• COVID-19

CATH Functional Families (FunFams) are coherent subsets of protein domain sequences that share the same function within the same CATH SuperFamily. The latest release of CATH, v4.3, was frozen before the COVID-19 pandemic, therefore structural domains from SARS-CoV-2 and the FunFams assignments are not part of the CATH website. The assignments in these files file were obtained by scanning the UniProt entries of SARS-CoV-2, SARS and MERS against the FunFams v4.3 Hidden Markov Models library using HMMER3 and resolved using cath-resolve-hits.

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

Raw data collected from the systematic review + outputs from analyses and models. The link to these data will be made publicly available upon completion of the peer-review process. For peer reviewers, please request access.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a deadly virus which is extended at the end of 2019 globally form seafood market, Wuhan, China and considered as novel coronavirus which has 70% similarity with SARS-CoV and MERS-CoV. SARS-CoV-2 considered as globally pandemic because of high mortality and fatality rate among worldwide by the World Health Organization (WHO). The disease caused by this called Coronavirus Disease 2019 (COVID-19) in which 19 referred to as the year of occurrence of disease. The intermediate sources are humans but it is not known seriously but it is confirmed that the spreading is done by human-to-human transmission rapidly and widely. This review highlights the whole insight and the understanding towards the SARS-CoV-2 and COVID-19 regarding its, spreading history, origin, epidemiology, prevalence rate, sources and modes of transmission, pathogenesis, life cycle entry mechanisms, clinical characteristics, symptoms, complications of comorbidities, diagnosis, treatment, research hindrances, preventive measures, potential pharmacological therapeutics (repurposing of main drugs) research with previous studies of SARS and MERS. The literature review databases were searched from the Scopus, MEDLINE, PUBMED, Elsevier, WHO situation reports. The SARS-CoV-2 infection has a high mortality rate and leads to a high global disaster to human well-being, social as well as economic. Lockdown phases are taken to prevent the spreading of the virus. Solitary confinement procedures followed by the clinical and health care services so, to inhibit the contamination of the areas with suspected patients. The research on the novel coronavirus (n-CoV) is still a concern and in the primary stage in which repurposing of the main pharmacological drugs which act on symptoms of COVID-19 trials are held. As such no clinically tested/approved vaccines/anti-viral drugs are prepared, approaches for preparation in respect to these viral outbreaks and against the COVID-19 and SARS-CoV-2. However, some broad-spectrum antibiotics, anti-viral drugs, angiotensin-converting enzymes 2 inhibitors (ACE 2) are clinically screened for the COVID-19 disease in clinical trials. This review article gives information publically about the COVID-19 and SARS-CoV-2 infection.

The relationship between the nasopharyngeal virus load, IgA and IgG antibodies to both the S1-RBD-protein and the N-protein, as well as the neutralizing activity (NAbs) against SARS-CoV-2 in the blood of moderately afflicted COVID-19 patients, needs further longitudinal investigation. Several new serological methods to examine these parameters were developed, validated and applied in three patients of a family which underwent an ambulatory course of COVID-19 for six months. The virus load had almost completely disappeared after about four weeks. Serum IgA levels to the S1-RBD-protein and, to a lesser extent, to the N-protein, peaked about three weeks after clinical disease onset but declined soon thereafter. IgG levels rose continuously, reaching a plateau at approximately six weeks, and stayed elevated over the observation period. Virus-neutralizing activity reached a peak about 4 weeks after disease onset but dropped slowly. The longitudinal associations of virus neutralization and the serological immune response suggest immunity in patients even after a mild clinical course of COVID-19.

