Lymphocytes Are the Major Reservoir for Foamy Viruses in Peripheral Blood

AbstractSimian and human foamy virus (FV) DNA can be readily detected in peripheral blood leukocytes. However, it is unknown which leukocyte populations harbor the virusin vivo.We, therefore, analyzed blood samples from nine African green monkeys, four chimpanzees, and two humans for the presence of foamy virus proviral DNA in different FACS-purified leukocyte populations, using a highly sensitive nested polymerase chain reaction (PCR). The CD8+lymphocytes were PCR positive in all 15 samples and the average viral burden was highest in this population. FV DNA was detected in 10 of 15 cell samples enriched for B lymphocytes, and 4 of 9 CD4+lymphocyte, 3 of 13 CD14+monocyte, and 4 of 13 polymorphonuclear leukocyte samples. A highly sensitive reverse transcriptase PCR was performed to detect viral transcripts in peripheral blood leukocytes. All samples were negative. In conclusion, lymphocytes, and especially CD8+T lymphocytes, were found to be a major target for foamy virus in the peripheral blood, but viral gene expression was not detected

No Evidence of HIV and SIV Sequences in Two Separate Lots of Polio Vaccines Used in the First U.S. Polio Vaccine Campaign

AbstractWe obtained sealed vials of two different polio vaccine lots, expiration date 1955, which were used in the first U.S. polio vaccine campaign. These early lots were pulled from the market because they contained live infectious poliovirus which caused polio in some of the vaccines. Theoretically, these vaccines could have contained other infectious retroviruses, including HIV. No viral sequences were detected using RT-PCR analyses with primers capable of amplifying chimpanzee SIV and HIV-1-related viruses nor with primers for macaque SIV, sooty mangabey SIV, and HIV-2-related viruses. Poliovirus sequences were readily amplified by RT-PCR, suggesting that the technique used would have detected SIV or HIV sequences, if present

Development of a Clinical MALDI-ToF Mass Spectrometry Assay for SARS-CoV-2: Rational Design and Multi-Disciplinary Team Work.

The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a country's population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high-throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology-multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct application to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 coronavirus detection-(Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; (1) ease of sampling, (2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution

SARS-CoV-2 Spike Protein Binding of Glycated Serum Albumin-Its Potential Role in the Pathogenesis of the COVID-19 Clinical Syndromes and Bias towards Individuals with Pre-Diabetes/Type 2 Diabetes and Metabolic Diseases

The immune response to SARS‐CoV‐2 infection requires antibody recognition of the spike protein. In a study designed to examine the molecular features of anti‐spike and anti‐nucleocapsid antibodies, patient plasma proteins binding to pre‐fusion stabilised complete spike and nucleocap-sid proteins were isolated and analysed by matrix‐assisted laser desorption ionisation–time of flight (MALDI‐ToF) mass spectrometry. Amongst the immunoglobulins, a high affinity for human serum albumin was evident in the anti‐spike preparations. Careful mass comparison revealed the preferential capture of advanced glycation end product (AGE) forms of glycated human serum albumin by the pre‐fusion spike protein. The ability of bacteria and viruses to surround themselves with serum proteins is a recognised immune evasion and pathogenic process. The preference of SARS‐ CoV‐2 for AGE forms of glycated serum albumin may in part explain the severity and pathology of acute respiratory distress and the bias towards the elderly and those with (pre)diabetic and athero-sclerotic/metabolic disease

Pathology caused by persistent murine norovirus infection.

Subclinical infection of murine norovirus (MNV) was detected in a mixed breeding group of WT and Stat1(-/-) mice with no outward evidence of morbidity or mortality. Investigations revealed the presence of an attenuated MNV variant that did not cause cytopathic effects in RAW264.7 cells or death in Stat1(-/-) mice. Histopathological analysis of tissues from WT, heterozygous and Stat1(-/-) mice revealed a surprising spectrum of lesions. An infectious molecular clone was derived directly from faeces (MNV-O7) and the sequence analysis confirmed it was a member of norovirus genogroup V. Experimental infection with MNV-O7 induced a subclinical infection with no weight loss in Stat1(-/-) or WT mice, and recapitulated the clinical and pathological picture of the naturally infected colony. Unexpectedly, by day 54 post-infection, 50 % of Stat1(-/-) mice had cleared MNV-O7. In contrast, all WT mice remained infected persistently. Most significantly, this was associated with liver lesions in all the subclinically infected WT mice. These data confirmed that long-term persistence in WT mice is established with specific variants of MNV and that despite a subclinical presentation, active foci of acute inflammation persist within the liver. The data also showed that STAT1-dependent responses are not required to protect mice from lethal infection with all strains of MNV

Cross-Neutralisation of Novel Bombali Virus by Ebola Virus Antibodies and Convalescent Plasma Using an Optimised Pseudotype-Based Neutralisation Assay.

