Metagenomic identification of human Gemykibivirus-2 (HuGkV-2) in parenterally infected blood donors from the Brazilian Amazon

•Human Gemykibivirus-2 (HuGkV-2) is an emerging virus.•HuGkV-2 DNA was identified by viral metagenomics in blood donors from the Brazilian Amazon.•HuGkV-2 was present as a co-infection with HIV, hepatitis B virus and syphilis.•HuGvK-2 may show a possible parenteral route of transmission. To metagenomically analyse blood units originating from the Brazilian Amazon and positive for parenterally transmitted infections (human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-lymphotropic virus (HTLV), Chagas disease or syphilis). Twenty plasma samples (35% HBV-positive, 10% HIV-positive, 10% HCV-positive, 20% positive for syphilis, 20% for Chagas disease, and 5% for HTLV) assembled in pools were analysed by metagenomic next-generation sequencing. The obtained raw sequencing data were submitted to a bioinformatic pipeline set up for identification of emerging viruses. The viral reads of interest were phylogenetically analysed and confirmed by PCR in the individual samples. The metagenomic analysis identified contigs belonging to the emerging human Gemykibivirus-2 (HuGkV-2) in two pools. The HuGkV-1 phylogeny demonstrated that the Amazonian isolate formed a separate cluster with other HuGkV-2 strains obtained from human hosts. The PCR confirmation detected HuGkV-1 DNA in three individual samples (15%). HuGkV-2 is an emerging virus with unknown clinical impact. The detection of HuGkV-2 DNA in blood donations positive for parenterally transmitted infections showed that HuGkV-2 can be considered as an opportunistic viral agent with a hypothetic parenteral transmission route.