As part of the Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa (HAALSI), we investigated sleep habits and their interactions with HIV or non-communicable diseases (NCDs) in 5059 participants (median age: 61, interquartile range: 52-71, 54% females). Self-reported sleep duration was 8.2 ± 1.6h, and bed and rise times were 20:48 ± 1:15 and 05:31 ± 1:05 respectively. Ratings of insufficient sleep were associated with older age, lack of formal education, unemployment, and obesity (p < 0.05). Ratings of restless sleep were associated with being older, female, having more education, being unemployed, and single. Hypertension was associated with shorter self-reported sleep duration, poor sleep quality, restless sleep, and periods of stopping breathing during the night (p < 0.05). HIV positive individuals not on antiretroviral treatment (ART) reported more nocturnal awakenings than those on ART (p = 0.029) and HIV negative individuals (p = 0.024), suggesting a negative net effect of untreated infection, but not of ART, on sleep quality. In this cohort, shorter, poor-quality sleep was associated with hypertension, but average self-reported sleep duration was longer than reported in other regions globally. It remains to be determined whether this is particular to this cohort, South Africa in general, or low- to middle-income countries undergoing transition.

Recently a number of novel adenoviruses have been isolated from diverse bat species and from diverse geographical locations. We describe the isolation of a novel adenovirus (Family Adenoviridae, genus Mastadenovirus) from a pool of liver and spleen tissue of an apparently healthy wild-caught Egyptian fruit bat (Rousettus aegyptiacus) in South Africa. Genetically the virus is most closely related to four mastadenoviruses recently isolated in China, from Miniopterus schreibersi and Rousettus leschenaultii bats, which are highly divergent from previously identified bat adenoviruses. The length of the Rousettus aegyptiacus adenovirus-3085 (RaegAdV-3085) genome, at 29,342 bp is similar to its closest relatives, and contains 27 open reading frames. The RaegAdV-3085 genome has a low G + C content (36.4%) relative to other viruses in the genus (between 43.6 and 63.9%) but similar to its closest relatives. The inverted terminal repeat (ITR) of RaegAdV-3085 is only 40 bp compared to between 61 and 178 bp of its closest relatives. The discovery of RaegAdV-3085 expands the diversity of known adenoviruses in bats and might represent a member of a new mastadenovirus species in bats.

The gut microbiota of mosquitoes is a crucial determinant of their fitness. As such, the biology of the gut microbiota of Anopheles arabiensis, a major malaria vector of Southern Africa, was investigated. Two laboratory strains of An. arabiensis were used; SENN, an insecticide susceptible strain, and SENN-DDT, a resistant strain. The strains were supplemented with either non-commensal bacteria or antibiotics via a sucrose source to sterilize the gut. The strains were fed the broad-spectrum bactericidal antibiotic gentamicin, or a preferentially gram-positive bactericidal (vancomycin), gram-negative bactericidal (streptomycin) or broad-spectrum bacteriostatic (erythromycin), either by sugar supplementation or by artificially-spiked blood-meal. The effects on adult mosquito longevity and insecticide resistance phenotype were assessed. Bacteria from the midgut of both strains were characterised by MALDI-TOF mass spectroscopy. Bactericidal antibiotics increased longevity in SENN-DDT. Bacterial supplementation increased insecticide tolerance. Antibiotic supplementation via sugar decreased tolerance to the insecticides deltamethrin and malathion. Blood-supplemented vancomycin decreased insecticide resistance, while gentamicin and streptomycin increased resistance. SENN showed a greater gut bacterial diversity than SENN-DDT, with both strains dominated by Gram-negative bacteria. This study suggests a crucial role for bacteria in An. arabiensis life history, and that gut microflora play variable roles in insecticide resistant and susceptible mosquitoes.

The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 h. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.

Rift Valley fever (RVF) is a mosquito-borne viral zoonosis showing complex epidemiological patterns that are poorly understood in South Africa. Large outbreaks occur in the central interior at long, irregular intervals, most recently in 2010-2011; however, the level of herd immunity of ruminant livestock, a key determinant of outbreaks, is unknown. During 2015-2016 a cross-sectional study on 234 randomly-selected farms investigated the prevalence, patterns of, and factors associated with, antibodies to RVF virus (RVFV) in livestock in an area heavily affected by that outbreak. A RVFV inhibition ELISA was used to screen 977 cattle, 1,549 sheep and 523 goats and information on potential risk factors was collected using a comprehensive questionnaire. The estimated RVFV seroprevalence, adjusted for survey design, was 42.9% in cattle, 28.0% in sheep and 9.3% in goats, showing a high degree of farm-level clustering. Seroprevalence increased with age and was higher on private vs. communal land, on farms with seasonal pans (temporary, shallow wetlands) and perennial rivers and in recently vaccinated animals. Seropositivity amongst unvaccinated animals born after the last outbreak indicates likely viral circulation during the post-epidemic period. The current level of herd immunity in livestock may be insufficient to prevent another large outbreak, should suitable conditions recur.

