Unsuccessful Cassava Brown Streak Disease (CBSD) evaluation attempts in western Democratic Republic of Congo and implications with cassava root necrosis disease (CRND) etiology

Open Access ArticleCassava brown streak disease (CBSD) is the second most important virus disease after Cassava mosaic disease (CMD), infecting cassava (ManihotesculetaCrantz) in Africa. The disease is caused by two distinct viruses, Cassava brown streak virus [2, 3] and Ugandan Cassava brown streak virus (family, Potyviridae: genus, Ipomovirus). Transmission of CBSV from one plant to another is reported to occur through grafting CBSV-free with infected cuttings and subsequent dissemination by infected cuttings. The basic approach to control of CBSD is selecting planting material from symptomless mother plants. Graft inoculation is the most efficient and effective of the techniques for CBSD virus transmission and consequently cuttings are the most effective way of the disease spreading. In early 2000s, cassava root necrosis similar to those of CBSD were reported in western provinces of Democratic Republic of Congo (RDC) (Kinshasa and Kongo Central) and up to date PCR diagnoses did not detect any causal agent related to the observed symptoms and the disease which was still referred as ‘CBSD-like disease’. Due to lack of molecular data and the similarity of root symptoms with CBSD, the existence of a virus has always been suspected to be the cause of CBSD-like propagation. Thus, 2 field experiments were proposed in order to verify the existence of a systematic transmission of a possible CBSD related virus, knowing that CBSD viruses are transmitted efficiently by cuttings. The first trial focused on the field evaluation of CBSD – like infected and apparently uninfected planting materials, while the second trial involved the importation of tanzanian CBSD resistant genotypes for evaluation in INERA Mvuazi research center under CBSD-like infection conditions. Results of the first trial did not show a systemic transmission of any CBSD-like pathogen while CBSD-resistant parents involved in the second trial all succumbed to CBSD-like disease

First report and preliminary evaluation of cassava root necrosis in Angola

Open Access ArticleCassava is a main staple food for 800 million people world-wide. Production is limited by pest and pathogens. The most devastating cassava viruses are Cassava Brown Streak Virus and Uganda Cassava Brown Streak Virusboth causing severe root necrosis called Cassava Brown Streak Disease. In the last 10 years, the Cassava Brown Streak Disease (CBSD)has spread across Africa from the east coast of Africa to central Africa. Similar root necrosis to cassava brown streak disease has also been identified in the Democratic Republic of Congo where the first symptoms were identified in 2002 in Kinshasa and Kongo central province. In 2012, the presence of CBSD was confirmed in eastern Democratic Republic of Congo. All attempts since 2002 in western Democratic Republic of Congo to identify the cause of these root necrosis have failed. In 2017, a team of scientists surveying the Songololo Territory in the Kongo central province at the northern Angola, identified the same root necrosis similar to CBSD in several localities bordering Angola. These unexpected results will foreshadow the presence of cassava root necrosis in Angola. This preliminary investigation in northern Angola was conducted specifically in the Zaire province and the territory of Mbanza Kongo at approximatively 62 kms from the Democratic Republic of Congo border in order to verify, whether or not, these root necrosis are present in Angola. Results obtained from this exploratory survey in several fields of the Zaire province and territory of Mbanza Kongo confirmed, for the first time, the presence of cassava root necrosis in Angola, similar to CBSD, as identified in western DRC

Assessing the severity and the incidence of Cassava Root Necrosis Disease (CRND) in western Democratic Republic of Congo

Open Access ArticleCassava is the staple food in the Democratic Republic of Congo (DRC) where both the roots and leaves are consumed. This crop is susceptible to several viral diseases, including Cassava Mosaic Disease(CMD) and Cassava Brown Streak Disease(CBSD) in eastern DRC. Following earlier studies that show root necrosis occurring in western DR Care not due to CBSD but to Cassava Root Necrosis Disease (CRND), an exploratory survey was conducted in western DRC from 2016 to 2017 in order to determine the distribution, the severity and the incidence of this disease (previously known as CBSD-like disease). NGS ( Next Generation Sequencing) results confirmed all the previous negative results obtained using PCR and CBSV primers. This suggests that microorganisms such as bacteria or fungi could be responsible for cassava root necrosis in western DRC and is not CBSD as predicted. Five provinces (Bas-Congo, Kinshasa, Bandundu, Equateur and Kasai-Oriental) were surveyed and data were collected according to the harmonized protocols adopted by countries within the West African Virus Epidemiology (WAVE) project. Statistical tests (ANOVA) performed on our data showed that CRND severity did not vary significantly among the provinces of Kinshasa, Bandundu and Bas-Congo which are the areas most affected by the disease. Bas-Congo and Kinshasa provinces presented the highest maximum disease severity (score 3 and 5 respectively), while Equateur province had the lowest disease severity score. Equateur province also had the highest percentage of healthy plants and few plants presented mild symptoms. The overall average of cassava root necrosis severity in western DRC ranged around 1.88 ± 0.08, an approximate score of 2. The overall mean incidence of CRND in western DRC was 22.24 ± 2.4% but reached 100% in localities considered as hotspots (Lukuakua in Bas-Congo and Nguma in Plateau des Batékés). The behaviour of cassava varieties against CRND is similar with CBSD in East Africa, most of improved varieties and landraces are susceptible to both diseases. Correlation analyses showed a positive correlation (r = 0.6940) between severity and incidence of CRND. Therefore, Bas-Congo province is the most affected province, while the province of Equateur is the least affected province in western DRC. Further investigations, including genomic surveillance, should also be conducted in the eastern DRC where CBSD is confirmed to know if CRND is found in conjunction with CBSD and to report possible instances of mixed infections. For medium-term disease control, our study suggests that the development and deployment of control measures including cultivars with resistance to CRND and CBSD should be a priority

