CoVnita, an end-to-end privacy-preserving framework for SARS-CoV-2 classification.

Classification of viral strains is essential in monitoring and managing the COVID-19 pandemic, but patient privacy and data security concerns often limit the extent of the open sharing of full viral genome sequencing data. We propose a framework called CoVnita, that supports private training of a classification model and secure inference with the same model. Using genomic sequences from eight common SARS-CoV-2 strains, we simulated scenarios where the data was distributed across multiple data providers. Our framework produces a private federated model, over 8 parties, with a classification AUROC of 0.99, given a privacy budget of [Formula: see text]. The roundtrip time, from encryption to decryption, took a total of 0.298 s, with an amortized time of 74.5 ms per sample.

Co-factors for abnormal lactate levels among persons with HIV disease at a tertiary HIV care setting in South India.

BACKGROUND: The co-factors underlying abnormal lactate level remains to be determined in resource-limited settings. In a cross-sectional study conducted between January 2004 and July 2006, we determined the proportion of HIV-infected persons with abnormal lactate levels and correlated the association of certain co-factors of abnormal lactate levels at a tertiary HIV care centre in Chennai, Southern India. METHODS: Lactate was estimated by the enzymatic method using an Olympus AU 400 autoanalyzer. Absolute CD4+T lymphocyte count was determined by the Guava personal cell analyser (Guava Technologies Inc., Hayward, CA, USA). Subjects were classified to have normal or abnormal values of lactate based on the reference interval (0.3-2.2 mmol/L). A p value 0.05 was considered statistically significant. RESULTS: A total of 225 HIV-infected individuals (HAART experienced 213 (95%) and HAART naïve (5%)) were included in the analysis. Mean age was 34+/-8 and 36+/-9 years for the individuals with normal and abnormal lactate levels respectively. Of these 185 (82%) had normal (0.3-2.2 mmol/L) and 40 (18%) had abnormal (>2.2 mmol/L) lactate levels. Significant difference in relation to female gender was observed between the normal and abnormal groups (p=0.03). Among the abnormal group, 39 (97.5%) subjects were HAART experienced compared to 174 (94.1%) normal group. Among the abnormal group, 24 (60%) individuals had a CD4 count of <200 cells/microL as compared to 76 (41.1%) normal subjects. CONCLUSION: Female gender should be carefully monitored with respect to their clinical, laboratory and biological data to diminish the occurrence of lactic acidosis.

Changes in antioxidant profile among HIV-infected individuals on generic highly active antiretroviral therapy in southern India.

OBJECTIVE: The role of oxidative stress in disease progression has been shown to be more complicated in HIV-infected individuals receiving highly active antiretroviral therapy (HAART) compared to those who remain treatment-naïve. This study examined the changes in the antioxidant profile of HIV-infected subjects who remained HAART-naïve due to a high CD4 cell count and HIV-negative controls, over a 12-month follow-up period at YRG CARE, a tertiary HIV referral centre in southern India. METHODS: We prospectively studied 35 HIV-infected participants (18 on d4T+3TC+EFV (stavudine+lamivudine+efavirenz), eight on AZT+3TC+EFV (zidovudine+lamivudine+efavirenz), and nine who were antiretroviral therapy-naïve) and 20 HIV-negative controls. Antioxidant profile (total antioxidant status, glutathione reductase, glutathione peroxidase, uric acid, ceruloplasmin, zinc, and albumin), CD4 cell count, plasma viral load, dietary intake, and history of smoking and alcohol use were determined at baseline and at twelve months. RESULTS: At 12 months, participants on HAART showed a significant increase in glutathione peroxidase (baseline: 1765 vs. 12 months: 2850U/l; p<0.001) and albumin (3.6 vs. 4.4g/dl; p<0.001), and a significant decrease in glutathione reductase (52.6 vs. 50.5U/l; p=0.054) and uric acid (5.4 vs. 4.8mg/dl; p=0.027) compared to baseline. Also HAART-naïve participants had a significant increase in albumin (baseline: 3.7 vs.12 months: 4.3g/dl; p=0.023) and a significant decrease in zinc levels (baseline: 79.0 vs.12 months: 74.5microg/dl; p=0.052) from baseline to 12 months. HIV-negative subjects had a significant increase in glutathione reductase at 12 months from baseline (baseline: 37 vs.12 months: 39U/l; p=0.002). No significant difference in total antioxidant status, ceruloplasmin, and zinc levels were observed in HAART-experienced subjects and negative controls over the 12-month follow-up period. CONCLUSION: This study documents changes in antioxidants over a period of time in HAART-experienced subjects in a southern India setting.

GB virus infection: a silent anti-HIV panacea within?

The GB virus (GBV)/hepatitis G virus is a member of the Flaviviridae family and belongs to the hepatitis group of viruses transmitted parenterally, common among intravenous drug users. The strong association between GBV and HIV infection suggests that the two viruses may share similar epidemiological and transmission features. GBV infection is widely believed to prolong HIV disease progression as well as decreasing the HIV viral load and increasing the CD4(+) T-cell level. GBV-driven anti-E2 antibodies have been shown to inhibit HIV replication in vitro. Preliminary studies also suggest that GBV infection of peripheral blood mononuclear cells leads to increased production of beta-chemokines, which may explain the in vitro inhibitory effects and warrants further studies. With sufficient knowledge of resistance patterns studied in tropical south India, researchers are now keen to study the competitive interactions between GBV-induced chemokines and HIV ligands to bind CCR5.