The inference of HIV-1 transmission direction between HIV-1 positive couples based on the sequences of HIV-1 quasi-species

Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs

Identifying the transmission direction between individuals provides unparalleled power to understand infectious disease epidemiology. With epidemiological and clinical information typically unavailable to infer transmission direction, phylogenetic analysis of pathogen sequence data offers an alternative approach. While the success of this phylogenetic analysis varies, the reasons remain unknown. We analyze sequence data from over 100 transmission pairs for which both the transmission direction of HIV is known and detailed additional information is available. We find that easily quantifiable phylogenetic and sampling characteristics discriminate whether a phylogenetically inferred transmission direction is correct. Our analysis highlights that while phylogenetic approaches to infer transmission direction are unsuitable for individual-level analysis, such as forensic investigations, confidence in source attribution can be incorporated in population-level analyses.

Inferring the transmission direction between linked individuals living with HIV provides unparalleled power to understand the epidemiology that determines transmission. Phylogenetic ancestral-state reconstruction approaches infer the transmission direction by identifying the individual in whom the most recent common ancestor of the virus populations originated. While these methods vary in accuracy, it is unclear why. To evaluate the performance of phylogenetic ancestral-state reconstruction to determine the transmission direction of HIV-1 infection, we inferred the transmission direction for 112 transmission pairs where transmission direction and detailed additional information were available. We then fit a statistical model to evaluate the extent to which epidemiological, sampling, genetic, and phylogenetic factors influenced the outcome of the inference. Finally, we repeated the analysis under real-life conditions with only routinely available data. We found that whether ancestral-state reconstruction correctly infers the transmission direction depends principally on the phylogeny's topology. For example, under real-life conditions, the probability of identifying the correct transmission direction increases from 32%—when a monophyletic–monophyletic or paraphyletic–polyphyletic tree topology is observed and when the tip closest to the root does not agree with the state at the root—to 93% when a paraphyletic–monophyletic topology is observed and when the tip closest to the root agrees with the root state. Our results suggest that documenting larger differences in relative intrahost diversity increases our confidence in the transmission direction inference of linked pairs for population-level studies of HIV. These findings provide a practical starting point to determine our confidence in transmission direction inference from ancestral-state reconstruction.

Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases

For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.

The inference of HIV-1 transmission direction between a man who has sex with men and his heterosexual wife based on the sequences of HIV-1 quasi-species

Currently, homosexual transmission has become one of the main routes of HIV-1 spread in China. Furthermore, about 80% Chinese men, who have sex with men (MSM), feel forced to enter eventually into heterosexual marriages due to the Chinese traditional marriage culture, which may cause HIV-1 infection in families. In this study, we identified HIV-1 transmission in a family and the direction of HIV-1 transmission from a MSM to his wife and infant, which indicated Chinese MSM may have become a potential bridge of HIV-1 transmission to their wives and children. Therefore, we need to develop more effective defence measures to prevent the spread of HIV-1 in MSM families in China.

Health related behaviors among HIV-infected people who are successfully linked to care: an institutional-based cross-sectional study

BACKGROUND

By the end of October 2019, there were 958 thousand people were reported living with HIV/AIDS in China. Unhealthy lifestyle factors, such as smoking, drinking alcohol, using illicit drugs and no physical activity have been found to mitigate the positive impact of antiretroviral therapy (ART) on viral load and HIV-related quality of life. Moreover, risky sexual behavior among HIV-positive persons places their partners at risk for HIV transmission and other sexually transmitted infections. The aim of the study is to determine the prevalence of unhealthy behavior of people living with HIV/AIDS and related influencing factors, particularly those that are closely connected with HIV infection and ART effects.

METHODS

An institutional based cross-sectional study design was used to collect data from people living with HIV/AIDS (PLWHA) in Beijing and Yunnan Province. The following information was included in the questionnaire survey: social-demographic characteristics, health behavior information, sexual risk behaviors. Binary logistic regression model was conducted to analyze the influencing factors of unhealthy general health behaviors and risky sexual behaviors.

RESULTS

In total, 2575 PLWHA were included in the study and 78.3% (2017/2575) were male. For the general health behaviors, 34.2% (987/2544) smoke; 33.8% (870/2575) drank alcohol and 2.3% (49/2134) reported the use of illicit drugs in the previous 6 months. From the sexual behaviors perspective, 59.0% (1519/2575) had sex in the previous 6 months. Among people who had sex, 92.0% (1398/1519) had fixed sexual partners. Among those with no fixed sexual partner, 38.0% (46/121) had more than three partners. Among men who had sex, 34.7% (448/1292) reported having sex with men in the previous 6 months and 16.7% (75/448) of these had group sexual activity. Among participants, 72.2% (1053/1458) used condoms every time they had sex while 6.4% (94/1458) of people never used condom. Male people living with HIV/AIDS were more likely to have sexual risk behaviors (adjusted odds ratio [OR] = 2.208, 95% confidence interval [CI]: 1.147-4.252) and unhealthy general health behaviors (adjusted OR = 2.029, 95% CI: 1.480-2.783). The odds of higher risk sexual behaviors was 1.546 times (95% CI: 1.302-1.827, P = 0.001) greater among participants who drank alcohol compared with their non-drinking counterparts.

CONCLUSIONS

PLWHA is a group that is vulnerable to problematic health behaviors, especially for men who were more likely to drink alcohol, have more sexual partners, more sexual risk behaviors including group sexual activity, not using condoms and using drugs. Therefore, interventions focusing on gender-specific risk behaviors reduction for people living with HIV/AIDS are now necessary to control the spread of HIV infection and improve the efficacy of antiviral treatment.