Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

Efficacy and Tolerance of Thymus Vulgaris Extract in Patients with Covid-19

The coronavirus disease 19 (COVID-19) has been a pandemic since February 2020. So far, no effective treatment has been found. WHO has recommended research on medicinal plants as an alternative treatment course. Several studies conducted on Thymus vulgaris have established its antioxidant, antiviral and immunomodulatory properties that induce the elimination of viruses such as Herpes simplex Virus 1 and 2. Following this, we initiated a study entitled Efficacy and tolerance of Thymus vulgaris extract in patients with coronavirus 2019. Material and method: Thymus vulgaris powder was used in this study. A consent letter and a questionnaire about the patients’ symptoms were prepared to be used by a research investigator. According to the statistical calculations of this cohort study, 161 patients testing positive for COVID-19 PCR were consecutively recruited, of which 75 patients were not exposed to Thymus vulgaris and 86 patients were exposed. Information from the questionnaire was gathered from the patients before the initiation of conventional treatment (vitamin C 1000 1 tablet/day, Zinc 20 mg 1tablet/day, Azithromycin 500 1cp day and amoxicillin/clavulamic acid 1g/125 1 tablet per 12 hours for six days in both cohorts) and by combining Thymus vulgaris (1 teaspoon, i.e. 5g, in 100 ml of hot water to be taken every 8 hours) by the patients in the exposed cohort. After three days of this treatment, the evaluative part of the questionnaire was completed to assess the impact of taking or not taking Thymus vulgaris on early symptoms and tolerance; on the 10th day after the start of treatment, the PCR control test was carried out. Thereafter, the various statistical analyses were performed. Results: Statistical evaluation after three days of treatment shows that taking Thymus vulgaris has a statistically significant positive effect on cough (p <0.01), dyspnoea (p <0.001), dizziness (p <0.029), fatigue (p <0.001), anorexia (p <0.001), chest pain (p <0.001), fever (p <0.024), agueusia (p <0.029) and anosmia (p <0.001). There was a significant decrease in neutrophils (p <0.01); in addition, the lymphocyte count increased significantly (p <0.001) as did the serum calcium level (p <0.03). Blood urea level decreased significantly (p <0.01). Significant negative results of the COVID-19 PCR were obtained at Day 10 in the exposed group (p <0.001). In addition, there was no significant change in other biological parameters such as creatinine, blood glucose, aspartate amino transferase. Conclusion: Results of this study show that the use of the powder of Thymus vulgaris, a medicinal plant, with antioxidant, immunomodulatory and antiviral properties, was very effective on coronavirus-induced symptoms and virus elimination. Moreover, there was good tolerance after taking Thymus vulgaris.

Proposed approaches for coronaviruses elimination from wastewater: Membrane techniques and nanotechnology solutions

Since the beginning of the third Millennium, specifically during the last 18 years, three outbreaks of diseases have been recorded caused by coronaviruses (CoVs). The latest outbreak of these diseases was Coronavirus Disease 2019 (COVID-19), which has been declared by the World Health Organization (WHO) as a pandemic. For this reason, current efforts of the environmental, epidemiology scientists, engineers, and water sector professionals are ongoing to detect CoV in environmental components, especially water, and assess the relative risk of exposure to these systems and any measures needed to protect the public health, workers, and public, in general. This review presents a brief overview of CoV in water, wastewater, and surface water based on a literature search providing different solutions to keep water protected from CoV. Membrane techniques are very attractive solutions for virus elimination in water. In addition, another essential solution is nanotechnology and its applications in the detection and protection of human and water systems.

Endocrinopathies in the era of coronavirus infection

Difficulties in the treatment of COVID-19 have determined the need to systematize the factors for the development of complications, critical conditions and death. Endocrine and metabolic disorders associated with obesity, insulin resistance, chronic inflammation, and lipid and fatty acid metabolism disorders increase immunological dysregulation and make these patients vulnerable to infection. The data from the observations made it possible to single out diabetes mellitus, obesity as a risk factor aggravating the course of COVID-19, and to state the duration of the virus elimination period, potentiation of cardiovascular diseases, an increase in the production of pro-inflammatory cytokines, coagulopathy - factors in the development of unfavorable outcomes. The article presents generalized data on the organization of medical care for patients with endocrine pathology during the coronavirus pandemic

Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses.

Destruction mechanisms of ozone over SARS-CoV-2

In this pandemic SARS-CoV-2 crisis, any attempt to contain and eliminate the virus will also stop its spread and consequently decrease the risk of severe illness and death. While ozone treatment has been suggested as an effective disinfection process, no precise mechanism of action has been previously reported. This study aimed to further investigate the effect of ozone treatment on SARS-CoV-2. Therefore, virus collected from nasopharyngeal and oropharyngeal swab and sputum samples from symptomatic patients was exposed to ozone for different exposure times. The virus morphology and structure were monitored and analyzed through Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), Atomic Absorption Spectroscopy (AAS), and ATR-FTIR. The obtained results showed that ozone treatment not only unsettles the virus morphology but also alters the virus proteins’ structure and conformation through amino acid disturbance and Zn ion release from the virus non-structural proteins. These results could provide a clearer pathway for virus elimination and therapeutics preparation.

Australia could miss the WHO hepatitis C virus elimination targets due to declining treatment uptake and ongoing burden of advanced liver disease complications

Australia was one of the first countries to introduce government-funded unrestricted access to direct-acting antiviral (DAA) therapy, with 88,790 treated since March 2016. However, treatment uptake is declining which could potentially undermine Australia’s progress towards the WHO HCV elimination targets. Using mathematical modelling, we updated estimates for those living with chronic HCV in Australia, new cases of decompensated cirrhosis (DC), hepatocellular carcinoma (HCC), and liver-related mortality among the HCV-cured and viraemic populations from 2015 to 2030. We considered various DAA treatment scenarios incorporating annual treatment numbers to 2020, and subsequent uptake per year of 6,790 (pessimistic), 8,100 (intermediate), and 11,310 (optimistic). We incorporated the effects of excess alcohol consumption and reduction in progression to DC and HCC among cirrhosis-cured versus viraemic individuals. At the end of 2020, we estimated 117,810 Australians were living with chronic HCV. New cases per year of DC, HCC, and liver-related mortality among the HCV viraemic population decreased rapidly from 2015 (almost eliminated by 2030). In contrast, the growing population size of those cured with advanced liver disease meant DC, HCC, and liver-related mortality declined slowly. The estimated reduction in liver-related mortality from 2015 to 2030 in the combined HCV viraemic and cured population is 25% in the intermediate scenario. With declining HCV treatment uptake and ongoing individual-level risk of advanced liver disease complications, including among cirrhosis-cured individuals, Australia is unlikely to achieve all WHO HCV elimination targets by 2030.