Ebolaviruses continue to pose a significant outbreak threat, and while Ebola virus (EBOV)-specific vaccines and antivirals have been licensed, efforts to develop candidates offering broad species cross-protection are continuing. The use of pseudotyped virus in place of live virus is recognised as an alternative, safer, high-throughput platform to evaluate anti-ebolavirus antibodies towards their development, yet it requires optimisation. Here, we have shown that the target cell line impacts neutralisation assay results and cannot be selected purely based on permissiveness. In expanding the platform to incorporate each of the ebolavirus species envelope glycoprotein, allowing a comprehensive assessment of cross-neutralisation, we found that the recently discovered Bombali virus has a point mutation in the receptor-binding domain which prevents entry into a hamster cell line and, importantly, shows that this virus can be cross-neutralised by EBOV antibodies and convalescent plasma

Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa.

Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa

Gobierno universitario : entre la autogestión estamental y la responsabilidad social

<p>Low doses of the relatively neutralization resistant SHIV _SF162P3 isolate were incubated at 37⁰C for four hours with concentrations of the human monoclonal antibody IgG1 b12. The mixture was then added to GHOST cells and allowed to absorb for 24 hours. The cells were washed and cultured for a further 24 hours (4/24/2 assays). Four duplicate cultures were used for each point within a replicate. Data are fitted to a second-order (quadratic) equation. Dotted lines are extrapolations to the horizontal axis calculated from the quadratic plots. Axes are truncated and some symbols are excluded to improve clarity, especially around the origin. <b>A</b>. SHIV_SF162P3 exposed to GHOST cells from passage 7 (1 replicate) and 9 (2 replicates). Gray: control cultures where virus were incubated without monoclonal antibody: y = -0.00285 x² + 1.310 x -6.009; green: Virus pre-incubated with 0.625 µg/ml IgG1 b12: y = -0.00284 x² + 0.939 x -0.517. <b>B</b>. Gray same as for A. blue: Virus pre-incubated with 0.25 µg/ml IgG1 b12: y = -0.000606 x² + 0.870 x + 3.152. <b>C</b>. SHIV_SF162P3 exposed to GHOST cells from passages 15, 17 and 21. Gray: control cultures where virus were incubated without monoclonal antibody: y = 0.00182 x² + 0.665 x + 11.01; green: Virus pre-incubated with 0.625 µg/ml IgG1 b12: y = + 0.00135 x² + 0.487 x + 8.334. <b>D</b>. Gray same as for C. blue: where cultures are exposed to virus pre-incubated with 0.25 µg/ml IgG1 b12: y = 0.00140x² + 0.616x + 5.768. Interval between points where control and 0.25 µg/ml IgG1 b12 plots cut x-axis: 7.81 infectious virus.</p

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.

The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.This work was supported by Wellcome Trust WT091501MAThis is the author accepted manuscript. It is currently under an indefinite embargo pending publication by PLOS

Correlation between pseudotyped virus and authentic virus neutralisation assays, a systematic review and meta-analysis of the literature

Background: The virus neutralization assay is a principal method to assess the efficacy of antibodies in blocking viral entry. Due to biosafety handling requirements of viruses classified as hazard group 3 or 4, pseudotyped viruses can be used as a safer alternative. However, it is often queried how well the results derived from pseudotyped viruses correlate with authentic virus. This systematic review and meta-analysis was designed to comprehensively evaluate the correlation between the two assays. Methods: Using PubMed and Google Scholar, reports that incorporated neutralisation assays with both pseudotyped virus, authentic virus, and the application of a mathematical formula to assess the relationship between the results, were selected for review. Our searches identified 67 reports, of which 22 underwent a three-level meta-analysis. Results: The three-level meta-analysis revealed a high level of correlation between pseudotyped viruses and authentic viruses when used in an neutralisation assay. Reports that were not included in the meta-analysis also showed a high degree of correlation, with the exception of lentiviral-based pseudotyped Ebola viruses. Conclusion: Pseudotyped viruses identified in this report can be used as a surrogate for authentic virus, though care must be taken in considering which pseudotype core to use when generating new uncharacterised pseudotyped viruses