SIV infection in wild gorillas

Heuverswyn, Fran Van; Li, Yingying; Neel, Cécile; Bailes, Elizabeth; Keele, Brandon F.; Liu, Weimin; Loul, Sévérin; Butel, Christelle; Liégeois, Florian; Bienvenue, Yanga; Ngolle, E. Mpoudi; Sharp, Paul M.; Shaw, George M.; Delaporte, Eric; Hahn, Beatrice H.; Peeters, Martine

doi:10.1038/444164a

Cited by 324 publications

(122 citation statements)

References 5 publications

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“…Regarding subtype C, the excellent and similar sensitivities and specificities reported for all the automatic subtyping tools indicate the suitability of all tools in discriminating subtype C viruses (24,33) and their possible routine use in settings with subtype C predominance like southern Africa, eastern Africa, India, Nepal, and part of China (2,5,34). On one hand, Stanford-v8.1 showed excellent performance in sensitivity (97.4% to 100%) on other pure subtypes (D, F1, and F2) in contrast to other rapid tools (reporting Ͻ90% sensitivity); this indicates that Stanford-v8.1 might be acceptable in assigning D or F strains.…”

Section: Discussionmentioning

confidence: 99%

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Comparative Evaluation of Subtyping Tools for Surveillance of Newly Emerging HIV-1 Strains

et al. 2017

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HIV-1 non-B subtypes/circulating recombinant forms (CRFs) are increasing worldwide. Since subtype identification can be clinically relevant, we assessed the added value in HIV-1 subtyping using updated molecular phylogeny (Mphy) and the performance of routinely used automated tools. Updated Mphy (2015 updated reference sequences), used as a gold standard, was performed to subtype 13,116 HIV-1 protease/reverse transcriptase sequences and then compared with previous Mphy (reference sequences until 2014) and with COMET, REGA, SCUEAL, and Stanford subtyping tools. Updated Mphy classified subtype B as the most prevalent (73.4%), followed by CRF02_AG (7.9%), C (4.6%), F1 (3.4%), A1 (2.2%), G (1.6%), CRF12_BF (1.2%), and other subtypes (5.7%). A 2.3% proportion of sequences were reassigned as different subtypes or CRFs because of misclassification by previous Mphy. Overall, the tool most concordant with updated Mphy was Stanford-v8.1 (95.4%), followed by COMET (93.8%), REGA-v3 (92.5%), Stanford-old (91.1%), and SCUEAL (85.9%). All the tools had a high sensitivity (Ն98.0%) and specificity (Ն95.7%) for subtype B. Regarding non-B subtypes, Stanford-v8.1 was the best tool for C, D, and F subtypes and for CRFs 01, 02, 06, 11, and 36 (sensitivity, Ն92.6%; specificity, Ն99.1%). A1 and G subtypes were better classified by COMET (92.3%) and REGA-v3 (98.6%), respectively. Our findings confirm Mphy as the gold standard for accurate HIV-1 subtyping, although Stanford-v8.1, occasionally combined with COMET or REGA-v3, represents an effective subtyping approach in clinical settings. Periodic updating of HIV-1 reference sequences is fundamental to improving subtype characterization in the context of an effective epidemiological surveillance of non-B strains.

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Section: Discussionmentioning

confidence: 99%

“…The HIV-1 pandemic has been mainly caused by group M (1)(2)(3)5), which is subdivided into 9 subtypes (A to D, F to H, J, and K) and at least 79 circulating recombinant forms (CRFs) (http://www .hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html, accessed 25 February 2017) and multiple unique recombinant forms (URFs) widely spread across the globe.…”

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confidence: 99%

Comparative Evaluation of Subtyping Tools for Surveillance of Newly Emerging HIV-1 Strains

et al. 2017

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“…SIV infection is endemic in wild-living apes throughout equatorial Africa, yet only certain lineages of SIVcpz and SIVgor have been found to infect and cause disease in humans (1)(2)(3). This has raised the question of whether certain strains of SIVcpz/SIVgor are more prone than others to cross from apes to humans.…”

Section: Discussionmentioning

confidence: 99%

“…It is now well established that HIV-1, the main cause of AIDS, emerged as a consequence of at least 4 cross-species transmissions of SIVs infecting wild-living apes (1,2). Both SIVcpz-infected chimpanzees (Pan troglodytes troglodytes) and SIVgor-infected gorillas (Gorilla gorilla gorilla) transmitted their viruses to humans, generating HIV-1 groups M, N, O, and P (1)(2)(3)(4). Of these, groups, M and N have been traced to geographically isolated chimpanzee communities in southeastern Cameroon (3).…”

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confidence: 99%

Efficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation

Bibollet-Ruche¹,

Heigele²,

Keele³

et al. 2012

J. Clin. Invest.

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“…Further analyses of ape faecal samples from across Cameroon revealed group O-related viruses in gorillas (Gorilla gorilla gorilla) (Van Heuverswyn et al 2006;Takehisa et al 2009). Very recently, Plantier et al (2009) have reported an HIV-1 strain that does not fall within any of the three described groups, and so must represent a fourth cross-species transmission; if viruses from this lineage are found in other individuals, they will constitute a fourth group, P. This new strain of HIV-1 is very closely related to the gorilla viruses (SIVgor), and has most probably resulted from gorilla-to-human transmission.…”

Section: The Origins Of Hiv-1 and Hiv-2mentioning

confidence: 99%

The evolution of HIV-1 and the origin of AIDS

Sharp

Hahn

2010

Phil. Trans. R. Soc. B

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The major cause of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus type 1 (HIV-1). We have been using evolutionary comparisons to trace (i) the origin(s) of HIV-1 and (ii) the origin(s) of AIDS. The closest relatives of HIV-1 are simian immunodeficiency viruses (SIVs) infecting wild-living chimpanzees ( Pan troglodytes troglodytes ) and gorillas ( Gorilla gorilla gorilla ) in west central Africa. Phylogenetic analyses have revealed the origins of HIV-1: chimpanzees were the original hosts of this clade of viruses; four lineages of HIV-1 have arisen by independent cross-species transmissions to humans and one or two of those transmissions may have been via gorillas. However, SIVs are primarily monkey viruses: more than 40 species of African monkeys are infected with their own, species-specific, SIV and in at least some host species, the infection seems non-pathogenic. Chimpanzees acquired from monkeys two distinct forms of SIVs that recombined to produce a virus with a unique genome structure. We have found that SIV infection causes CD4 + T-cell depletion and increases mortality in wild chimpanzees, and so the origin of AIDS is more ancient than the origin of HIV-1. Tracing the genetic changes that occurred as monkey viruses adapted to infect first chimpanzees and then humans may provide insights into the causes of the pathogenicity of these viruses.

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SIV infection in wild gorillas

Cited by 324 publications

References 5 publications

Comparative Evaluation of Subtyping Tools for Surveillance of Newly Emerging HIV-1 Strains

Comparative Evaluation of Subtyping Tools for Surveillance of Newly Emerging HIV-1 Strains

Efficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation

The evolution of HIV-1 and the origin of AIDS

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