Detection and comparative genomic analysis of a fossil pithovirus-like giant virus from clinical samples

We report the existence of a novel pithovirus, denoted pithovirus swab (PTVSW), in clinical samples from 70 patients with acute respiratory infections and febrile illness in Shandong Province in China. A near-complete genome sequence of PTVSW was assembled. Similar to the prototype 'fossil' pithoviruses pithovirus sibericum (PTVS) and pithovirus mammoth (PTVMM), PTVSW comprised a genome -611-kb in length with 36.34% of GC content, and sharing over 96.7% average nucleotide identity with the fossil strains. Interestingly, a unique insertion domain was observed in the RNApolB gene sequences of PTVSW, as well as pithovirus massiliensis isolated from sewage, yet was absent in PTVS and PTVMM. Among the 59,981 sites detected with single nucleotide variations (SNVs), 14,445 had shifted from PTVS, and over 75% of the observed variations were intra-host-SNVs. PTVSW also exhibited high transcriptional activity within clinical samples and several highly expressed genes were identified to be associated with viral replication, transcription, and translation.