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In early 2020 the World Health Organization (WHO) declared a COVID-19 pandemic outbreak. As of March 2023, the Kingdom of Saudi Arabia has reported over 829 thousand cases and over 9 thousand deaths. Due to the public health emergency, the wild-type SARS-CoV-2 genome was fully sequenced early on the pandemic course. Afterward, different viral variants emerged around the world. The variant prevalence fluctuates over time, with some strains presenting increased transmissibility, changes in disease severity, and decreased efficacy of containment measures. In this respect, genomic surveillance and timely data sharing to public repositories represent a tool to track and detect emerging changes that require addressing with public health measurements. However, the Kingdom's genome contribution to the GISAID database represents merely 0.27% of the reported cases. To address this gap, we incorporated whole genome sequencing and the available metadata, to track the circulating viral lineages and identify the variants of concern (VOC) and variants of interest (VOI) over 14 months, from December 2021 to January 2023. We sequenced 581 genomes using the MinION MK1C platform of Oxford Nanopore Technologies (ONT) and assigned the viral lineages, the data primarily derived from COVID-19-positive patients from the city of Jeddah. The VOC Omicron was the principal circulating variant in the country (~99%), which aligns with the global trend. Our report included the sublineages BA.2.75, BQ.1, CH.1.1, XBB, and XBB.1.5, which are under WHO monitoring. We also reported the VOC Delta and the recombinant strains XF, XZ, and XPB. Finally, to validate the use of ONT for genomic surveillance, we compared the data quality of 93 samples sequenced in both ONT MinION and Illumina NaovaSeq platforms. There was 90% correspondence in the Nextstrain clade assignment (84/93) and 78% correspondence in the Pangolin sublineage assignment (73/93). MinION offered a shorter turnaround time, while Illumina produced a consistently higher breadth of genome coverage. In conclusion, the continued viral evolution patterns are reflected in the Kingdom's variant prevalence, where only Omicron circulated by January 2023. Likewise, current Variants Under Monitoring (VUM) were already identified in KSA, highlighting the need for increased genomic surveillance.

<p> Over 40 years since the emergence of the AIDS epidemic and still no cure exists for AIDS or its causative HIV-1 infection. Protease inhibitors are an integral part of the most effective treatment regimen for HIV-1 infected patients known as combination antiretroviral therapy (cART), which is extremely effective at decreasing viral loads to nearly undetectable levels. One of the most alarming issues with current treatments is the emergence of multi-drug resistant strains. Even darunavir, which has shown exceptional activity against drug resistant strains, has experienced this issue. Herein we designed a novel series of heterocyclic based P2 ligand HIV-1 protease inhibitors based on kinase inhibitors such as imatinib and dasatinib. These inhibitors were designed to promote hydrogen bonding with the peptide backbone atoms of HIV-1 protease. Compounds were synthesized, biologically evaluated, and underwent X-ray structural studies. Inhibitors displayed activity as low as sub-nanomolar potency and low nanomolar antiviral activity. Important ligand-binding site interactions were determined through two X-ray crystal structures.</p> <p>Emergence of SARS-CoV-2 at the end of 2019 resulted in a global pandemic that has affected millions. Researchers all over the world turned their attention to developing drug therapies aimed at preventing and treating the viral infection. One such target became the main viral protease, or 3-chymotrypsin like protease (3CLpro). 3CLpro is an essential viral enzyme responsible for polypeptide cleavage during the viral replication cycle to produce 16 nonstructural proteins (nsps). Thus, it has been a highly researched area for effective SARS-CoV-2 drug therapies. Therefore, we designed, synthesized, and biologically evaluated a series of competitive reversible SARS-CoV-2 3CLpro inhibitors. </p>

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as a global pandemic with an unprecedented death toll worldwide. Although it primarily affects the respiratory tract presenting as pneumonia or acute respiratory failure, it is also known to cause significant cardiovascular complications, including acute coronary syndrome (ACS), arrhythmia, myopericarditis, cardiomyopathy, venous thromboembolism, heart failure, and cardiogenic shock. Morbidity and mortality secondary to cardiovascular complications are higher in patients with preexisting cardiovascular risk factors. Here, we present a case report of a 69-year-old male who was recently diagnosed with COVID-19 illness presenting with ST-elevation myocardial infarction (STEMI) and eventually with Takotsubo cardiomyopathy (TTC), and the course was complicated by right atrial thrombus and a pulmonary embolism (PE).

This policy paper reviews the history, use and significance of telehealth in primary care. The emergence of telehealth as a primary strategy to continue to deliver value based, timely primary care during COVID-19 is discussed with recommendations for future applications, payment and preparation of providers to continue to provide quality care of clients in the future using telehealth.

