HIV-1 and HCV sequences from Libyan outbreak

Oliveira, Túlio de; Pybus, Oliver G.; Rambaut, Andrew; Salemi, Marco; Cassol, Sharon; Ciccozzi, Massimo; Rezza, Giovanni; Gattinara, Guido Castelli; D’Arrigo, Roberta; Amicosante, Massimo; Perrin, Luc; Colizzi, Vittorio; Perno, Carlo Federico

doi:10.1038/444836a

Cited by 114 publications

(94 citation statements)

References 10 publications

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“…It is becoming apparent from this discussion that it is very unlikely the virus originated from a single human being and spread to 500+ children in a short time period by the nosocomial infection, regardless of how inappropriate the infection control unit was. One can see this kind of scenario all over the developing nations and, yet, no one has encountered the kind of outbreak that is described in El-Fatah children hospital [3][4][5][6]. The alternate explanation is that the children were infected with two cloned HIV-1 viruses (first with an attenuated HIV-1 and then with a pathogenic strain of HIV-1).…”

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

“…It is possible that due to years of sanctions the Libyan Government was unable to provide sufficient number of sterilized needles and reuse of blood laden needles served as the main source of epidemic [3][4][5][6]. However, several credible reports refute this theory (reviewed in [24][25].…”

Section: Case Of Unsafe Medical Practices and Reuse Of Unsterilized Nmentioning

confidence: 99%

“…It is entirely another thing if 400+ children got infected over a long period of time and showed a monophyletic subtype years after exposure [4][5][6].…”

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

“…What is a statistical possibility that 500+ children carry the same monophyletic HIV-1 strain? Bear in mind that, according to all three scientific articles, it is a unique sequence that did not exist previously (CRF02-AG: [4][5][6]). What is the possibility that all the children carry the same monophyletic strain if the infection was initiated by a drug abuser at ElFatah children hospital and due to inappropriate infection control the contaminated needles were reused that spread HIV-1, HCV and HBV to more then 500 children?…”

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

“…d) From the above discussion it must be clear that if a single HIV-1 infected child was admitted a number of times within 1-2 years and he or she served as the index case, that individual would not be able to maintain the same viral subtype for that long and may transmit different quasispecies to different children [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23]. These subtypes will further recombine into the new hosts and therefore, it is highly unlikely that the virus will remain monophyletic [4][5][6].…”

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

See 4 more Smart Citations

The Libyan HIV Outbreak How do we find the truth?

Bagasra

Alsayari

Bullard-Dillard

et al. 2007

Libyan Journal of Medicine

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Section: Case Of Monophyletic Virusmentioning

confidence: 99%

Section: Case Of Unsafe Medical Practices and Reuse Of Unsterilized Nmentioning

confidence: 99%

“…It is entirely another thing if 400+ children got infected over a long period of time and showed a monophyletic subtype years after exposure [4][5][6].…”

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

Section: Case Of Monophyletic Virusmentioning

confidence: 99%

See 3 more Smart Citations

The Libyan HIV Outbreak How do we find the truth?

Bagasra

Alsayari

Bullard-Dillard

et al. 2007

Libyan Journal of Medicine

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Methodologies for Phylogenetic Inference

Gil

Anisimova

2015

Encyclopedia of Life Sciences

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Phylogenetic inference from homologous molecular sequences is key to hypothesis testing and problem solving not only in evolutionary biology but also in a wide variety of other fields – from medicine to ecology. Model‐based phylogenetic methods rely on Markov substitution models to describe the molecular evolution as a stochastic process of character substitution over time on a phylogenetic tree relating the sequences. Model parameters are estimated with standard statistical inference methods, namely, Bayesian and maximum likelihood approaches. A typical phylogenetic analysis first infers a multiple sequence alignment. Given this alignment, a phylogenetic tree is then estimated together with branch lengths and model parameters. Ideally, the alignment and phylogeny should be estimated simultaneously, amongst others to take alignment uncertainty into account. Key Concepts Sequence Alignment estimates an assignment of homologous molecular characters, that is, nucleotides, amino acids or codons related by common ancestry. Phylogenetic Tree is the hierarchical representation of evolutionary relationships between homologous molecular sequences. The leaves of the tree usually represent the present day sequences, while the internal nodes represent the common ancestors. Model of Molecular Evolution is the mathematical description of the process of sequence change through time, such as character substitutions, insertions and deletions. Phylogenetic Likelihood is the probability function of observing the sequence data given the model of molecular evolution and phylogenetic tree. Frequentist Phylogenetic Inference relies on optimised phylogenetic likelihood to estimate parameters of a model of molecular evolution and a phylogenetic tree. Bayesian Phylogenetic Inference relies on phylogenetic likelihood and a prior probability distribution of parameters to obtain a posterior probability distribution of parameters of a model of molecular evolution and a phylogenetic tree. Branch Support quantifies the uncertainty of phylogenetic inference by assigning statistical confidence to the inferred partitions (i.e. clades) on a phylogenetic tree. Alignment Uncertainty quantifies the statistical confidence of sequence alignment, which compounds the uncertainty of phylogenetic inference.

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Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark

Eriksen¹,

Jørgensen²,

Krarup³

et al. 2010

Journal of Medical Virology

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The prevalence of hepatitis C virus (HCV) genotype 4 has increased throughout Europe. This is an epidemiological study of patients infected chronically with HCV genotype 4 in Denmark. The HCV strains analyzed originated from patient samples collected between 1999 and 2007 as part of the national Danish hepatitis B and C network, DANHEP. Sequence analyses were based on the envelope 1 region of HCV. Results from a total of 72 patients indicated a high degree of genetic heterogeneity. Fifty‐six patients (78%) were infected with one of the three dominating subtypes: 4d, 4a, or 4r. The remaining 16 patients (22%) were infected with subtypes 4h, 4k, 4l, 4n, 4o, or 4Unclassified. Three epidemiological profiles were identified: (1) patients infected with HCV by intravenous drug use were infected solely with subtype 4d. They were all of European origin, and 15 of the 16 patients were ethnic Danes. No single transmission event could be confirmed, but the pairwise nucleotide identity within the patients of Danish origin was relatively high (∼95%), suggesting a recent introduction into Denmark. (2) The 21 patients infected with subtype 4a all came from Northern Africa, Egypt, Pakistan, or the Middle East. (3) Patients from Southern Africa dominated among patients infected with subtype 4r (10 of 12 patients). This study demonstrates that HCV genotype 4d has been introduced in and spread among Danish intravenous drug users. The remaining subtypes show restricted distribution, infecting almost exclusively patients from geographical areas with a relatively high prevalence of HCV genotype 4 infections. J. Med. Virol. 82:1869–1877, 2010. © 2010 Wiley‐Liss, Inc.

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HIV-1 and HCV sequences from Libyan outbreak

Cited by 114 publications

References 10 publications

The Libyan HIV Outbreak How do we find the truth?

The Libyan HIV Outbreak How do we find the truth?

Methodologies for Phylogenetic Inference

Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark

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