Genomic epidemiology of SARS-CoV-2 virus with a bioinformatics platform

Introduction: viral epidemics have presented a risk to human health since they can turn into pandemics and affect a large part of the population, especially for poor developing countries. In 2020, the worldwide pandemic of COVID-19 is underway. Research is currently being carried out showing data that combines genetic and social information that can change our understanding of the dynamics of the epidemic.Objective: to describe data science-based technology tool called Nextstrain that allows epidemics to be visualized with data as up to date as possible using academic databases.Development: there are currently viral sequences from 57 countries on 6 continents. The common ancestor of the virus circulating in the world emerged in Wuhan, China, in late November or early December 2019, and from where it is supposed to have mutated towards humans, from bats and pangolins. Regarding monitoring, research work is already being carried out using this tool, such as in Taiwan, France, and Finland, which were able to determine where the SARS-CoV-2 strains that were causing outbreaks in their respective country originated. Besides, Nextstrain allows to freely share the phylogenetic analyzes of various authors from different countries and allows us to see the great work in the epidemiology of the virus.Conclusions: Nextstrain is a tool based on big data that gives us a better view of the worldwide epidemiology of pathogens of interest. Its use is based on bioinformatic tools and it shows us this information through a pleasant and understandable ecosystem

The global emergency of novel coronavirus (SARS-CoV-2). An update of the current status and forecasting

Over the past two decades, there have been two major outbreaks where the crossover of animal Betacoronaviruses to humans has resulted in severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In December 2019, a global public health concern started with the emergence of a new strain of coronavirus (SARS-CoV-2 or 2019 novel coronavirus, 2019-nCoV) which has rapidly spread all over the world from its origin in Wuhan, China. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes human SARS-CoV, MERS and two other human coronaviruses (HCoVs), HCoV-OC43 and HCoV-HKU1. The fatality rate of SARS-CoV-2 is lower than the two previous coronavirus epidemics, but it is faster spreading and the large number of infected people with severe viral pneumonia and respiratory illness, showed SARS-CoV-2 to be highly contagious. Based on the current published evidence, herein we summarize the origin, genetics, epidemiology, clinical manifestations, preventions, diagnosis and up to date treatments of SARS-CoV-2 infections in comparison with those caused by SARS-CoV and MERS-CoV. Moreover, the possible impact of weather conditions on the transmission of SARS-CoV-2 is also discussed. Therefore, the aim of the present review is to reconsider the two previous pandemics and provide a reference for future studies as well as therapeutic approaches

COVID 19: RECENT VACCINE AND VACCINE UNDER TRAIL

Since 2002, there has been a record ofCoronavirus disease outbreak caused by SARS-CoV,MERS-CoV, as well as the novel SARS-CoV-2, the causalagent of the Coronavirus Disease 2019 that broke outin Wuhan, China in December the same year and hassince become widespread across several countries andcontinents leading to thousands of deaths More than 180 vaccine candidates, based on several different platforms(Fig. vaccine platform used for SARS-CoV-2 vaccine developement), are currently in development against SARS-CoV-2(57) (Fig. overview of the SARS-CoV-2 vaccine development landscape). TheWorld Health Organization (WHO) maintains a working document(57)that includes most of the vaccines in development and is available at https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines. Clinical trials are evaluating COVID-19 vaccines in tens of thousands of study participants to Generate the scientific data and other information needed to determine safety and effectiveness These clinical trials are being conducted by manufacturers according to rigorous standards

Summary of the available molecular methods for detection of SARS-CoV-2 during the ongoing pandemic

Since early 2020, the COVID-19 pandemic has caused an excess in morbidity and mortality rates worldwide. Containment strategies rely firstly on rapid and sensitive laboratory diagnosis, with molecular detection of the viral genome in respiratory samples being the gold standard. The reliability of diagnostic protocols could be affected by SARS-CoV-2 genetic variability. In fact, mutations occurring during SARS-CoV-2 genomic evolution can involve the regions targeted by the diagnostic probes. Following a review of the literature and an in silico analysis of the most recently described virus variants (including the UK B 1.1.7 and the South Africa 501Y.V2 variants), we conclude that the described genetic variability should have minimal or no effect on the sensitivity of existing diagnostic protocols for SARS-CoV-2 genome detection. However, given the continuous emergence of new variants, the situation should be monitored in the future, and protocols including multiple targets should be preferred

Reporte de un brote de infección por SARS-CoV-2 por transmisión aérea: evidencia epidemiológica y molecular