Aim: The 21st Century has already witnessed three outbreaks caused by the same family of coronaviruses, the Severe Acute Respiratory Syndrome (SARS), the Middle East Respiratory Syndrome (MERS) and recently, The Noval Coronavirus Disease 2019 (COVID-19). The main aim of this study is to analyze the overall scientific publications indexed in Science Citation Index Expanded (SCI-E) about these three outbreaks. And the secondary aim is to compare first scientific reactions to SARS, MERS and COVID-19 outbreaks in their early phases by using the dates of first 4 months of them.Material and Method: Web of Science (WoS) software was used for the search and the analysis. Allscientific papers, included in SCI-E, related with each outbreaks of SARS, MERS and COVID-19 from 1980 to April15.2020, were searched and analyzed by using the terms of “SARS”, “SARS-CoV” and “Severe Acute Respiratory Syndrome” for SARS; “MERS”, “MERS-CoV”, “HCoV-EMC” and “Middle East Respiratory Disease” for MERS and “COVID-19”, “2019-n-CoV”, “SARS-CoV-2”, “Coronavirus disease 19” and “2019 novel coronavirus” for COVID-19 in the topic section of the software.Results: Overall; 3690, 1517 and 730 papers, indexed by SCI-E, were found related to SARS, MERS and COVID-19 respectively. The biggest contribution for publications was from People’s Republic of China (PRC) for SARS and COVID-19 and was from The United States of America (USA) for MERS.Conclusion: In this study, it was revealed that scientific contribution to COVID-19 is faster and greatful then SARS and MERS in the early phase of the outbreak. But the pandemic potential of betacoronaviruses, especially SARS-CoV-2, remains a threat for public health globally. Therefore further research into the pathogenesis of these infections in order to find appropriate targets for treatment is imperative. Amaç: 21. yüzyıl, aynı koronavirüs ailesinin neden olduğu üç salgına, Şiddetli Akut Solunum Sendromu (SARS), Orta Doğu Solunum Sendromu (MERS) ve yakın zamanda Noval Koronavirüs Hastalığı 2019’un (COVID-19) tanık olmuştur. Bu çalışmanın amacı, bu üç salgın ile ilgili, Science Citation Index Expanded (SCI-E) dergilerde indekslenen genel bilimsel yayınları analiz etmektir. İkincil amacı ise SARS, MERS ve COVID-19 salgınlarına yönelik ilk bilimsel reaksiyonları erken evrelerinde, ilk 4 aylık süreçlerinde, karşılaştırmaktır.Materyal ve Metot: Arama ve analiz için ISI-Web of Knowledge- Web of Science (WoS) yazılımı kullanılmıştır. 1975’ten 15 Nisan 2020’ye kadar SARS, MERS ve COVID-19 salgını ile ilgili SCI-E indexlenen tüm bilimsel makaleler Şiddetli Akut Solunum Sendromu (SARS) için “SARS”, “SARS-CoV” ve “Şiddetli Akut Solunum Sendromu” terimleri kullanılarak; Orta Doğu Solunum Sendromu (MERS) için “MERS”, “MERS-CoV”, “HCoV-EMC” ve “Orta Doğu Solunum Sendromu” terimleri kullanılarak ve COVID-19 için “COVID-19”, “2019-n-CoV”, “SARS-CoV-2”, “Koronavirüs hastalığı 19” ve “2019 yeni koronavirüs” erimleri kullanılarak arştırma yapıldı.Bulgular: SCI-E tarafından indekslenen 3690 yayın SARS ile, 1517 yayın MERS ile ve 730 yayın COVID-19 ile ilgili bulunmuştur. Yayınlara en büyük katkı, SARS ve COVID-19 için Çin Halk Cumhuriyeti’nden (PRC); MERS için Amerika Birleşik Devletlerindendir (ABD).Sonuç: Bu çalışma ile, COVID-19’a bilimsel katkının salgının erken evresindeki SARS ve MERS’den daha hızlı ve daha büyük olduğunu gösterdik. Ancak, HCoV’lerin, özellikle SARS-CoV-2’nin pandemik potansiyeli, küresel olarak halk sağlığı için bir tehdit olmaya devam etmektedir. Bu nedenle, tedavi için uygun hedefleri bulmak için HCoV enfeksiyonlarının patogenezine yönelik daha fazla araştırma yapılması zorunludur.

