Forensic application of phylogenetic analyses – Exploration of suspected HIV-1 transmission case

Šiljić, Marina; Salemović, Dubravka; Ćirković, Valentina; Pešić-Pavlović, Ivana; Ranin, Jovan; Todorović, Marija; Nikolic, Slobodan; Jevtović, Djordje; Stanojević, Maja

doi:10.1016/j.fsigen.2016.12.006

Cited by 10 publications

(9 citation statements)

References 22 publications

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“…A set of analyses was performed for a definition of HIV transmission clusters, following the strategy of “statistical support of clades plus similarity” that proved to be suitable in our previous investigation of transmission chains in Serbia (Siljic et al, 2013, 2017). Evidence of transmission cluster was characterized by two criteria sets: according to the first set of criteria, transmission clusters were assigned as those monophyletic phylogenetic clades consisting of three or more sequences, fulfilling the conditions of genetic distance of 1.5% or less, with minimal bootstrap support of 90%, and the Bayesian posterior probability of higher than 0.9.…”

Section: Methodsmentioning

confidence: 99%

Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach

et al. 2019

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Previous molecular studies of Serbian HIV epidemic identified the dominance of subtype B and presence of clusters related HIV-1 transmission, in particular among men who have sex with men (MSM). In order to get a deeper understanding of the complexities of HIV sub-epidemics in Serbia, epidemic trends, temporal origin and phylodynamic characteristics in general population and subpopulations were analyzed by means of mathematical modeling, phylogenetic analysis and latent class analysis (LCA). Fitting of the logistic curve of trends for a cumulative annual number of new HIV cases in 1984–2016, in general population and MSM transmission group, was performed. Both datasets fitted the logistic growth model, showing the early exponential phase of the growth curve. According to the suggested model, in the year 2030, the number of newly diagnosed HIV cases in Serbia will continue to grow, in particular in the MSM transmission group. Further, a detailed phylogenetic analysis was performed on 385 sequences from the period 1997–2015. Identification of transmission clusters, estimation of population growth (Ne), of the effective reproductive number (Re) and time of the most recent common ancestor (tMRCA) were estimated employing Bayesian and maximum likelihood methods. A substantial proportion of 53% of subtype B sequences was found within transmission clusters/network. Phylodynamic analysis revealed Re over one during the whole period investigated, with the steepest slopes and a recent tMRCA for MSM transmission group subtype B clades, in line with a growing trend in the number of transmissions in years approaching the end of the study period. Contrary, heterosexual clades in both studied subtypes – B and C – showed modest growth and stagnation. LCA analysis identified five latent classes, with transmission clusters dominantly present in 2/5 classes, linked to MSM transmission living in the capital city and with the high prevalence of co-infection with HBV and/or other STIs.Presented findings imply that HIV epidemic in Serbia is still in the exponential growth phase, in particular, related to the MSM transmission, with estimated steep growth curve until 2030. The obtained results imply that an average new HIV patient in Serbia is a young man with concomitant sexually transmitted infection.

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Section: Methodsmentioning

confidence: 99%

Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach

et al. 2019

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“…Therefore, relationships between queried and control samples are usually obtained under the light of evolutionary analyses since those samples most likely belong to distant generations [ 52 ]. The evolutionary analysis not only provides the identification of genetic relationships (dealing with questions like, “is the suspect the cause of the studied transmission or outbreak?” or “which individuals were infected by the suspect and which individuals were infected or coinfected from other sources?”) [e.g., 31 – 36 , 53 , 54 , 55 ], but also allows the estimation of the timing of transmission events (i.e., infection date of each individual, including the individual that generated the outbreak) [e.g., 53 , 54 ].…”

Section: Evolutionary Analysis Of Genetic Data In Forensic Geneticsmentioning

confidence: 99%

“…In NHFG, this statistical parameter can provide a measure of the reliability of relationships between the pathogen genetic sequences of the investigated individuals. For example, a number of forensic studies based on phylogenetic inferences showed a classification of all control individuals in significantly separated clades, whereas individuals related with the studied outbreak or transmission clustered in a unique clade [e.g., 31 , 32 , 34 , 35 , 53 , 54 , 55 ]. Likelihood ratio tests can also be useful for hypothesis testing (i.e., testing if control sequences group or not with the studied outbreak) [e.g., 54 ].…”

Section: Evolutionary Analysis Of Genetic Data In Forensic Geneticsmentioning

confidence: 99%

“…Applications of MF in biocrimes also include the tracking of sexually transmitted diseases and healthcare malpractice linked to the transmission of HIV [e.g., 31 – 36 , 53 , 184 ] and HCV [e.g., 54 , 55 ]. Moreover, this discipline is also used to determine responsibilities in cases of hospital-acquired infections [e.g., 185 , 186 ] or sudden death syndrome [e.g., 187 , 188 ].…”

Section: Microbiologymentioning

confidence: 99%

“…In addition, as noted above, evolutionary processes that exchange genetic material (e.g., recombination) can bias phylogenetic tree inferences [ 60 ]. However, to our knowledge, all existing NHFG studies including phylogenetic tree inferences from pathogens that usually evolve with high recombination rates (i.e., HIV and HCV) ignored recombination [e.g., 31 – 36 , 53 , 54 , 55 ]. We strongly recommend considering these aspects in future NHFG studies.…”

Section: The Future Of Nhfgmentioning

confidence: 99%

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While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material—including other animal species, plants, or microorganisms—is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.

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Forensic application of phylogenetic analyses – Exploration of suspected HIV-1 transmission case

Cited by 10 publications

References 22 publications

Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach

Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach

Forensic genetics and genomics: Much more than just a human affair

Genomic insights into deciphering bacterial outbreaks

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