The applications of machine learning in HIV neutralizing antibodies research-A systematic review

Machine learning algorithms play an essential role in bioinformatics and allow exploring the vast and noisy biological data in unrivaled ways. This paper is a systematic review of the applications of machine learning in the study of HIV neutralizing antibodies. This significant and vast research domain can pave the way to novel treatments and to a vaccine. We selected the relevant papers by investigating the available literature from the Web of Science and PubMed databases in the last decade. The computational methods are applied in neutralization potency prediction, neutralization span prediction against multiple viral strains, antibody-virus binding sites detection, enhanced antibodies design, and the study of the antibody-induced immune response. These methods are viewed from multiple angles spanning data processing, model description, feature selection, evaluation, and sometimes paper comparisons. The algorithms are diverse and include supervised, unsupervised, and generative types. Both classical machine learning and modern deep learning were taken into account. The review ends with our ideas regarding future research directions and challenges.

Reaching 95-95-95 targets: The role of private sector health facilities in closing the HIV detection gap-Kisumu Kenya, 2018

BACKGROUND

HIV testing efficiency could be improved by focusing on high yield populations and identifying types of health facilities where people with undiagnosed HIV infection are more likely to attend.

METHODS

A retrospective cohort analysis of data collected during an integrated TB/HIV active case-finding intervention in Western Kenya. Data were analyzed from health facilities' registers on individuals who reported TB-suggestive symptoms between 1 July and 31 December 2018 and who had an HIV test result within one month following symptom screening. We used logistic regression with general estimating equations adjusting for sub-county level data to identify health facility-level predictors of new HIV diagnoses.

RESULTS

Of 11,376 adults with presumptive TB identified in 143 health facilities, 1038 (9%) tested HIV positive. The median HIV positivity per health facility was 6% (IQR = 2-15%). Patients with TB symptoms were over three times as likely to have a new HIV diagnosis in private not-for-profit facilities compared to those in government facilities (adjusted odds ratio (aOR) 3.40; 95% CI = 1.96-5.90). Patients tested in hospitals were over two times as likely to have a new HIV diagnosis as those tested in smaller facilities (i.e., health centers and dispensaries) (aOR 2.26; 95% CI = 1.60-3.21).

CONCLUSION

Individuals with presumptive TB who attended larger health facilities and private not-for-profit facilities had a higher likelihood of being newly diagnosed with HIV. Strengthening HIV services at these facilities and outreach to populations that use them could help to close the HIV diagnosis gap.

The Relationship Between HIV Antibody Titer, HIV Viral Load, HIV p24 Antigen, and CD4 T-cell Count Among Iranian HIV-positive Patients

OBJECTIVE

This study aimed to simultaneously measure and assess the correlation between the available HIV infection parameters including HIV antibody, p24 Antigen, CD4 cell count, and viral load at the different stages of HIV disease among HIV-positive individuals in Iran.

MATERIALS AND METHODS

Fifty HIV-positive individuals were classified into three stages (1, 2, and 3) according to the HIV disease stages classification, available in Control of Disease and Prevention (CDC) guideline. 10 ml of the venous blood sample was collected to run the tests for HIV antibody and p24 Ag levels, CD4 cell counts, and viral load. Pearson's correlation test was employed to calculate the coefficients for the in-between correlation of different HIV parameters in each stage.

RESULTS

Of 50 participants, 17 (34%), 25 (50%), and 8 (16%) patients belonged to stages 1, 2, and 3, respectively. Sexual relationship was the main route of HIV transmission among the patients (36%); however, injecting drug use (20%) was also reported frequently. There was no significant correlation between the parameters of HIV disease in different stages in the present study.

CONCLUSION

The findings showed no correlation between HIV parameters in the present study. Considering the fact that the association of HIV antibodies with HIV disease progression in infected individuals is independent of HIV-1 RNA levels, combined measurement of HIV-1 RNA and CD4 cell counts should be routinely carried out in HIV infected patients follow up.

Delayed seroreversion of specifical antibody against HIV in HIV-exposed infants: A retrospective cohort study

OBJECTIVES

To investigate the seroreversion time in HIV-1-exposed but uninfected infants from two tertiary hospitals in China.

METHODS

This study retrospectively investigated the data of perinatal, HIV-1-exposed infants from hospitals in Beijing and Shenzhen. Maternal and infant medical records from both hospitals from January 2009 to December 2019 were reviewed, and the HIV antibody seroreversion times of infants were determined. From 2009 to 2019, a total of 485 HIV-1-exposed but uninfected infants were enrolled. The majority of infants were born at term with normal birth weight.

RESULTS

The seroreversion rates were 89.3%, 94.2% and 100% at 12, 18 and 24 months of age, respectively. There were no significant associations between seroreversion and several risk factors, such as gender, birth weight, gestational age, mode of delivery, postpartum prophylaxis and antiretroviral treatment duration. The mean value of HIV-specific immunoglobulin G concentration decreased from 15.4 at day 42 to 0.03 after 24 months in HIV-exposed, uninfected infants.

