The coronavirus disease 2019 (COVID-19) has led to more than 3,000,000 deaths globally. During the first year of the pandemic, countries have focused their response strategies on non-pharmaceutical interventions (NPIs) such as lockdowns and use of facial coverings. Because of collateral effects (psycho-social, and economical) by NPIs, investigating their effectiveness is increasingly important for optimal policies. The aim of this study is to investigate whether varying degrees of response strategies affect the rate of change in mortality at specific time points in the epidemic. The containment and health index (CHI) is used to identify the degree of response measures adopted by each country. Six time points around the peak of daily mortality are identified for the first two epidemiological waves for 40 European countries. The response was then correlated to the rate of change of mortality observed over one week 26 days later (time lag for the intervention to take effect). Spearman’s rank correlation coefficient was used for the unadjusted analysis, and multiple linear regression is used in the adjusted analysis. The intensity of CHI reduced the rate of increase of mortality before the first epidemic peak but had no detectable effect at any other time point. Different covariates and interactions between CHI and covariates such as population density and GDP, affected the rate of change of mortality at different time points during the two waves. NPIs may be effective, as suggested by a significant effect of CHI on mortality early in the first wave. However, the effect is not consistent across time points, and the extent of collateral damage suggests a closer look at other factors influencing the epidemic is necessary.

Introduktion: Coronavirus är RNA-virus med ett lipidhölje som är täckt utav karaktäristiska spikprotein. De mest kända coronavirusvarianterna är SARS-CoV-1 som var aktiv mellan 2002-2004, MERS-CoV som har varit aktiv sedan 2012 och SARS-CoV-2 som har varit aktiv sedan 2019–tillsvidare. SARS-CoV-2 infektionen betecknades januari 30 2020 som en pandemi. Flera läkemedelsföretag har forcerat ??? till att framställa vaccin riktad mot SARS-CoV-2, “The United States Food and Drug Administration” (FDA) och “European Medicines Agency” (EMA) har nödgats att ge ut “Emergency Use Authorization (EUA) i hopp om att få kontroll på dess spridining. Syfte och mål: Syftet med arbetet är att undersöka säkerheten och effektiviteten hos de EMA-godkända vaccinerna riktade mot SARS-CoV-2. Metod: Studierna för vardera vaccin hittades och valdes ut genom World Health Organizations (WHO) “Draft landscape and tracker of COVID-19 candidate vaccines”. Totalt inkluderades åtta studier baserade på tio kliniska prövningar som undersökte säkerheten och effektiviteten hos de fyra ledande vaccinerna från Pfizer BioNTech, Moderna, AstraZeneca och Johnson & Johnson. Resultat: De fyra undersökta vaccinerna visade en god säkerhet utan grövre biverkningar. De vanligaste biverkningarna hos samtliga vaccin var lokal smärta, trötthet och huvudverk. Dessa biverkningar varade mellan en till två dagar efter vaccination och var till större del milda. Större skillnader kunde ses hos de olika vaccinernas effektivitet, Pfizer BioNTech och Modernas mRNA-vacciner visade på effektiviteter runt 95% medan AstraZeneca och Johnson & Johnsons adenovirus-vektor-vacciner visade på effektiviteter runt 66-70%. Diskussion: Inga större skillnader i säkerhet kunde ses mellan de undersökta vaccinerna. AstraZeneca använde ett influensa vaccin istället för isoton vattenlösning till deras kontrollgrupper. Detta kan ha haft en påverkan på placebo och resultaten från deras prövningar. En tydlig skillnad i effektivitet kunde ses mellan de olika vaccintyperna, vilket har ett stort inflytande på hur lätt man kan inducera flockimmunitet hos en befolkning. Eftersom flockimmunitet har en stor roll i både att bromsa spridningen men även i att förebygga förekomsten av nya virus varianter så bör endast mRNA vacciner rekomenderas om möjligt. / Introduction: Coronaviruses are RNA viruses with a lipid envelope that is covered by characteristic spike protein. The most well-known coronaviruses are SARS-CoV-1 which were active between 2002-2004, MERS-CoV which is active since 2012 and SARS-CoV-2 which is active since 2019. SARS-CoV-2 was designated a pandemic January 30, 2020. Several pharmaceutical companies have been rushing to produce vaccines targeting SARS-CoV-2, The United States Food and Drug Administration (FDA) and the European Medicines Agency (EMA) have had to issue Emergency Use Authorization (EUA) in the hope of gaining control of its spread. Objective: The purpose of this study is to investigate the safety and efficacy of the EMA-approved vaccines targeting SARS-CoV-2. Method: The studies for each vaccine were found and selected through the World Health Organizations' (WHO) "Draft landscape and tracker of COVID-19 candidate vaccines". A total of eight studies were included based on ten clinical trials examining the safety and efficacy of the four leading vaccines from Pfizer BioNTech, Moderna, AstraZeneca and Johnson & Johnson. Results: The four vaccines examined showed good safety without any serious side effects, the most common side effects with all vaccines were local pain, fatigue, and headache. These side effects lasted between one to two days after vaccination and were mostly mild. Larger differences could be seen in the efficacy of the different vaccines, with Pfizer BioNTech and Moderna's mRNA vaccines showing efficacies of around 95%. While AstraZeneca and Johnson & Johnson's adenovirus vector vaccines showed efficacies of around 66-70%. Discussion: No major differences in safety could be seen between the vaccines examined. AstraZeneca used an influenza vaccine instead of isotonic aqueous solution for their control groups, this may have had an impact on placebo and thus the results of their trials. A clear difference in efficacy could be seen between the different types of vaccines. This has a great influence on how easily one could induce herd immunity to a population. Herd immunity plays a major role in both slowing the spread but also in preventing the occurrence of new virus variants, therefore mRNA vaccines should be recommended if possible.

