foot‐and‐mouth disease virus (FMDV) still lacks a reliable explanation, as its etiology and maintenance are intricate and potentially involve concurrent infections with multiple pathogens. In this study, we utilized the nanopore platform for direct sequencing of clinical samples obtained from cattle persistently infected with FMDV serotype O and investigated the distribution characteristics of coinfecting pathogens in their pharyngeal region. Briefly, we exploited Oxford Nanopore sequencing technology to generate high‐quality and sufficient sequence data for the comprehensive characterization of microbial genomes. Furthermore, we performed sequence comparison, alignment, and phylogenetic tree construction. Our findings revealed a total of 23 viruses in FMDV carrier bovine, with FMDV, bovine orthopneumovirus, and Choristoneura fumiferana granulovirus emerging as the top three identified pathogens. The analysis unexpectedly revealed the presence of porcine circovirus type 2 and pepper mild mottle virus among the viral genes detected in the bovine FMDV carrier. Compared to noncarrier, carrier bovine of FMDV exhibited a greater diversity and abundance of mycoplasma types as well as reads counts. Therefore, we propose that the establishment and perpetuation of persistent FMDV infection may be attributed to the simultaneous presence of other viral agents and mycoplasmas. These findings highlight the significance of investigating multipathogen coinfection in elucidating the etiology of persistent FMD virus infection.