Experience in the use of phylogenetic analysis in the investigation of cases of HIV-infected patients

Abstract

Objective. To establish a probable source of infection using phylogenetic analysis in the investigation of cases of HIV infection. Materials and methods. HIV genome sequencing was carried out using the kit ViroSeq (Celera). The phylogenetic tree was constructed using the maximum likelihood method in the Mega 6 program. As a comparison group, 40 samples of HIV-infected patients from the Krasnoyarsk region were used, as well as 25 nucleotide sequences of various HIV subtypes taken from the international GenBank database. The reliability of the resulting tree was evaluated in bootstrap analysis, a branch rotation test for a thousand random constructions.Results and discussion. The paper presents five cases of epidemiological investigations with a probable nosocomial and occupational mechanism of HIV infection transmission in the Krasnoyarsk region. In 2013, a study was conducted on the infection of three persons treated in the same hospital with an HIV-infected patient. A close genetic relationship of HIV was shown in newly identified individuals, the probable source could not be examined due to death. Second epidemiological investigation in 2013. The association of cases of infection between a newly diagnosed woman with HIV infection and a patient with a previously established HIV status is shown. Both persons were simultaneously in the same medical institution. To determine the direction of transmission of the virus, a test for the duration of infection was used. In 2014, after receiving medical care in four medical organizations, the patient was confirmed to be HIV positive. In all hospitals there were persons with a confirmed diagnosis of HIV infection. Three of them have been examined. The absence of a phylogenetic relationship was confirmed, the fourth died, the material could not be obtained from him. In 2015, a nurse was injured while caring for an HIV-positive patient. Phylogenetic analysis showed a high degree of genetic relationship between these cases of infection. In 2016, after a car accident, two patients were hospitalized in the intensive care unit. After some time, both were diagnosed with HIV infection. Four HIV-infected patients were in intensive care at the same time. Phylogenetic analysis was carried out in two newly identified individuals and one putative source. The association of infections in newly identified patients was shown, the alleged source could not be established.Conclusion. The use of molecular genetic methods in epidemiological investigations significantly improves the quality and accuracy of deciphering epidemic chains of HIV infection.