El desarrollo y producción de vacunas seguras y eficaces contra la enfermedad por coronavirus 2019 (COVID- 19) ofrece la esperanza para el control de la pandemia actual. Los eventos adversos posteriores a la inmunización son respuestas indeseadas o acontecimientos involuntarios que siguen a la vacunación, y que deben ser cuidadosamente vigilados, ya que todas las vacunas, incluyendo las desarrolladas contra el SARSCoV- 2, requieren cumplir con los criterios de seguridad para su administración en humanos. Se recopiló la información de la base de datos de PubMed/Medline durante los meses de agosto de 2020 a noviembre de 2021. La mayoría de los eventos adversos identificados en los ensayos clínicos fueron leves o moderados; sin embargo, se identificaron eventos trombóticos asociados a algunas vacunas basadas en vectores virales contra la COVID-19 en estudios de seguimiento, aunque se requiere la conclusión de los distintos estudios en curso y vigilancia poscomercialización para determinar todos los posibles eventos adversos y de especial interés.

Se describe la evidencia actual del efecto del SARS-CoV-2 a nivel de tejido renal. Se realizó una revisión narrativa de los artículos publicados en SCOPUS y PUBMED hasta septiembre de 2020. Los resultados se dividieron en las siguientes secciones: evidencia del efecto directo del virus en el riñón, mecanismos de invasión celular, mecanismos de injuria celular y las potenciales implicaciones terapéuticas de estos hallazgos. El SARS-CoV-2 invade las células del túbulo proximal y los podocitos, a través del receptor ECA-2. La invasión y replicación viral podrían producir daño mediante un efecto citopático directo aunado a un daño mediado por la respuesta inmune. Debido a la expresión celular de ECA-2, se ha propuesto a los Inhibidores del Sistema Renina–Angiotensina–Aldosterona como un potencial tratamiento contra la COVID-19. Sin embargo, a la fecha, la evidencia no apoya su uso. / We describe evidence on SARS-CoV-2 effect on the kidney. We carried a narrative review of articles published in SCOPUS and PUBMED until September 2020. The results were divided into six topics: evidence of direct effect of virus on the kidney, mechanisms of cellular invasion, mechanisms of kidney injury, and potential therapeutic implications. SARS-Cov-2 gains access to proximal tubule cells and podocytes via ACE-2 receptors. Viral invasion and replication may induce kidney damage through a direct cytopathic effect and immune-mediated damage. Due to ACE-2 cellular expression, Renin–Angiotensin–Aldosterone System Inhibitors have been proposed as potential treatment for COVID-19. However, current evidence does not support its therapeutic use. / Trabajo de investigación

