Vector Competence of the Invasive Mosquito Species Aedes koreicus for Arboviruses and Interference with a Novel Insect Specific Virus

The global spread of invasive mosquito species increases arbovirus infections. In addition to the invasive species Aedes albopictus and Aedes japonicus, Aedes koreicus has spread within Central Europe. Extensive information on its vector competence is missing. Ae. koreicus from Germany were investigated for their vector competence for chikungunya virus (CHIKV), Zika virus (ZIKV) and West Nile virus (WNV). Experiments were performed under different climate conditions (27 ± 5 °C; 24 ± 5 °C) for fourteen days. Ae. koreicus had the potential to transmit CHIKV and ZIKV but not WNV. Transmission was exclusively observed at the higher temperature, and transmission efficiency was rather low, at 4.6% (CHIKV) or 4.7% (ZIKV). Using a whole virome analysis, a novel mosquito-associated virus, designated Wiesbaden virus (WBDV), was identified in Ae. koreicus. Linking the WBDV infection status of single specimens to their transmission capability for the arboviruses revealed no influence on ZIKV transmission. In contrast, a coinfection of WBDV and CHIKV likely has a boost effect on CHIKV transmission. Due to its current distribution, the risk of arbovirus transmission by Ae. koreicus in Europe is rather low but might gain importance, especially in regions with higher temperatures. The impact of WBDV on arbovirus transmission should be analyzed in more detail.

Personalized Virus Load Curves for Acute Viral Infections

We introduce an explicit function that describes virus-load curves on a patient-specific level. This function is based on simple and intuitive model parameters. It allows virus load analysis of acute viral infections without solving a full virus load dynamic model. We validate our model on data from mice influenza A, human rhinovirus data, human influenza A data, and monkey and human SARS-CoV-2 data. We find wide distributions for the model parameters, reflecting large variability in the disease outcomes between individuals. Further, we compare the virus load function to an established target model of virus dynamics, and we provide a new way to estimate the exponential growth rates of the corresponding infection phases. The virus load function, the target model, and the exponential approximations show excellent fits for the data considered. Our virus-load function offers a new way to analyze patient-specific virus load data, and it can be used as input for higher level models for the physiological effects of a virus infection, for models of tissue damage, and to estimate patient risks.

SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator

SARS coronavirus-2 (SARS-CoV-2) is causing a global pandemic with large variation in COVID-19 disease spectrum. SARS-CoV-2 infection requires host receptor ACE2 on lung epithelium, but epithelial underpinnings of variation are largely unknown. We capitalized on comprehensive organoid assays to report remarkable variation in SARS-CoV-2 infection rates of lung organoids from different subjects. Tropism is highest for TUBA- and MUC5AC-positive organoid cells, but levels of TUBA-, MUC5A-, or ACE2- positive cells do not predict infection rate. We identify surface molecule Tetraspanin 8 (TSPAN8) as novel mediator of SARS-CoV-2 infection, which is not downregulated by this specific virus. TSPAN8 levels, prior to infection, strongly correlate with infection rate and TSPAN8-blocking antibodies diminish SARS-CoV-2 infection. We propose TSPAN8 as novel functional biomarker and potential therapeutic target for COVID-19.

SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator

SARS coronavirus-2 (SARS-CoV-2) is causing a global pandemic with large variation in COVID-19 disease spectrum. SARS-CoV-2 infection requires host receptor ACE2 on lung epithelium, but epithelial underpinnings of variation are largely unknown. We capitalized on comprehensive organoid assays to report remarkable variation in SARS-CoV-2 infection rates of lung organoids from different subjects. Tropism is highest for TUBA- and MUC5AC-positive organoid cells, but levels of TUBA-, MUC5A-, or ACE2- positive cells do not predict infection rate. We identify surface molecule Tetraspanin 8 (TSPAN8) as novel mediator of SARS-CoV-2 infection, which is not downregulated by this specific virus. TSPAN8 levels, prior to infection, strongly correlate with infection rate and TSPAN8-blocking antibodies diminish SARS-CoV-2 infection. We propose TSPAN8 as novel functional biomarker and potential therapeutic target for COVID-19.

Aptamer BC 007’s Affinity to Specific and Less-Specific Anti-SARS-CoV-2 Neutralizing Antibodies

COVID-19 is a pandemic respiratory disease that is caused by the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Anti-SARS-CoV-2 antibodies are essential weapons that a patient with COVID-19 has to combat the disease. When now repurposing a drug, namely an aptamer that interacts with SARS-CoV-2 proteins for COVID-19 treatment (BC 007), which is, however, a neutralizer of pathogenic autoantibodies in its original indication, the possibility of also binding and neutralizing anti-SARS-CoV-2 antibodies must be considered. Here, the highly specific virus-neutralizing antibodies have to be distinguished from the ones that also show cross-reactivity to tissues. The last-mentioned could be the origin of the widely reported SARS-CoV-2-induced autoimmunity, which should also become a target of therapy. We, therefore, used enzyme-linked immunosorbent assay (ELISA) technology to assess the binding of well-characterized publicly accessible anti-SARS-CoV-2 antibodies (CV07-209 and CV07-270) with BC 007. Nuclear magnetic resonance spectroscopy, isothermal calorimetric titration, and circular dichroism spectroscopy were additionally used to test the binding of BC 007 to DNA-binding sequence segments of these antibodies. BC 007 did not bind to the highly specific neutralizing anti-SARS-CoV-2 antibody but did bind to the less specific one. This, however, was a lot less compared to an autoantibody of its original indication (14.2%, range 11.0–21.5%). It was also interesting to see that the less-specific anti-SARS-CoV-2 antibody also showed a high background signal in the ELISA (binding on NeutrAvidin-coated or activated but noncoated plastic plate). These initial experiments suggest that the risk of binding and neutralizing highly specific anti-SARS CoV-2 antibodies by BC 007 should be low.

Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study

Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed. Many of them assign sequenced reads to specific taxa to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient virome data remains unknown. In this work, we conduct an extensive simulation study using public viral sequences to establish which tool is the most suitable for ancient virome studies. We compare the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulate reads by adding noise typical of ancient DNA to a randomly chosen set of publicly available viral sequences and to the human genome. We fragment the DNA into different lengths, add sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measure the resulting precision and sensitivity for all classifiers. Across most simulations, 119 out of the 120 simulated viruses are recovered by Centrifuge, Kraken2 and DIAMOND in contrast to MetaPhlAn2 which recovers only around one third. While deamination damage has little impact on the performance of the classifiers, DIAMOND and Kraken2 cannot classify very short reads. For data with longer fragments, if precision is strongly favoured over sensitivity, DIAMOND performs best. However, since Centrifuge can handle short reads and since it achieves the highest sensitivity and precision at the species level, it is our recommended tool overall. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, if the goal is to detect a specific virus, given the high variability observed among tested viral sequences, a simulation study to determine if a given tool can recover the virus of interest should be conducted prior to analysing real data.

Proteasome homeostasis is essential for a robust cauliflower mosaic virus infection

SummaryThe ubiquitin-proteasome system (UPS) is essential for the maintenance and shifts in protein homeostasis, and thereby forms a founding pillar in virtually all cellular processes including plant immunity and viral infections. According to its importance in fine-tuning the complex plant immune response, proteasomal defects result in divergent outcomes including both resistance and susceptibility phenotypes in response to viruses. The final outcome will largely depend on the specific virus and its specific co-adaptation with the UPS as well as the immune system. Here, we show that cauliflower mosaic virus (CaMV) relies on the proteasome for robust infection. The proteasome system is induced during infection via SA and supports systemic accumulation of the virus as well as plant growth performance during infection. This establishes the UPS as a win-win pathway for the plant and the virus, and together with our demonstration of a proteasome-suppressing viral effector, the intimacy between the proteasome and CaMV is fortified.

Thromboembolic complications in COVID-19 disease, a brief update

The role of coagulopathy in severe novel coronavirus infection remains to be clarified. Coagulopathy mechanisms can be summarised in two main pathways: inflammation-related and specific-virus related pathways. The incidence of thromboembolic events is high with pulmonary embolism being the most frequent thromboembolic complication. Low molecular weight heparin is considered the main prophylactic and therapeutic option in patients with COVID-19. Treatment of thromboembolic complications should be started without delay in all cases with certain or clinically suspected diagnosis, whether confirmed or not with specific diagnostic methods. The article reviews the following: mechanisms of development of coagulopathy in COVID-19 including those directly related to the action of the virus, the diagnostic value of biochemical markers and thromboelastography, the incidence of thromboembolic events, and approaches to the prevention and treatment of COVID-19-associated coagulopathy.

Polymerase Chain Reaction (PCR) and How Temperature Modifies Nucleotide Pairings

Polymerase Chain Reaction (PCR) is a molecular technique more suitable for accurate diagnoses because of its specificity in targeting and identifying specific pathogens. PCR technique is reliable to detect the genetic presence of the virus in the host since the very beginning of the infection, no matter how the immune system of the person might react. Moreover, the samples for the test contains the DNA information during quite a long time since the extraction. Programmable thermal operation cycler for controlling heating and cooling is the procedure to denaturation into two single strands, annealing and extension reactions of the DNA. The PCR is certainly having a clinical approach, because do not emphasized on how the immune system of the patient might reacts to the infection, only on whether the specific virus is present or not for the accurate diagnoses and subsequently proceed with an appropriated medical treatment to restore health.

Survey of five major grapevine viruses infecting Blatina and Žilavka cultivars in Bosnia and Herzegovina

The sanitary status of grapevines has not yet been considered sufficiently in vineyards throughout Bosnia and Herzegovina (BiH). An extensive survey of five major grapevine viruses in the country was carried out in 2019. A total of 630 samples from the two dominant autochthonous cultivars, named Žilavka and Blatina, were tested by DAS-ELISA for the presence of grapevine leafroll-associated viruses (GLRaV-1 and 3), grapevine fleck virus (GFkV), grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV). Eighty-eight % of the samples were positive for at least one virus, and all five viruses were detected, thought with different incidence, i.e. GLRaV-3 (84%), GFLV (43%), GLRaV-1 (14%), GFkV (10%) and ArMV (0.2%). The majority of infected plants (about 75%) were asymptomatic. Specific virus symptoms were observed in the remaining infected plants, together with the reported GLRaV vectors, Planococcus ficus and Parthenolecanium corni, while nematodes of the Xiphinema genus were not found in the GFLV- or ArMV-infected vineyards. The GLRaV-3 CP phylogenetic analyses showed 75–100% nucleotide identity between the BiH and reference isolates, and the BiH isolates clustered into the major group. The dNS/dS ratio indicated a negative selection of the virus population, and the lack of geographical structuring within the population was observed. In addition, putative GLRaV-3 recombinants with breakpoints in the 5’ of the CP gene were detected, while no recombinant strains were identified for the other four viruses. The obtained results indicate a deteriorated sanitary status of the cultivated grapevines, the prevalence and intraspecies genetic diversity of GLRaV-3 throughout the country. The establishment of certified grapevine material and adequate virus vector control is therefore of primary importance to prevent further spread of these viruses. This study presents the results of the first molecular characterisation of grapevine viruses in Bosnia and Herzegovina.