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Beginning in 2019 and quickly spreading internationally, the Coronavirus disease Covid-19 became the first pandemic that many people have witnessed firsthand along with the severe disruption to their daily lives. A key field of research for Covid-19 that is studied by epidemiologists, biologists, and computer scientists alike is modeling the spread of Covid-19 in order to better predict future outbreaks of the pandemic and evaluate potential strategies to reduce infections, hospitalizations, and deaths. This thesis proposes a method of modeling Covid-19 spread and interventions for local environments based on different levels of perspective. The goal for this thesis is to be able to present a model of Covid-19 in terms of surrounding areas in San Luis Obispo including the unique mobility dynamic currently held in the global pandemic. Furthermore, we use our model to explore different methods of ensuring a low infection rate such as isolation methods and mobility restrictions.

Infectious diseases caused by viruses such as influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose major threats to human health. Glycosylation, a post-translational modification critical for biological functions including receptor recognition and binding, cell adhesion, and protein folding, is a key mediator of the interaction between viruses and host cells. IAV and SARS-CoV-2 recognize and bind to glycans on host cells prior to uptake by the cells; by the same token, the glycoproteins hemagglutinin of IAV and the spike protein of SARS-CoV-2 are the targets of both host immune molecules and vaccines. The diversity of glycans, structures made up of oligosaccharide residues in complex, branched configurations, can in part be attributed to the push and pull of evolutionary pressures from infectious disease agents such as these viral pathogens. Evolving host glycans may gain the ability to evade recognition by viruses, and likewise, the evolution of viral glycans may result in viral evasion from immune responses. Thus, for a complete understanding of host-pathogen interactions, detailed characterization of glycoproteins that quantitatively measures changes in glycosylation is necessary. However, a number of factors makes quantitative characterization of glycoproteins difficult. Firstly, glycans are highly heterogeneous with dozens of possible glycans at a given glycosylation site and different occupancy levels at each site. Secondly, a particular glycoform may have very low abundance, making the signals difficult to detect. Thirdly, it is difficult to achieve deep, quantitative measurement of glycoprotein glycans using conventional liquid chromatography-mass spectrometry experiments. The usual mass spectrometry methods are not adequate because they are biased towards selecting higher abundance precursors, which leave many glycopeptide glycoforms undetected. This dissertation begins with an assessment of the current state-of-the-art of glycoproteomics using mass spectrometry to give context to our primary research discussed in subsequent chapters. Chapter 2 describes the use of a modified Tanimoto similarity coefficient to quantify the glycosylation similarity between two variants of a strain of IAV, wild-type and mutant, both expressed in embryonated chicken eggs. Our results indicate that even subtle changes in the amino acid sequence of hemagglutinin can result in measurably distinct glycosylation. Chapter 3 expands the number of comparisons of IAV strains made in the previous chapter to include strains produced in a mammalian expression vector, Madin-Darby canine kidney cells. We show that the choice of expression system can change the population of glycoforms at some but not necessarily all glycosylation sites. In addition, we explore data-independent acquisition mass spectrometry to improve upon sensitivity and selectivity of glycopeptide identification. In Chapter 4, this data-independent acquisition method is applied to the quantitative characterization of SARS-CoV-2 spike protein. The work presented here provides a significant contribution toward improving the confident detection and assignment of site-specific glycopeptides. Furthermore, understanding how to measure changes in glycosylation in related viral glycoprotein variants offers opportunities to include consideration of specific glycosylations in the design of vaccines to potentially improve efficacy against continually evolving viruses.

Yes / The on-going COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) has posed an extraordinary threat to global public health, wealth and well-being. As the carrier of human life and production, infrastructures need to be upgraded to mitigate and prevent the spread of viral diseases. Developing multifunctional/smart civil engineering materials to fight viruses is a promising approach to achieving this goal. In this perspective, the basic introduction on virus and its structure is provided. Then, the current design principles of antiviral materials and structures are examined. Subsequently, the possibility of developing active/passive antiviral civil engineering materials (including cementitious composites, ceramics, polymers and coatings) is proposed and envisaged. Finally, the future research needs and potential challenges to develop antiviral civil engineering materials are put forward. The proposed strategies to develop multifunctional/smart antiviral civil engineering materials will aid in the construction of smart infrastructures to prevent the spread viruses, thus improving human life and health as well as sustainability of human society. / The authors would like to thank the National Science Foundation of China (51978127, 52178188, and 51908103) and the Fundamental Research Funds for the Central Universities (DUT21RC(3)039) for providing funding to carry out this investigation.