Introduction The rapid expansion of the novel SARS-CoV-2 virus has raised serious public health concerns due to the possibility of misdiagnosis in regions where arboviral diseases are endemic. We performed the first study in northern Peru to describe the detection of SARSCoV-2 IgM antibodies in febrile patients with a suspected diagnosis of dengue and chikungunya fever. Materials and methods A consecutive cross-sectional study was performed in febrile patients attending primary healthcare centers from April 2020 through March 2021. Patients enrolled underwent serum sample collection for the molecular and serological detection of DENV and CHIKV. Also, serological detection of IgM antibodies against SARS-CoV-2 was performed. Results 464 patients were included during the study period, of which (40.51%) were positive for one pathogen, meanwhile (6.90%) presented co-infections between 2 or more pathogens. The majority of patients with monoinfections were positive for SARS-CoV-2 IgM with (73.40%), followed by DENV 18.09% and CHIKV (8.51%). The most frequent co-infection was DENV + SARS-CoV-2 with (65.63%), followed by DENV + CHIKV and DENV + CHIKV + SARSCoV-2, both with (12.50%). The presence of polyarthralgias in hands (43.75%, p<0.01) and feet (31.25%, p = 0.05) were more frequently reported in patients with CHIKV monoinfection. Also, conjunctivitis was more common in patients positive for SARS-CoV-2 IgM (11.45%, p<0.01). The rest of the symptoms were similar among all the study groups. Conclusion SARS-CoV-2 IgM antibodies were frequently detected in acute sera from febrile patients with a clinical suspicion of arboviral disease. The presence of polyarthralgias in hands and feet may be suggestive of CHIKV infection. These results reaffirm the need to consider SARS-CoV-2 infection as a main differential diagnosis of acute febrile illness in arboviruses endemic areas, as well as to consider co-infections between these pathogens. Copyright: / Revisión por pares

Background: The COVID-19 pandemic is caused by the SARS-CoV-2 virus, which enter the host cells through interactions between the receptor-binding domain (RBD) on the S-protein and the ACE-2 receptor on the host cell. A novel type of vaccine strategy is peptide vaccines, with great potential as a faster and more selective approach to conventional vaccine development. This study focuses on the possibility of generating an antibody response through synthetic peptides harboring B cell epitopes.  Aim: This project aims to investigate the potential of immunogenic peptides to generate an antibody response when used as synthetically produced peptides. As proof-of-concept, the project studies the interactions between previously identified monoclonal antibodies with defined B cell epitopes and the corresponding peptide sequences.  Method: The interactions are evaluated by different ELISA experiments. The candidate peptides are additionally investigated on their binding to polyclonal serum with established S reactive antibodies. Furthermore, the project includes synthesis of one peptide by solid phase peptide synthesis. Results: The ELISA experiments presented no interaction between the synthetic peptides and the monoclonal antibodies or human sera.  Conclusion: The project fulfilled its aim to study the interaction between the B cell epitopes and the monoclonal antibodies. However, no binding was observed. Despite the many advantages in production and stability, development of B cell epitope vaccines come with many challenges. Future will entail if synthetic peptides harboring B cell epitopes can be used as vaccines, or if peptide vaccines will be a focus when a T cell response is to be induced.

No description available.

