Unexpected higher convergence of human-great ape enteric viromes in central African forest than in a European zoo: A One Health analysis

Abstract

Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this holistic study elucidates these processes, integrating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. Surprisingly, we find more enteric virome sharing between Cameroonian humans and great apes than in the zoo, a virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. In addition to physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens explain these unexpected findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.

Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics

“…Using the central pipeline, all protocols (12/12) resulted in 100% qualitative detection of the synthetic viral sequences spiked in up to 99% human background sequences (viral loads 10 4 -10 7 copies/ml, C T values [24][25][26][27][28][29][30][31]. Coverages of the viral genomes were consistently 100% for viral loads of 10 6 copies/ml or higher (C T values of 24-26) when using the Illumina protocols, and ranged from 29% 3.…”

“…This report aims to assist the implementation of viral metagenomics for pathogen detection in clinical diagnostic settings by providing insight into the efficacy of platforms and key protocol steps. Gradel et al 20 Bigi et al 21 Gradel et al 22 Rodriguez et al 23 Penner et al 24 Morfopoulou et al 25 Atkinson et al2023 18 Alawi et al 26 Kufner et al 5 Narat et al 27 Vallet et al 28 Garzaro 29 and Aboudar et al 30 Cinek et al 31 Mourik et al 19 Carbo et al 11 Reyes et al 32 De Kleine et al 33 Vanmechelen et al 34 Wollants et al 35 Vanmechelen et al 36 Van Boheemen et al 6 Pichler et al 37 a; pre-nucleic acid extraction enrichment was applied to the ATCC Virome Mix dilutions containing whole viruses. WTA; whole transcriptome amplification, SISPA; sequence-independent, single-primer amplification.…”

“…No thresholds for defining a positive result were used; that is, qualitative detection results by horizontal genome coverage and unnormalized read counts were therefore equivalent. copies/ml, C T values [24][25][26][27][28][29][30][31]. Coverages of the viral genomes were consistently 100% for viral loads of 10 6 copies/ml or higher (C T values of 24-26) when using the Illumina protocols, and ranged from 29% 3.…”