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Enteric Virome Analysis of Non-Invasive Samples from Gorillas by Next-Generation Sequencing and Association with SIV Infection

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Enteric Virome Analysis of Non-Invasive Samples from Gorillas by Next-Generation Sequencing and Association with SIV Infection Enteric Virome Analysis of Non-Invasive Samples From Gorillas by Next-Generation Sequencing and Association With SIV Infection 1,2 1 1 3 3 1,2 Mirela D’arc , Carolina Furtado , Juliana D. Siqueira , Ahidjo Ayouba , Martine Peeters , Marcelo A. Soares 1 Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil 2 Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil 3 Institut de Recherche pour le Développement (IRD), Montpellier, France The ancestors of HIV-1 HIV-1 M HIV-1 N HIV-1 P HIV-1 O SIV Pathogenic Infections ✤ The infection in chimpanzees has already been associated with progression to an AIDS-like disease (Etienne et al., 2011; Keele et al., 2009; Rudicell et al., 2010; Moeller et al., 2013) ✤ SIVgor-infected gorilla showed different results, with bacteriome stability despite SIV infection (Moeller et al., 2015) ✤ Handley et al. (2012) reported the expansion of the ENTERIC VIROME Handley et al., 2012 associated with disease progression in an AIDS-like context Objective ✤ Identify and compare enteric virome of SIV-infected and uninfected gorillas, and to assess their impact on SIVgor pathogenesis Material & Methods: Samples Collection CAMEROON Etienne et al., 2012 Personal photos Material & Methods: RNA and DNA Libraries - 22 individuals well characterized (23 samples): - 11 SIV-infected individuals - ID74 with two samples : 8789 (31,497 cp/mL; collected in 2012) and 9725 (4,924 cp/mL; collected in 2013) - 11 uninfected individuals Material & Methods: NGS Analysis - Statistical Analyses: 99% Confidence in Fisher’s Exact Test with Bonferroni Correction Results ✤ Reads with good quality (Phred >30 and ~99 bp of length) ✤ RNA libraries: 473,357,985 reads (~14,327,235 / sample) ✤ DNA libraries: 559,920,656 reads (~24,344,376.3 / sample) Results ✤ The gorilla ID74 was resampled in two years consecutively (2012 and 2013), with different viral load results ✤ Despite the similar profiles for both samples, we noticed that the number of reads assigned for RNA libraries was higher in the sample with lower viral load (9725) than with higher viral load (8789) Results * ✤ Globally, the viral family profiles diverged significantly * * ✤ Sample 8789 (31,497 cp/mL): * Siphoviridae (p < 0.0001) and Unclassified Phages (p = 0.0068) * * ✤ Sample 9725 (4,924 cp/mL): Baculoviridae (p < 0.0001), * Marseilleviridae (p < 0.0001), Mimiviridae (p < 0.0001), Poxviridae (p < 0.0001) and Retroviridae (p = 0.0028) Mammalian Families Results ✤ A direct read square-root normalized comparison of reads for both inputs showed differences in the diversity of assigned viral families between SIV-infected and uninfected groups SIV+ SIV- Results ** ✤ SIV-infected group has 43 viral families represented (8 exclusive) ** ✤ Profile SIV+ : Adenoviridae**, Leviviridae**, Reoviridae**, Siphoviridae**, Unclassified Phages** and Virgaviridae** ✤ Uninfected group has 40 viral families represented (5 exclusive) ✤ Profile SIV- : Alphaflexiviridae**, Bromoviridae**, ** Caulimoviridae**, Myoviridae**, Picobirnaviridae* * , P o d o v i r i d a e * * , Rhabdoviridae**, Tectiviridae* and Tymoviridae** ✤ Adenoviridae reads were only found in SIV-infected group ! ✤ Handley et al. (2012) showed the association of adenovirus as well as parvovirus viremia in rhesus ** macaques with intestinal disease with advanced AIDS Total 48 Families / Mammalian Families / ** p < 0.0048 / * p = 0.0096 Results ** ✤ Without outliers the SIV-infected group has 22 viral families represented (3 exclusive) ✤ Profile SIV+ : Alloherpesviridae**, Herpesviridae**, Inoviridae** and ** Reoviridae** ✤ Without outliers the Uninfected group has 21 viral families represented (2 exclusive) ✤ Profile SIV- : Microviridae**, Myoviridae**, Phycodnaviridae*, ** Podoviridae**, Rhabdoviridae**, Siphoviridae** and Tymoviridae** Total 24 Families / Mammalian Families / ** p < 0.0024 / * p = 0.0072 Results ✤ Proxies for SIV infection: ✤ Reoviridae and Alloherpesviridae associated with SIV+ (POS) ✤ Tymoviridae, Microviridae and Rhabdoviridae associated with SIV- (NEG) Results ✤ Also, in the SIV-infected group, two distinct clusters were recognizable when a 1,000 cp/ mL cutoff of SIVgor viral load in faeces (dividing in 5 and 6 samples per group) was used to assess within-group diversity Results * ✤ <1,000 cp/mL group with 37 families represented (12 exclusive) § * ✤ Profile : Adenoviridae* , Alloherpesviridae*, Betaflexiviridae*, Circoviridae*, Iridoviridae*, Leviviridae*, Mimiviridae*, Myoviridae*, Phycodnaviridae*, Podoviridae*, §§ Poxviridae , Siphoviridae*, Unclassified §§ * dsDNA Viruses* and Unclassified Phages* ✤ >1,000 cp/mL group with 31 families represented (6 exclusive) § ✤ Profile : Dicistroviridae*, Parvoviridae , Reoviridae*, Retroviridae* , Rhabdoviridae*and Virgaviridae* * * Total 43 Families / Mammalian Families / * p ≤ 0.0043 /§ p = 0.0171 / §§ p = 0.038 Results ✤ Without outliers the <1,000 cp/mL ** group with 22 families represented (1 exclusive) ✤ Profile <1,000 cp/mL : Alloherpesviridae** and Nudiviridae** ✤ Without outliers the >1,000 cp/mL group with 22 families represented (1 exclusive) ** ✤ Profile >1,000 cp/mL : Baculoviridae**, Parvoviridae**, Picobirnaviridae** and Podoviridae* Total 23 Families / Mammalian Families / ** p ≤ 0.0023 / * p = 0.0046 Results ✤ Proxies for SIV viral load: ✤ Baculoviridae and Picobirnaviridae associated with >1,000 cp/mL (Up) ✤ A l l o h e r p e s v i r i d a e associated with <1,000 cp/ mL (Down) Conclusions ✤ The enteric virome dynamics in gorillas could be potentially associated with the SIVgor status ✤ First evidence for the association of some mammalian viral families (like Adenoviridae, Herpesviridae and Reoviridae) with the presence of the SIVgor in a putative dysbiosis context, linking this phenomenon to disease progression ✤ Virome stability studies are clearly providing better markers of pathogenic infection progression than bacteriomes ✤ Further studies are still needed to better understand the influence of SIV pathogenesis on infected gorilla populations in the wild, and to associate deeper taxa (virus genera and species) to SIV status in these animals Thank you!.
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