Analysis of HIV-1 diversity and inflammatory markers in HIV-associated neurocognitive disorders (HAND).

Pathology: Medical Virolog

Peripheral blood lymphocyte proviral DNA predicts neurocognitive impairment in clade C HIV

CITATION: Ruhanya, V. et al. 2020. Peripheral blood lymphocyte proviral DNA predicts neurocognitive impairment in clade C HIV. Journal of NeuroVirology, 26:920–928, doi:10.1007/s13365-020-00882-9.The original publication is available at https://link.springer.comIt is not known if proviral DNA in the periphery corresponds to cognitive status in clade C as it does in clade B and recombinant forms. A cross-sectional study was conducted on participants investigated for HIV-associated neurocognitive impairment in South Africa. HIV-1 proviral DNA was quantified using a PCR assay targeting a highly conserved HIV-1 LTR-gag region. Fifty-four (36.7%) participants were cognitively impaired and 93 (63.3%) were not impaired. Forty-three (79.6%) of the cognitively impaired participants were female and 11 (20.4%) were male. There was no significant age difference between cognitively impaired and unimpaired participants (p = 0.42). HIV-1 DNA in cognitively impaired PLWH was significantly higher than in cognitively normal individuals (p = .016). Considering impaired participants, lymphocyte HIV-1 DNA was significantly higher in males than females (p = 0.02). There was a modest positive correlation between lymphocyte HIV-1 DNA and global deficit scores (GDS) r = 0.176; p = 0.03). The two measures of viral load, lymphocyte HIV-1 DNA copies/million and plasma RNA copies/ml, were positively correlated (r = 0.39; p < .001). After adjusting for other covariates, age, sex, treatment status, and the interactions between impairment and treatment, the multivariate regression showed association between proviral load and neurocognitive impairment; omega effect size was 0.04, p value = 0.010. The burden of HIV-1 peripheral blood lymphocyte proviral DNA corresponds to neurocognitive impairment among individuals infected with clade C disease. Therefore, therapeutic strategies to reduce the HIV-1 proviral DNA reservoir in lymphocytes may improve neurocognitive outcomes in PLWH.Poliomyelitis Research Foundation (PRF)National Research Foundation (NRF)South African Medical Research Council (SAMRC)Publisher's versio

Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.

BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limite

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

Efficiency of glass wool adsorption-elution technique for the recovery of enteric viruses from water

One of the major obstacles to human health relates to unsafe water and poor sanitation. Faecal contamination of source and drinking water introduces enteric pathogens which result in disease outbreaks. Therefore monitoring the occurrence of human pathogens in source water and drinking water is necessary in order to limit the prevalence of environmentally transmitted infectious diseases. Knowledge of pathogen loads in source waters provides the basis for establishing treatment requirements and health standards stipulated by water regulatory authorities and assists in determining the efficacy of water treatment plants. Water quality monitoring and public health assurance is performed routinely by enumerating faecal indicator bacteria. Studies have demonstrated that there is no relationship between current bacterial indicator detection and the presence of enteric pathogenic viruses in treated and source water. There is therefore a need to monitor the levels of pathogenic enteric viruses in surface waters, irrigation water, sewage effluent as well as treated drinking water for public health safety and quality assessment. However due to the low concentration of viruses in water matrices and presence of inhibitors, efficient concentration methods from large quantities of water are essential. The analysis of water for enteric viruses is a two stage process: the first step is to apply efficient viral recovery and concentration procedures from large volumes (10–1000 ℓ) of water followed by viral detection. Glass wool adsorption-elution is a cost-effective and practical viral recovery method for use in resource-limiting settings. The main objective of this study was to determine the efficiency of the glass wool adsorptionelution method for the recovery of viruses of different genera from large water samples (10 ℓ) of different quality by a step-by-step evaluation of its performance using seeding experiments. Standard curves were prepared using quantitative reverse transcription-polymerase chain reactions (RT-PCR)(for RNA viruses) and PCR (for DNA viruses). The efficiency of recovery (EOR) of glass wool between tap water and turbid surface water was compared for six enteric viruses by examining the recovery and loss of viruses at each stage of the process. The generalised linear statistical model was applied to compare the EOR of each virus in each water type and results clearly indicated that the EOR varied for each virus type and was higher for tap water than for turbid surface water for each virus. There was extensive loss of virus in the flow through and this was also higher for the turbid water than the tap water. In this study it was also demonstrated that mengovirus behaved similarly to the pathogenic enteric viruses and was therefore a suitable process control to monitor viral recovery and nucleic acid extraction when recovering and detecting enteric viruses from environmental matrices using glass wool adsorption method. It was also demonstrated that EOR of glass wool for turbid surface water was underestimated as the poor sample quality affected the quantitative molecular detection assays. Adenovirus was shown to be a suitable indicator for virus contamination of water. Modification of the glass wool column preparation did not result in significant difference in EOR but an increase in the amount of glass wool used resulted in reduction in EOR. There were no significant differences between the two polyethylene glycol/sodium chloride (PEG6000/NaCl and PEG8000/NaCl) precipitation methods applied to the secondary concentration of the viruses, but it should be noted that the former has the disadvantage of overnight incubation. The EOR of glass wool was shown to be influenced by pH of the sample. The optimal sample pH for the recovery of hepatitis A virus in turbid surface water was pH 6.0. The study provides valuable new data on the EOR of enteric viruses using the glass wool adsorption-elution technique where virus quantities could be traced from seeding to detection by molecular-based methods.Dissertation (MSc)--University of Pretoria, 2013.Medical VirologyMScUnrestricte