Introduction: It has been shown that the transmission of SARS-CoV-2 occurs mainly by air, and the risk of infection is greater in closed spaces. Objective: Describe the epidemiology, virology and molecular characterization of a COVID-19 outbreak at a closed vaccination point during the third wave of SARS-CoV-2 in Colombia. Materials and methods: Diagnostic tests, interviews, sampling, cell cultures and viral sequencing were carried out, the latter being molecular characterization and lineage identification. Results: Seven workers were positive for SARS-CoV-2; among these, 3 samples were analyzed, plus an additional sample belonging to the mother of the presumed index case; all samples were identified with lineage B.1.625, with a maximum of 2 nucleotides difference between them. Conclusions: Variant B.1.625 was identified as the cause of the COVID-19 outbreak, and a co-worker was also identified as the index case. Unexpectedly, attending a vaccination day became a risk factor for acquiring the infection.Introducción. Se ha demostrado que la transmisión de SARS-CoV-2 se da principalmente por vía aérea y el riesgo de infección es mayor en espacios cerrados con alta concentración de personas; este último factor se presentó en algunos de los puestos de vacunación de la ciudad de Medellín. Objetivo. Describir la epidemiología, virología y caracterización molecular de un brote de COVID-19 en un punto de vacunación cerrado durante la tercera ola de SARS-CoV-2 en Colombia. Materiales y métodos. Se realizaron test diagnósticos, entrevistas, toma de muestras, aislamiento viral y secuenciación genómica. Con esta última se realizó caracterización molecular e identificación de linaje. Resultados. Siete trabajadores fueron positivos para SARS-CoV-2, y de estos, tres muestras fueron secuenciadas, más una muestra adicional perteneciente a la madre del presunto caso índice. Todas las muestras fueron identificadas con el linaje B.1.625, con un máximo de 2 nucleótidos de diferencia entre ellas. Conclusiones. Se identificó la variante B.1.625 como la causante del brote de COVID-19, y también un compañero de trabajo fue identificado como el caso índice. De forma imprevista, asistir a una jornada de vacunación se convirtió en un factor de riesgo para adquirir la infección

Associated factors for mortality in a COVID-19 colombian cohort : is the third wave relevant when Mu variant was predominant epidemiologically?

Q1Q1Pacientes con COVID-19Objectives: To evaluate the association between Colombia's third wave when the Mu variant was predominant epidemiologically (until 75%) in Colombia and COVID-19 all-cause in-hospital mortality. Methods: In this retrospective cohort, we included hospitalized patients ≥18 years with SARS-CoV-2 infection between March 2020 to September 2021 in ten hospitals from three cities in Colombia. Description analysis, survival, and multivariate Cox regression analyses were performed to evaluate the association between the third epidemic wave and in-hospital mortality. Results: A total of 25,371 patients were included. The age-stratified time-to-mortality curves showed differences according to epidemic waves in patients ≥75 years (log-rank test p = 0.012). In the multivariate Cox analysis, the third wave was not associated with increased mortality relative to the first wave (aHR 0.95; 95%CI 0.84–1.08), but there was an interaction between age ≥75 years and the third wave finding a lower HR for mortality (aHR 0.56, 95%CI 0.36–0.86). Conclusions: We did not find an increase in in-hospital mortality during the third epidemic wave in which the Mu variant was predominant in Colombia. The reduced hazard in mortality in patients ≥75 years hospitalized in the third wave could be explained by the high coverage of SARS-CoV-2 vaccination in this population and patients with underlying conditions.https://orcid.org/0000-0003-1833-1599https://orcid.org/0000-0001-5363-5729https://orcid.org/0000-0001-6964-2229https://orcid.org/0000-0003-3975-2835https://orcid.org/0000-0001-9441-4375Revista Internacional - IndexadaA1N

Application of Transmission Electron Microscopy Techniques in the Veterinary Diagnosis of Viral Gastroenteritis in Livestock Animals

Gastroenteritis caused by viruses is considered to be one of the most important diseases in livestock, being the main cause of morbidity and mortality in young animals, culminating in serious economic losses due to costs with prophylaxis and treatment, increased susceptibility of animals to secondary infections, developmental delay and death. Stressful factors may support the onset of illness. Several viral agents can cause gastroenteritis in various animal species. Rotaviruses are considered the main cause of enteric infections in various animals, including humans constituting important zoonosis. Due to genetic diversity and their ability to cross the species barrier, the coronaviruses infect many species. In cattle, they cause “Winter Dysentery” in adult animals and “Neonatal Diarrhea” in newborn calves. In swine, they are responsible for “Transmissible Gastroenteritis” and “Swine Epidemic Diarrhea.” Equines infected with coronavirus also develop severe gastroenteritis. Bovine viral diarrhea (BVD) caused by a flavivirus of the genus Pestivirus is related to digestive and reproductive disorders, affecting any productive sector, are it cut, milk or confinement. Transmission electron microscopy is an indispensable tool in the diagnosis of viral gastroenteric infectious diseases. Negative staining is a simple, fast and efficient technique, being ideal for the detection of gastroenteric viruses, being easily visualized. The immunoelectron microscopy (IEM) technique allows increasing the sensitivity of virus detection where low concentrations of virus are aggregated so that they may be more easily seen. The immunolabeling with colloidal gold technique utilizes specific antibodies tagged with particles of colloidal gold to label the antigen antibody reaction. Embedding resin technique allows obtaining information on the virus–cell interaction. The different transmission electron microscopy modalities promotes a fast and accurate diagnosis of the different gastroenteric viral agents, allowing prophylactic measures of control and prevention in the creations to be promptly instituted, avoiding animal losses and disastrous economic losses, and collaborating with the National Porcine and Bovine Agribusiness

Which Plagues are Coming Next?

Plagues and pandemics are no longer distant thoughts of the past. Previously referred as moments in history, infectious diseases have re-emerged as potential existential threats to mankind. International Health Security researchers have repeatedly warned society about impending pandemics and in 2020, the world experienced its first major pandemic in over a century. The SARS-CoV-2/COVID-19 pandemic came fast and hit hard, impacting the entire world within months of discovery. Although SARS-CoV-2 was a completely novel virus, there are an assortment of novel and timeworn pathogens fostering the potential to become the next pandemic. This chapter focuses on pathogens ranging from yeast to virus, capable of transmission through food, water, air, or animal, that could emerge as the next International Health Security threat