<p>  </p> <p>Designing and developing a diagnostic technology that is capable of highly sensitive and specific, multiplexed, high-throughput, and quantitative biomarker assays for disease diagnosis and progression is of the upmost importance in modern medicine and patient care. Current diagnostic assays capable of multiplexed and high-throughput analysis include mass spectrometry, electrochemistry, polymerase chain reaction (PCR), and fluorescence-based techniques, however, these techniques suffer from a lack in sensitivity, false responses, or extensive sample processing that are detrimental to clinical diagnostics. To overcome these sensitivity challenges, the field of nanoplasmonics has become utilized when developing diagnostic assays. Plasmonic-based diagnostic tests utilize the unique optical, chemical, and physical property of nanoparticles to increase the sensitivity of the assay. In this dissertation, novel diagnostic platforms that utilize nanoparticles and their localized surface plasmon resonance (LSPR) property will be introduced. LSPR is an optical property in noble metallic nanoparticles that is referred to as the collective oscillation of free electrons upon light irradiation. It is highly dependent on the shape, size, and dielectric constant (refractive index) of the surrounding medium of the nanoparticle and LSPR sensing is based on a change in these properties. In this dissertation, the LSPR property is utilized to fabricate nanoplasmonic-based diagnostic platforms that are capable of multiplexed and high-throughput biomarker assays, with high sensitivity and specificity. The work presented in this dissertation is presented as six chapters, (1) Introduction. (2) Methods, (3) Fabrication of a LSPR-based multiplexed and high-throughput biosensor platform and its application in performing microRNA assays for the diagnosis of bladder cancer. In this chapter, the advancement of single-plex solid state LSPR-based biosensors into a multiplexed and high-throughput diagnostic biosensor platform is reported for the first time. The diagnostic biosensor platform is first fabricated utilizing different gold nanoparticles (spherical nanoparticles, nanorods, and triangular nanoprisms), and then with the gold triangular nanoprisms as the nanoparticle of choice, microRNA assays were performed. The developed biosensor platform is capable of assaying five different types of microRNAs simultaneously at an attomolar limit of detection. Additionally, five microRNA were assayed in 20-bladder cancer patient plasma samples. (4) Development/optimization of the biosensor platform presented in Chapter 3 for the detection of COVID-19 biomarkers. In this chapter, the biosensor platform utilized in Chapter 3 was designed to assay 10 different COVID-19 specific biomarkers from three classes (six viral nucleic acid gene sequences, two spike protein subunits, and two antibodies) with limit of detections in the attomolar range and with high specificity. The high-throughput capability of the biosensor platform was advanced, with the platform performing analysis of a single biomarker in 92 patient samples simultaneously. Additionally, the biomarker platform was utilized to assay all 10 biomarkers in a total of 80 COVID-19 patient samples.  (5) Further optimization of the biosensor platform for the development of a highly specific antibody detection test for COVID-19. During the COVID-19 pandemic, knowledge was gained on the specificity of antibodies produced against COVID-19. In this chapter, that knowledge was applied towards the optimization of the biosensor platform presented in Chapter 4 in order to assay SARS-CoV-2 neutralizing antibody IgG. The optimization of the biosensor platform included the size of the gold triangular nanoprisms and the receptor molecule of choice. The biosensor platform assayed this highly specific COVID-19 IgG antibody with a limit of detection as low as 30.0 attomolar with high specificity and no cross reactivity. Additionally, as a proof of concept, the biosensor platform was utilized in a high-throughput format to assay SARS-CoV-2 IgG in a large cohort of 121 COVID-19 patient samples simultaneously. (6) Advancement of the biosensor platform from a 96-well plate to a 384-well plate and its application in assaying microRNA for early diagnosis of pancreatic cancer. In this chapter, the high-throughput capabilities of the biosensor platform presented in Chapters 3-5 was expanded by increasing the sensor amount in one platform from 92 to 359. The 384-well plate biosensor platform was designed, optimized, and utilized to perform microRNA assays for early-stage pancreatic cancer diagnosis. The optimization of the biosensor platform included the manipulation of LSPR-based parameters and the -ssDNA receptor molecule in order to obtain low limit of detections (high sensitivity). Additionally, the biosensor platform assayed two microRNA in a large cohort (n=110) of pancreatic cancer and chronic pancreatitis patient samples. </p>

