Clustering of hepatitis c virus nucleotide sequences among people with hepatitis C mono-infection and co-infected with HIV



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Abstract

Despite extensive investigation of hepatitis C virus (HCV) molecular and biological properties, assessing clustering of hepatitis C virus (HCV) circulating in Russia and separately in the Far Eastern federal district was understudied.

Objective – to conduct a phylogenetic analysis and evaluate clustering of HCV obtained from HCV monoinfected and HIV+HCV co-infected patients in the Far Eastern federal district.

Materials and methods. In the study, 277 HCV NS5B nucleotide sequences (233 - HCV mono-infected and 44 – HIV-HCV co-infected) including 152 sequences originated from the Far Eastern Federal district (122 – HCV mono-infected and 30 - HIV-HCV co-infected) were analyzed. Phylogenetic reconstruction was performed using the BEAST v.2.6.7 software package. Assortative mixing assessment was based on geographical origin and HIV status. Significance level was verified by permutation test (10000 repeats), cluster comparisons (with posterior probability of ≥0.9) – by Chi-square and Fisher exact tests.

Results and discussion. Here, the study revealed a limited mixing between Russia-originated, predominantly Far Eastern and foreign isolates (r=0.22; p=0.0001), which is consistent with cluster analysis data. For foreign isolates, they were assigned to three clusters only: two clusters of subtype 2a included isolates from China and Vietnam, one cluster of subtype 3a – from Sweden. At the same time, the HIV-HCV coinfection subgroup demonstrated moderate regional assortativity (r=0.63; p=0.005). Similar data were obtained in cluster analysis carried out in HIV-HCV coinfection and HCV-monoinfection subgroups: frequency of cluster formation in the former totaled 36.8% versus 18.8% in the latter (OR=2.7; p=0.019).

The Far Eastern sample group demonstrated moderate regional assortativity (r=0.56; p=0.001), while stratification showed that in HIV+HCV co-infection subgroup assortativity was close to zero (r=0.027; p=0.9), likely due to small sample size.

Some of the Far Eastern clusters were mixed, i.e., contained sequences isolated from HIV+HCV co-infected subjects and HCV mono-infected individuals.

Conclusion. HCV circulation in the Far Eastern federal district occurs on a geographic basis and according to a risk group including chronic HCV plus HIV infection. Detecting mixed clusters may evidence about a potential exchange of HCV variants between HIV-positive and HIV-negative subjects, which, however, required to be verified in further studies with larger sample size.

About the authors

Elena Anatolyevna Bazykina

FBUN Khabarovsk research institute of epidemiology and microbiology of the Federal Service for surveillance on consumer rights protection and human wellbeing, Russian Federation, Khabarovsk

Email: alyonaf@yandex.ru
ORCID iD: 0000-0002-5695-6752

junior research associate of the laboratory of epidemiology and prophylaxis of viral hepatitis and AIDS.

Russian Federation, Russian Federation, 680000, Khabarovsk, Shevchenko str., 2.

Valeria Olegovna Kotova

FBUN Khabarovsk research institute of epidemiology and microbiology of the Federal Service for surveillance on consumer rights protection and human wellbeing, Russian Federation, Khabarovsk

Email: dvaids@mail.ru
ORCID iD: 0000-0001-9824-7025

chief of the laboratory of epidemiology and prevention of viral hepatitis and AIDS.

Russian Federation, Russian Federation, 680000, Khabarovsk, Shevchenko str., 2.

Olga Evgenyevna Trotsenko

FBUN Khabarovsk research institute of epidemiology and microbiology of the Federal Service for surveillance on consumer rights protection and human wellbeing, Russian Federation, Khabarovsk

Email: trotsenko_oe@hniiem.ru
ORCID iD: 0000-0003-3050-4472

MD PHD, director of the FBUN Khabarovsk research institute of epidemiology and microbiology of the Federal Service for surveillance on consumer rights protection and human wellbeing.

Russian Federation, Russian Federation, 680000, Khabarovsk, Shevchenko str., 2.

Sergei Vladimirovich Balakhonov

FKUZ Irkutsk antiplague research institute of Siberia and Far East of the Federal service for surveillance on consumers rights protection and human wellbeing (Rospotrebnadzor), Irkutsk
 

Email: dvaids@mail.ru
ORCID iD: 0000-0003-4201-5828

MD PHD, professor, director of the FKUZ Irkutsk antiplague research institute of Siberia and Far East of the Federal service for surveillance on consumers rights protection and human wellbeing (Rospotrebnadzor).

Russian Federation, Russian Federation, 664047, Irkutsk, Trilisser str., 78

Ludmila Anatolyevna Balakhontseva

FKUZ Irkutsk antiplague research institute of Siberia and Far East of the Federal service for surveillance on consumers rights protection and human wellbeing (Rospotrebnadzor), Irkutsk

Author for correspondence.
Email: dvaids@mail.ru
ORCID iD: 0000-0002-3209-7623

chief of the Far Eastern regional center on prevention and combat against AIDS.

Russian Federation, Russian Federation, 680000, Khabarovsk, Shevchenko str., 2.

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Copyright (c) Bazykina E.A., Bondaruk A.N., Kotova V.O., Trotsenko O.E., Balakhonov S.V., Balakhontseva L.A.

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