HIV/AIDS vaccines for Africa: scientific opportunities, challenges and strategies

More than decades have already elapsed since human immunodeficiency virus (HIV) was identified as the causative agent of acquired immunodeficiency syndrome (AIDS). The HIV has since spread to all parts of the world with devastating effects. In sub-saharan Africa, the HIV/AIDS epidemic has reached unprecedented proportions. Safe, effective and affordable HIV/AIDS vaccines for Africans are therefore urgently needed to contain this public health problem. Although, there are challenges, there are also scientific opportunities and strategies that can be exploited in the development of HIV/AIDS vaccines for Africa. The recent RV144 Phase III trial in Thailand has demonstrated that it is possible to develop a vaccine that can potentially elicit modest protective immunity against HIV infection. The main objective of this review is to outline the key scientific opportunities, challenges and strategies in HIV/AIDS vaccine development in Africa

Human papillomavirus genotypes in cervical cancer and vaccination challenges in Zimbabwe

Cervical cancer is one of the major causes of morbidity and mortality in women in Zimbabwe. This is mainly due to the high prevalence of high-risk human papillomavirus (HPV) genotypes in the population. So far, few studies have been done that showed the presence of high-risk genital HPV genotypes such as 16, 18, 31, 33, 52, 58 and 70 in Zimbabwean women with cervical cancer. The prevalence of HPV DNA in women with cervical cancer has been shown to range from 63% to 98%. The high-risk HPV 16, 18, 31, 33 and 58 were the most common genotypes in all the studies. The introduction of the new HPV vaccines, HPV2 and HPV4, which protect against HPV genotypes 16 and 18 into Zimbabwe is likely to go a long way in reducing deaths due to cervical cancer. However, there are few challenges to the introduction of the vaccines. The target population for HPV vaccination is at the moment not well-defined. The other challenge is that the current HPV vaccines confer only type-specific (HPV 16 and 18) immunity leaving a small proportion of Zimbabwean women unprotected against other high-risk HPV genotypes such as 31, 33 and 58. Future HPV vaccines such as the nanovalent vaccine will be more useful to Zimbabwe as they will protect women against more genotypes

Occurrence of HBV/HIV coinfection by laboratory values in Roma, Lesotho

OBJECTIVE: This study was an assessment of the coinfection status of patients with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) in Lesotho, and this has been rarely reported. METHODS: This was a retrospective study, in a laboratory setting, on HBV/HIV coinfection among 304 HIV-positive patients who were screened for HBsAg in St Joseph's Hospital records between March 2011 and December 2013. Demographic characteristics, HIV status, indications for HBsAg screening, HBsAg results and liver function test results including alanine transaminase (ALT), aspartate transaminase (AST) and alkaline phosphatase were reviewed from the patient and laboratory registers. RESULTS: In this study 10.5% of 304 HIV-positive patients had HBV/HIV coinfection. With respect to gender, males had a significantly higher (p=0.048) rate of HBV/HIV coinfection in this study. Increased levels of ALT (p=0.013) and AST (p=0.014) were significantly associated with HBV/HIV coinfection status. CONCLUSION: Gender and liver function tests are important predictors for HBV/HIV coinfection. Screening for HBV coinfection in HIV-positive patients is recommended