CONCLUSIONS

Clearance of HIV antibodies could take more than 18 months in a small number of perinatally exposed infants. Caution should be used in excluding or diagnosing perinatal HIV infection in children with long persistence of HIV antibodies.

[Analysis on influencing factors that leading to nonspecific responses to indeterminate results of HIV antibodies]

Objective: To identify the influencing factors that leading to nonspecific responses to indeterminate HIV antibody tests, to provide scientific evidence for the differential diagnosis of HIV infection and control strategy. Methods: A case control study was conducted. The samples of HIV antibody indeterminate in confirmed Western blot (WB) tests, but were negative in HIV nucleic acid tests, were collected as HIV antibody indeterminate group from WB results of HIV confirmatory laboratories of Fujian province in 2015-2016. The general population matched group with HIV antibody screening negative samples and WB negative matched group with WB negative samples were selected as the two compared groups by matching gender and age from HIV antibody screening in Fujian province in the same period. Blood concentrations of hepatitis B surface antigen (HBsAg), anti-hepatitis C virus (HCV) antibody, anti-treponema pallidum (TP) antibody, antinuclear antibody (ANA), anti-human T-cell leukemia virus (HTLV) antibody, and alpha-fetoprotein (AFP) were detected by using enzyme-linked immunosorbent assay (ELISA). χ(2) test and multivariate non-conditional logistic regression analysis were performed to identify the influencing factors that leading to nonspecific responses, to indeterminate HIV antibody tests. Results: A total of 13 WB band patterns were observed in 110 HIV antibody indeterminate samples, in which a single p24 band (58.18%, 64/110), a single gp160 band (17.27%, 19/110) and a single p17 band (7.27%, 8/110) were the three most common patterns. The positive rate of anti-TP antibody was significantly higher in HIV antibody indeterminate samples than general population control group and WB negative control group (10.91%, 12/110 vs. 1.77%, 4/226 and 3.64%, 4/110), compared with two control groups (χ(2)=13.627 and 4.314, P<0.05). The positive rate of AFP was significantly higher in HIV antibody indeterminate samples than general population control group (18.18%, 20/110 vs. 0.44%, 1/226, χ(2)=39.736, P<0.05), the different was not significant compared with WB negative control group (18.18%, 20/110 vs. 23.64%, 26/110, χ(2)=0.990, P>0.05) While no significant differences were found between HIV antibody indeterminate group and two control groups in terms of the positive rates of ANA, HBsAg, anti-HCV antibody or anti-HTLV antibody. Conclusions: The influencing factors that leading to nonspecific responses to indeterminate HIV antibody tests appeared complicate, and the anti-TP antibody positivity might be an influencing factor responsible for nonspecific responses to indeterminate HIV antibody tests.

The prevalence of HBV, HCV and HIV infections among Iranian infertile couples referring to Royan institute infertility clinic: A cross-sectional study

BACKGROUND

The role of the screening protocol for viral hepatitis and human immuunodeficiency virus (HIV) infections among infertile couples were seldom investigated.

OBJECTIVE

The present study was performed to assess the prevalence of hepatitis B virus (HBV), hepatitis C virus (HCV) and HIV infections among infertile couples referring to infertility clinic of Royan Institute.

MATERIALS AND METHODS

This analytical cross-sectional study was performed on 21673 infertile couples referring to infertility clinic of Royan Institute between 2009 and 2014. Serological findings for viral hepatitis B, C and HIV infection were gathered herewith demographic data of the study participants through the study checklist. Ultimately, 302 couples who had at least one positive result in their serological tests were included in the statistical analysis.

RESULTS

The HBV and HCV infections prevalence among study participants were 0.57% and 0.148% respectively; only two cases had HIV infection. HBV and HCV infections prevalence had significant association with the gender of participants, but there was no significant relationship between these infections and infertility types.

CONCLUSION

Viral hepatitis infections screening among infertile couples undergoing assisted reproductive techniques needs more attention.

All-in-one dry-reagent time-resolved immunofluorometric assay for the rapid detection of HIV-1 and -2 infections

An all-in-one (AIO) dry-reagent time-resolved fluorometric immunoassay that requires minimal liquid handling was developed for the detection of anti-HIV-1 and -2 antibodies. To prepare the AIO wells, in vivo biotinylated capture antigens (r-Bio-HIV-1env and r-Bio-HIV-2env) were immobilized on streptavidin-coated microtitration wells and Eu(III) chelate labelled non-biotinylated tracer antigens [r-HIV-1env-Eu(III) and r-HIV-2env-Eu(III)] were dried in stable form in the same wells. The HIV AIO assay was evaluated with serum/plasma samples (n=148) from in-house and commercial panels at two different incubation times of 15 min and 1h. The overall sensitivity of the AIO assay was 98.6% and specificity was 100% for both the incubation times. The AIO assay can accept whole blood matrix. This assay is envisioned to fill the gap between the rapid point-of-care assays and traditional enzyme immunoassays (EIA) in terms of complexity and turnaround time, without compromising the performance.