Validation of a commercially available indirect assay for SARS-CoV-2 neutralising antibodies using a pseudotyped virus assay.

Objectives To assess whether a commercially available CE-IVD, ELISA-based surrogate neutralisation assay (cPass, Genscript) provides a genuine measure of SARS-CoV-2 neutralisation by human sera, and further to establish whether measuring responses against the RBD of S was a diagnostically useful proxy for responses against the whole S protein. Methods Serum samples from 30 patients were assayed for anti-NP responses, for ‘neutralisation’ by the surrogate neutralisation assay and for neutralisation by SARS-CoV-2 S pseudotyped virus assays utilising two target cell lines. Correlation between assays was measured using linear regression. Results The responses observed within the surrogate neutralisation assay demonstrated an extremely strong, highly significant positive correlation with those observed in both pseudotyped virus assays. Conclusions The tested ELISA-based surrogate assay provides an immunologically useful measure of functional immune responses in a much quicker and highly automatable fashion. It also reinforces that detection of anti-RBD neutralising antibodies alone is a powerful measure of the capacity to neutralise viral infection

Comparison of two interferon-gamma release assays (QuantiFERON-TB Gold In-Tube and T-SPOT.TB) in testing for latent tuberculosis infection among HIV-infected adults.

There is currently no 'gold standard' for diagnosis of latent tuberculosis infection (LTBI), and both the tuberculin skin test and interferon-gamma release assays (IGRAs) are used for diagnosis; the latter have a higher sensitivity than tuberculin skin tests for diagnosis of LTBI in HIV-infected individuals with lower CD4 counts. No evidence base exists for selection of IGRA methodology to identify LTBI among human immunodeficiency virus-infected patients in the UK. We prospectively evaluated two commercially available IGRA methods (QuantiFERON-TB Gold In Tube [QFG] and T-SPOT.TB) for testing LTBI among HIV-infected patients potentially nosocomially exposed to an HIV-infected patient with 'smear-positive' pulmonary tuberculosis. Among the exposed patients median CD4 count was 550 cells/µL; 105 (90%) of 117 were receiving antiretroviral therapy, of who 104 (99%) had an undetectable plasma HIV load. IGRAs were positive in 12 patients (10.3%); QFG positive in 11 (9.4%) and T-SPOT.TB positive in six (5.1%); both IGRAs were positive in five patients (4.3%). There was one indeterminate QFG and one borderline T-SPOT.TB result. Concordance between the two IGRAs was moderate (κ = 0.56, 95% confidence interval = 0.27-0.85). IGRAs were positive in only 4 (29%) of 14 patients with previous culture-proven tuberculosis. No patient developed tuberculosis during 20 months of follow-up

Attempts to identify Cassava Brown Streak Virus in western Democratic Republic of Congo

Open Access ArticleRoot necrosis similar to those of the cassava brown streak disease (CBSD) were observed on cassava in western provinces of the Democratic Republic of Congo (DR.Congo) in the early 2000’s. However molecular laboratory diagnosis were not able to detect any causative agent responsible for the attacks, hence, the disease related to these symptoms was named CBSD-like disease. In order to assess the distribution and the incidence of the CBSD-like disease, surveys were carried out in four western provinces, comprising, Kwango and Kwilu, Sud Ubangi, Kinshasa and Kongo Central. CBSD-like disease was observed in all surveyed provinces on the basis of root symptoms because foliar symptoms were different to those of the documented cases of CBSD in other parts of east Africa. CBSD-like disease incidence was high in Kongo Central and Sud Ubangi, exceeding an average of 50 %, but low in Kwango and Kwilu (32.8%) and in Kinshasa (19.1%). During the surveys, cassava leaf samples were collected for lab identification of the causal agent. PCR diagnosis was done on these samples using primers specific for the two known CBSVs. All samples tested negative with no amplification of DNA fragments of the correct size. Thus, further analysis on the causative organism is needed using Next Generation Sequencing (NGS) approaches. NGS approaches will help also to identify the causative organism in other Central Africa countries (Angola, Congo-Brazzaville and Gabon) where such cassava root necrosis have been reported or are suspected

Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics

BACKGROUND: COVID-19 is infrequently complicated by bacterial co-infection, but antibiotic prescriptions are common. We used community-acquired pneumonia (CAP) as a benchmark to define the processes that occur in bacterial pulmonary infections, testing the hypothesis that baseline inflammatory markers and their response to antibiotic therapy could distinguish bacterial co-infection from COVID-19. METHODS: Retrospective cohort study of CAP (lobar consolidation on chest radiograph) and COVID-19 (PCR detection of SARS-CoV-2) patients admitted to Royal Free Hospital (RFH) and Barnet Hospital (BH), serving as independent discovery and validation cohorts. All CAP and >90% COVID-19 patients received antibiotics on hospital admission. RESULTS: We identified 106 CAP and 619 COVID-19 patients at RFH. Compared with COVID-19, CAP was characterized by elevated baseline white cell count (WCC) [median 12.48 (IQR 8.2-15.3) versus 6.78 (IQR 5.2-9.5) ×106 cells/mL, P 8.2 × 106 cells/mL or falling CRP identified 94% of CAP cases, and excluded bacterial co-infection in 46% of COVID-19 patients. CONCLUSIONS: We propose that in COVID-19, absence of both elevated baseline WCC and antibiotic-related decrease in CRP can exclude bacterial co-infection and facilitate antibiotic stewardship efforts

The Cytomegalovirus gB/MF59 vaccine candidate induces antibodies against an antigenic domain controlling cell-to-cell spread

Vaccination against human cytomegalovirus (CMV) infection remains high priority. A recombinant form of a protein essential for CMV entry, glycoprotein B (gB), demonstrated partial protection in a clinical trial (NCT00299260) when delivered with the MF59 adjuvant. Although the antibody titre against gB correlated with protection poor neutralising responses against the 5 known antigenic domains (AD) of gB were evident. Here, we show that vaccination of CMV seronegative patients induces an antibody response against a region of gB we term AD-6. Responses to the polypeptide AD-6 are detected in >70% of vaccine recipients yet in <5% of naturally infected people. An AD-6 antibody binds to gB and to infected cells but not the virion directly. Consistent with this, the AD-6 antibody is non-neutralising but, instead, prevents cell-cell spread of CMV in vitro. The discovery of AD-6 responses has the potential to explain part of the protection mediated by gB vaccines against CMV following transplantation

Detection of low-frequency K103N mutants after unstructured discontinuation of efavirenz in the presence of the CYP2B6 516 TT polymorphism

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Post-vaccination COVID-19: A case-control study and genomic analysis of 119 breakthrough infections in partially vaccinated individuals

BACKGROUND: Post-vaccination infections challenge the control of the COVID-19 pandemic. METHODS: We matched 119 cases of post-vaccination SARS-CoV-2 infection with BNT162b2 mRNA, or ChAdOx1 nCOV-19, to 476 unvaccinated patients with COVID-19 (Sept 2020-March 2021), according to age and sex. Differences in 60-day all-cause mortality, hospital admission, and hospital length of stay were evaluated. Phylogenetic, single nucleotide polymorphism (SNP) and minority variant allele (MVA) full genome sequencing analysis was performed. RESULTS: 116/119 cases developed COVID-19 post first vaccination dose (median 14 days, IQR 9 - 24 days). Overall, 13/119 (10∙9%) cases and 158/476 (33∙2%) controls died (p<0.001), corresponding to 4∙5 number needed to treat (NNT). Multivariably, vaccination was associated with 69∙3% (95%CI 45∙8 - 82∙6) relative risk (RR) reduction in mortality. Similar results were seen in subgroup analysis for patients with infection onset ≥14 days after first vaccination (RR reduction 65∙1%, 95%CI 27∙2 - 83∙2, NNT 4∙5), and across vaccine subgroups (BNT162b2: RR reduction 66%, 95%CI 34∙9 - 82∙2, NNT 4∙7, ChAdOx1: RR reduction 78∙4%, 95%CI 30∙4 - 93∙3, NNT 4∙1). Hospital admissions (OR 0∙80, 95%CI 0∙51 - 1∙28), and length of stay (-1∙89 days, 95%CI -4∙57 - 0∙78) were lower for cases, while Ct values were higher (30∙8 versus 28∙8, p = 0.053). B.1.1.7 was the predominant lineage in cases (100/108, 92.6%) and controls (341/446, 76.5%). Genomic analysis identified one post-vaccination case harboring the E484K vaccine escape mutation (B.1.525 lineage). CONCLUSIONS: Previous vaccination reduces mortality when B.1.1.7 is the predominant lineage. No significant lineage-specific genomic changes during phylogenetic, SNP and MVA analysis were detected