In June-September 2021, we investigated severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections in domestic dogs and cats (n = 225) in Bangkok and the vicinities, Thailand. SARS-CoV-2 was detected in a dog and a cat from COVID-19 positive households. Whole genome sequence analysis identified SARS-CoV-2 delta variant of concern (B.1.617.2). Phylogenetic analysis showed that SARS-CoV-2 isolated from dog and cat were grouped into sublineage AY.30 and AY.85, respectively. Antibodies against SARS-CoV-2 could be detected in both dog (day 9) and cat (day 14) after viral RNA detection. This study raises awareness on spill-over of variant of concern in domestic animals due to human-animal interface. Thus, surveillance of SARS-CoV-2 in domestic pets should be routinely conducted.

Estimates for prevalence of high blood pressure (BP) among adolescents in Africa vary widely and few studies, if any, have documented the results of the recommended stepwise BP screening. In this cross-sectional study in Tanzania, we aimed to estimate prevalence of sustained high BP in 3 public secondary schools using the American Academy of Pediatrics BP screening strategy. On Day 1, one screening automated office BP (AOBP) measurement (Step 1) was followed by two more AOBP measurements (Step 2). Repeat AOBP measurements were obtained after about one month on adolescents with high AOBP measurements on Day 1 (Step 3). Participants with sustained high BP underwent 24-h ambulatory BP monitoring (step 4). Of all 500 enrolled participants, the prevalence of high blood pressure at each step in the process was 36.6% (183), 25.6% (128), 10.2% (51), and 2.6%(13) respectively for Steps 1-4. All except 6 students completed all 4 steps of the BP screening algorithm as indicated. We conclude that diagnosis of hypertension in African adolescents should use multiple AOBP measurements over multiple days followed by 24-h ABPM. Screening for high BP in school settings appears to be feasible and could provide a platform for cardiovascular disease education and health promotion.

Severe fever with thrombocytopenia syndrome (SFTS) is emerging and the number of SFTS cases increased year by year in China. In order to explore the epidemiology trend, we analyzed the changing epidemiological characteristics of SFTS cases in different years and compare characteristics in different provinces. From 2011 to 2016, a total of 5360 laboratory-confirmed SFTS cases were reported and annual case numbers increased year by year. Most SFTS cases occurred in individuals aged between 40 years and 80 years (91.57%), but age distributions of SFTS cases in different years were significantly different and the median ages increased slightly year by year. The numbers of affected counties from 2011 to 2016 increased sharply from 98 to 167. Of note, the seasonal distributions of SFTS cases in different provinces were significantly different (Fisher = 712.157, P = 0.000) and provinces in south regions showed earlier epidemic peak and longer epidemics durations. The median time from illness onset to confirmation of different years was significantly different (χ2 = 896.088, P = 0.000) and it peaked in 2014. Furthermore, case fatality rate was associated with province, year, and age of SFTS cases. These results may be helpful for authorities to better preventive strategy and improve interventions against SFTS.

Wildlife is a reservoir of emerging infectious diseases of humans and domestic animals. Marmota himalayana mainly resides 2800-4000 m above sea level in the Qinghai-Tibetan Plateau, and is the primary animal reservoir of plague pathogen Yersinia pestis. Recently we isolated a new species, Escherichia marmotae from the faeces of M. himalayana. In this study we characterised E. marmotae by genomic analysis and in vitro virulence testing to determine its potential as a human pathogen. We sequenced the genomes of the seven E. marmotae strains and found that they contained a plasmid that carried a Shigella-like type III secretion system (T3SS) and their effectors, and shared the same O antigen gene cluster as Shigella dysenterae 8 and E. coli O38. We also showed that E. marmotae was invasive to HEp-2 cells although it was much less invasive than Shigella. Thus E. marmotae is likely to be an invasive pathogen. However, E. marmotae has a truncated IpaA invasin, and lacks the environmental response regulator VirF and the IcsA-actin based intracellular motility, rendering it far less invasive in comparison to Shigella. E. marmotae also carried a diverse set of virulence factors in addition to the T3SS, including an IS1414 encoded enterotoxin gene astA with 37 copies, E. coli virulence genes lifA/efa, cif, and epeA, and the sfp gene cluster, Yersinia T3SS effector yopJ, one Type II secretion system and two Type VI secretion systems. Therefore, E. marmotae is a potential invasive pathogen.