Coronaviruses have caused three large outbreaks in the past century. The most recent one, also still ongoing, is represented by the SARS-CoV-2/Covid-19 pandemic. Efforts have been taken to develop efficient vaccines and antivirals and one of the major virus-based targets in drug development is represented by the main protease of these viruses. Main proteases are proteins (cysteine hydrolases) with high level of conservation among different coronaviruses and have an important role in the virus life cycle. Due to the need of developing broad-spectrum antivirals against Coronaviruses, this study aimed to set up a CPE-based assay for testing compounds against the main protease of human coronavirus 229E. An optimized TCID50 protocol was established by using MRC-5 cells, at a density of 1x104 cells/ml with a 3h incubation prior infection with a concentration of 10-1 of HCoV-229E. The cell viability was assessed through MTT assay. Using reference compounds, with previously demonstrated antiviral potency against the main protease of different coronaviruses (GC-376, Nirmatrelvir), the efficiency of the conceived assay was validated (GC-376 EC50 = 1.24 μM; Nirmatrelvir Ec50= 0.72 μM). Compound 19 was proved to also be active against the main protease of HCoV-229E (EC50 = 0.22 μM), and together with previous findings, it was concluded that this compound has a broad-spectrum activity. Newly developed compounds MP17 and MP19 were also demonstrated to be efficient against HCoV-229E. As a future perspective, further investigations of these compounds should take place for the identification of EC50 values.

Time-resolved cryo-EM has already provided ground-breaking discoveries in various fields, including structural biology, biochemistry, and drug development. Compared to traditional structural biology methods where mostly stabilized conformations are reconstructed, the main advantage of time-resolved cryo-EM is its ability to capture dynamic processes in biological samples at near-atomic resolution, which allows for studying biological structures as they change and interact in real-time. In this project, I focused on the expression and purification of the individual proteins of two dynamic molecular complexes – Staphylococcus aureus (S. aureus) DNA gyrase and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication-transcription complex – and attempted to assemble them into their functional forms for cryo-EM imaging.  Both of these complexes are interesting drug targets as they play an essential role in nucleic acid replication. The function of DNA gyrase is to modulate DNA supercoiling, facilitate DNA replication, and resolve intertwined DNA molecules. The replication-transcription complex of SARS-CoV-2 comprises, among other proteins, the RNA-dependent RNA polymerase, which, together with non-structural proteins 7 and 8, is responsible for the replication of the viral genome. There are still many questions about the underlying mechanisms of these key processes, and time-resolved cryo-EM studies will provide valuable information to advance our understanding of them. Here I present expression and purification protocols for S. aureus DNA gyrase subunits A and B and SARS-CoV-2 non-structural proteins 7, 8 and 12. DNA gyrase subunits A and B were expressed in Escherichia coli (E. coli) and purified in several steps, including affinity chromatography (His-Trap), ion exchange chromatography (IEX) and size exclusion chromatography (SEC). Despite many challenges with gyrase A precipitation, I obtained enough of both subunits for the intended cryo-EM. Different strategies to assemble them into a functional tetramer were tested but did not result in the expected outcome. The gained knowledge about the behaviour of the subunits in solution will serve as a basis for further optimization of the protocols before the assembly of the complex can be attempted again. Non-structural proteins 7 and 8 were expressed in E. coli as a polyprotein and successfully purified using His-Trap and SEC. I obtained a great amount of the polyprotein and established a protocol for its cleavage. Nsp12 was expressed using the baculovirus-insect cell expression system. The immunofluorescence assay data showed that the tested lipofection protocol works, and nsp12 is being produced in sufficient quantities. This result provides a solid base for further experiments to establish a purification method and assemble the nsp12-nsp7-nsp8 complex for cryo-EM imaging.