You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

Abstract

JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level

“…Another special component of TRACESPipe is the analysis of mitogenomes. Besides serving as a control for external contamination, the cross-association of the viral types with the geographical distribution of this marker can be extremely valuable in epidemiological or archaeovirological studies, as well as in forensic investigations, to evaluate the origins of unidentified individuals [ 43 , 44 ].…”

The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder

“…We searched all available JC Virus complete genomes from the NCBI database (http://www.ncbi.nlm.nih.gov/, last accessed September 14, 2021) and combined with previous research databases that identified JC Virus subtypes and population distribution (Shackelton et al, 2006;Garretto et al, 2018;Forni et al, 2020). Next, 672 available JC Virus complete genomes and 24 JC Virus genomes identified through mNGS were compared, using MUSCLE to align the sequences through Geneious (Version 10.1.2).…”

“…In reality, JC Virus may infect healthy persons latently, resulting in asymptomatic replication and sporadic detection of the virus in the urine in up to 30% of the general population (White and Khalili, 2011). Previous studies have determined the subtype of JC Virus and global distribution (Forni et al, 2020). The main subtype of JC Virus strains detected in urine of OAB patients were subtype 7B (n = 8) and subtype 7A (n = 7) and these two subtypes of JC Viruses are mainly prevalent in Asia, which was obviously inconsistent with the subtype measured by Wolfe et al, since their samples were mainly from Caucasians and African Americans (Garretto et al, 2018).…”

The landscape of persistent human DNA viruses in femoral bone

“…DNA viruses commonly establish persisting infections in humans, remaining thus, their genetic material imprinted in the tissues throughout life. These DNAs exhibit phylogeographies resembling those of humans [1], pointing to shared evolutionary and dispersal paths that can, together, add to the understanding of human population history and migrations [2][3][4][5][6][7][8]. In addition, the specific geographical distributions of DNA viruses, in both global [2,9] and local [10][11][12] scales, may provide new insights into the origins of unidentified individuals.…”

“…JCPyV´s genotypespecific global spread has been proposed as an indicator of the provenances of both modern [12] and ancient humans [13][14][15]. Although its timescale of evolution has been debated [16][17][18], recent work by Forni et al, [8] based on ~1100 worldwide strains, supports co-dispersal of this virus with major human migratory routes as well as its co-divergence with human mitochondrial and nuclear markers.…”