Journal of Clinical Virology 30 (2004) 11–18 Genetic and phylogenetic analyses of HIV-1 corroborate the transmission link hypothesis Mauro Pistello a,∗ , Barbara Del Santo a , Stefano Buttò b , Marino Bargagna c,1 , Ranieri Domenici c , Mauro Bendinelli a a Retrovirus Center and Virology Section, Department of Experimental Pathology, University of Pisa, Via San Zeno 35, I-56127 Pisa, Italy b Laboratory of Virology, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Rome, Italy c Forensic Medicine, Department of Neurosciences, University of Pisa, Via Roma 55, I-56100 Pisa, Italy Received 21 January 2003; received in revised form 13 August 2003; accepted 21 August 2003 Abstract Background: Phylogenetic and genetic analyses have proven a valuable tool to infer epidemiological links between human immunode- ficiency virus type-1 (HIV-1) isolates. These methods were applied in the present report for studying the genetic relatedness of the viral strains involved in two episodes of suspected HIV-1 transmission. Objectives: Provide any evidence that may help establish or refute the transmission link. Study design: In the first case, a leukemic patient became HIV-1 positive following the transfusion of platelets from a donor who was subsequently found to have tested false HIV-seronegative and to be sexual partner to an infected woman. In the second, a wife claimed to have acquired the infection from her husband who had concealed his infected status. Results and conclusions: The viral pairs detected in each of the suspected transmission cases exhibited common amino acid signatures and low genetic distances and seg- regated together in phylogenetic trees, thus showing a level of genetic relatedness similar to reference pairs known with certainty to be epidemiologically linked. These findings corroborated the existence of a direct transmission link in both the episodes with a high level of confidence. © 2003 Elsevier B.V. All rights reserved. Keywords: HIV-1 transmission; Genetic analysis; HIV-1; Phylogenetic analysis; VESPA 1. Introduction Human immunodeficiency virus (HIV) transmission may have important legal implications, as for example when it occurs as a consequence of medical practice, rape or unpro- tected sex with an individual aware of his/her infected status. In these circumstances, experts are required to provide any evidence that may help establish or refute the transmission link. The leading case is that of a dentist with overt AIDS who was suspected of having transmitted the infection to a number of patients during invasive procedures such as tooth Abbreviations: Aa, amino acid; HIV-1, human immunodeficiency virus type 1; Nt, nucleotide; PCR, polymerase chain reaction; VESPA, viral epidemiology signature pattern analysis ∗ Corresponding author. Tel.: +39-050-2213-781; fax: +39-050-2213-524. E-mail address: pistello@biomed.unipi.it (M. Pistello). 1 Deceased. extraction and endodontic therapy. By applying molecular techniques used for studying virus transmission in commu- nities, Ou et al. (1992) could demonstrate a close genetic correlation between the HIV strains harbored by the den- tist and five of his patients. Such evidence, together with clinical–epidemiological data, led to the conclusion that the dentist had indeed been the source of infection. Other situa- tions in which genetic analysis of HIV-1 isolates has proved valuable include rape (Albert et al., 1994; Banaschak et al., 2000; Machuca et al., 2001), health care worker-to-patient transmission (Blanchard et al., 1998; Goujon et al., 2000; Holmes et al., 1993), other forms of nosocomial infection (Arnold et al., 1998), and an outbreak in a Scottish prison (Yirrell et al., 1997). Thus, genetic analysis of viral se- quences to infer epidemiological links between HIV strains is a well-established procedure. In this study, an envelope (env) gene segment encom- passing the hypervariable region 3 (V3), that had already proven useful in similar investigations (Birch et al., 2000; 1386-6532/$ – see front matter © 2003 Elsevier B.V. All rights reserved. doi:10.1016/j.jcv.2003.08.008