Cardiovascular disease (CVD) is the leading cause of death and disability in people with diabetes mellitus (DM), since finding the correlation between DM and CVD risk factors can be effective in preventing the incidence of morbidity and mortality in patients. This study aimed to determine the prevalence of cardiovascular risk factors in people with and without metabolic syndrome (MtS) in DM. This cross-sectional study was part of the Rafsanjan Cohort Study as part of the comprehensive Persian (Prospective Epidemiological Research Studies in IRAN) on 35-70-year old adults with and without MtS in DM. Indicators of CVD risk factors, including gender, age, blood pressure, dyslipidemia, smoking, alcohol consumption, fasting blood sugar, creatinine, blood urea, waist circumference, body mass index, family history, physical inactivity, and fruit and vegetable consumption, were collected in the Persian Cohort Questionnaire. The data was analyzed by SPSS software version 22. The prevalence of MtS in 1933 participants was estimated to be 80% (95% confidence interval 78.1-81.8%). In the logistic regression model, smoking, alcohol consumption, and triglycerides were identified as the factors associated with MtS. Our results show that, based on our study, the prevalence of cardiovascular risk factors in DM was high. The suggested solutions in this field are to reduce smoking and alcohol consumption, as well as to control hypertension, hyperlipidemia, and being overweight.

Bacterial vaginosis (BV) is a highly prevalent disease in women, and increases the risk of pelvic inflammatory disease. It has been given wide attention because of the high recurrence rate. Traditional diagnostic methods based on microscope providing limited information on the vaginal microbiota increase the difficulty in tracing the development of the disease in bacteria resistance condition. In this study, we used deep-sequencing technology to observe dynamic variation of the vaginal microbiota at three major time points during treatment, at D0 (before treatment), D7 (stop using the antibiotics) and D30 (the 30-day follow-up visit). Sixty-five patients with BV were enrolled (48 were cured and 17 were not cured), and their bacterial composition of the vaginal microbiota was compared. Interestingly, we identified 9 patients might be recurrence. We also introduced a new measurement point of D7, although its microbiota were significantly inhabited by antibiotic and hard to be observed by traditional method. The vaginal microbiota in deep-sequencing-view present a strong correlation to the final outcome. Thus, coupled with detailed individual bioinformatics analysis and deep-sequencing technology, we may illustrate a more accurate map of vaginal microbial to BV patients, which provide a new opportunity to reduce the rate of recurrence of BV.

Coronary artery disease (CAD) is one of the most important cardiovascular diseases. Lifestyle and genetic factors play important roles in the development of CAD. The aim of the study is to examine the interaction of dietary patterns and genes on the likelihood of abnormal lipid profile and coronary artery stenosis in Iranians undergoing coronary angiography. This cross-sectional study was performed on 440 patients who underwent coronary angiography. The factor analysis method was used to extract dietary patterns. Commercial kits have been used to assess biochemical parameters. The detection of the rs28362491 genotype was carried out by the method of restriction fragment length polymorphism. Traditional (TDP) and western dietary pattern (WDP) were extracted. We observed an interaction of adherence to TDP and rs28362491 on the odds of having a high Gensini score. These interactions indicated that higher adherence to TDP was associated with higher odds of having a high Gensini score for patients with DD genotype than for those with II genotype. (OR 2.33, 95%CI 1.00-5.44; P = 0.05). These interactions remained statistically significant even after confounder variables. We observed an interaction between higher adherence to TDP and rs28362491 variants on the odds of high low-density lipoprotein cholesterol levels (P = 0.04) in the unadjusted model. We found a significant interaction of this polymorphism and higher adherence to WDP on the odds of having a high Gensini score in the unadjusted model (P = 0.04). This study provides a basis for future research on NF-KB1 gene and diet interaction. More large-scale longitudinal studies are needed to validate these findings.

To investigate the genetic diversity, spatiotemporal dynamics, and transmission networks of HIV-1 CRF55_01B epidemic in China. A total of 209 partial pol gene sequences of HIV-1 CRF55_01B were sampled during 2007-2015 from 7 provinces of China. Phylogenetic analyses and trait diffusion process of these sequences were performed using Bayesian methods. Distance-based molecular network analyses were performed to infer putative relationships. Characteristics of genetically linked individuals were analyzed. Our study identified that HIV-1 CRF55_01B likely originated among men who have sex with men (MSM) in Guangdong province in January 2003 (April 2000-April 2005), and that Guangdong province and MSM are major hubs for the spread of the HIV-1 CRF55_01B epidemic in China. A Bayesian Skygrid plot revealed that the effective population size of HIV-1 CRF55_01B experienced increased phase followed by a plateau. All sequences from persons of unknown risk clustered within groups who reported MSM risk. This could be because Chinese MSM may not report such risk due to HIV/AIDS-related stigmatization and discrimination. This study inferred the transmission dynamics of the HIV-1 CRF55_01B epidemic in China at high resolution. The methods developed in this study may be critical for designing effective HIV prevention strategies in China and beyond.

Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion of K. pneumoniae in support of hospital infection control. The epidemic curve of incident K. pneumoniae cases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested that K. pneumoniae strains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.