Las aplicaciones mHealth definidas por la OMS, como la práctica de medicina y salud pública mediante soportes digitales, inalámbricos o de telefonía móvil están alumbrando su posicionamiento esencial en el desarrollo actual y futuro de la salud. Su desarrollo ofrece una mejora sustancial en la calidad de la atención sanitaria (envejecimiento poblacional, enfermedades crónicas, etc..), así su potencial en actuaciones preventivas, sostenibilidad del sistema sanitario o telemedicina propiamente, están cambiando el modelo sanitario a la par que convirtiéndose en una de las categorías de aplicaciones móviles de mayor crecimiento. Este TFG tiene como objetivo realizar un análisis del estado actual de una de las subramas de la tecnología mHealth, las aplicaciones destinadas al COVID-19. Para este propósito se llevado a cabo una búsqueda masiva entre las aplicaciones disponibles, desarrollada en base a una metodología apoyada en el seguimiento de los distintos diagramas de flujo que marcan los criterios de búsqueda y elección entre las mismas. Se ha comenzado con la realización de una búsqueda de las aplicaciones existentes en las dos plataformas virtuales de almacenamiento, que mayor número de estos sistemas recogen en la actualidad en el mundo: Google Play y App Store, referenciándose ambas a los sistemas operativos Android y IOS, respectivamente. Se han recogido todas las aplicaciones que, además de cumplir los criterios establecidos presentan correlaciones con el campo del SARS-COV-2. En este caso, se han examinado en profundidad 24 aplicaciones disponibles en una de las dos tiendas virtuales o en ambas a la vez. Una vez realizada la recopilación muestra, se han elaborado estudios estadísticos a partir de los resultados ofrecidos, llegando a la inferencia de diversas conclusiones. En segundo lugar, realizado el estudio y constatadas carencias de funcionalidades en las aplicaciones actuales publicadas en las tiendas virtuales, se ha desarrollado una aplicación para Android. Esta aplicación pretende ser el medio para participar al médico sobre el avance de los síntomas del paciente, sin tener que realizar una llamada telefónica o asistir presencialmente a consulta. En definitiva se pretende el desarrollo de una aplicación para telefonía digital, cuyas funcionalidades e interacción médico/paciente la sitúen en el estrato de consideración como producto sanitario. Por lo tanto, este TFG nos da una visión global del estado actual de un conjunto de aplicaciones eHealth, cual ha sido y está siendo su crecimiento en la gestión del dato de salud. El desarrollo de las app, la tasa de penetración de trasvase de información digital/móvil, la futura integración de estas aplicaciones en los sistemas hospitalarios y solventar los problemas de ciberseguridad implícitos, no dan una visión de la revolución y salto de calidad que estos sistemas van implementar en el campo sanitario. mHealth applications, defined by the WHO as the practice of medicine and public health using digital, wireless or mobile phone supports, are becoming essential in the current and future development of health. Its development offers a substantial improvement in the quality of health care (population ageing, chronic diseases, etc.), and its potential in preventive actions, sustainability of the health system or telemedicine itself, are changing the health model at the same time as becoming one of the fastest growing categories of mobile applications. This TFG aims to carry out an analysis of the current state of one of the sub-branches of mHealth technology, applications for COVID-19. For this purpose, a massive search was carried out among the available applications, developed on the basis of a methodology based on the monitoring of the different flow diagrams that mark the search criteria and the choice between them. We began with a search of existing applications on the two virtual storage platforms that currently have the largest number of these systems in the world: Google Play and App Store, both referring to the Android and IOS operating systems, respectively. All the applications that, in addition to meeting the established criteria, have correlations with the SARS-COV-2 field have been collected. In this case, 24 apps available in one or both of the two online shops were examined in depth. After the sample collection, statistical studies have been carried out on the basis of the results provided, leading to the inference of several conclusions. Secondly, once the study had been carried out and the lack of functionalities in the current applications published in the virtual shops had been identified, an application for Android was developed. This application is intended to be a means of informing the doctor about the progress of the patient's symptoms, without having to make a phone call or go to the doctor's surgery in person. In short, the aim is to develop an application for digital telephony, whose functionalities and doctor/patient interaction place it in the stratum of consideration as a health product. Therefore, this TFG gives us an overview of the current state of a set of eHealth applications, which has been and is being its growth in the management of health data. The development of apps, the penetration rate of digital/mobile information transfer, the future integration of these applications in hospital systems and solving the implicit cybersecurity problems, do not give a vision of the revolution and leap in quality that these systems will implement in the healthcare field. Grado en Ingeniería de Tecnologías de Telecomunicación