SARS-CoV-2 and COVID-19: The most important research questions

Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic

Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.

Transcriptome & viral growth analysis of SARS-CoV-2-infected Vero CCL-81 cells

Background & objectives:

The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belonging to the family Coronaviridae, encodes for structural, non-structural, and accessory proteins, which are required for replication of the virus. These proteins are encoded by different genes present on the SARS-CoV-2 genome. The expression pattern of these genes in the host cells needs to be assessed. This study was undertaken to understand the transcription pattern of the SARS-CoV-2 genes in the Vero CCL-81 cells during the course of infection.

Methods:

Vero CCL-81 cells were infected with the SARS-CoV-2 virus inoculum having a 0.1 multiplicity of infection. The supernatants and cell pellets were harvested after centrifugation at different time points, post-infection. The 50% tissue culture infective dose (TCID₅₀) and cycle threshold (C_t) values of the E and the RdRp-2 genes were calculated. Next-generation sequencing of the harvested sample was carried out to observe the expression pattern of the virus by mapping to the SARS-CoV-2 Wuhan HU-1 reference sequence. The expressions were in terms of the reads per kilobase million (RPKM) values.

Results:

In the inital six hours post-infection, the copy numbers of E and RdRp-2 genes were approximately constant, which raised 10 log-fold and continued to increase till the 12 h post-infection (hpi). The TCID₅₀ was observed in the supernatant after 7 hpi, indicating the release of the viral progeny. ORF8 and ORF7a, along with the nucleocapsid transcript, were found to express at higher levels.

Interpretation & conclusions:

This study was a step towards understanding the growth kinetics of the SARS-CoV-2 replication cycle. The findings indicated that ORF8 and ORF7b gene transcripts were expressed in higher amounts indicating their essential role in viral replication. Future studies need to be conducted to explore their role in the SARS-CoV-2 replication.

One disease, many faces-typical and atypical presentations of SARS-CoV-2 infection-related COVID-19 disease

Since the appearance of the novel coronavirus (severe acute respiratory syndrome-coronavirus-2) and related coronavirus disease 2019 (COVID-19) in China in December 2019, a very high number of small and large patient series have been published in literature from around the world. Even though the classical presentation of COVID-19 is one with respiratory symptoms with or without pneumonia that can be self-limiting or evolve into severe respiratory distress syndrome with multiple organ failure, and secondary bacterial sepsis, a large body of evidence suggests a plethora of other types of clinical presentation. In this exhaustive review, we reviewed all of the published literature on COVID-19 to identify different types of clinical presentations affecting various organ systems, to provide an in-depth analysis that may prove useful for clinicians and health-workers on the frontline, battling the severe pandemic.

Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19)

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), known to cause the disease COVID-19, was declared a pandemic in early 2020. The objective of this review was to collate information regarding the potential of plants and natural products to inhibit coronavirus and targets associated with infection in humans and to highlight known drugs, which may have potential activity against SARS-CoV-2. Due to the similarity in the RNA genome, main proteases, and primary host receptor between SARS-CoV and SARS-CoV-2, a review was conducted on plants and secondary metabolites, which have shown activity against SARS-CoV. Numerous scientific reports on the potential of plants and secondary metabolites against SARS-CoV infection were found, providing important information on their possible activity against SARS-CoV-2. Based on current literature, 83 compounds have been identified with the potential to inhibit COVID-19. The most prominent selectivity was found for the alkaloid, lycorine, the lignan, savinin, and the abietane terpenoid, 8-beta-hydroxyabieta-9(11),13-dien-12-one with selectivity index values greater than 945, 667, and 510, respectively. Plants and their secondary metabolites, with activity against targets associated with the SARS-CoV infection, could provide valuable leads for the development into drugs for the novel SARS-CoV-2. The prospects of using computational methods to screen secondary metabolites against SARS-CoV targets are briefly discussed, and the drawbacks have been highlighted. Finally, we discuss plants traditionally used in Southern Africa for symptoms associated with respiratory viral infections and influenza, such as coughs, fever, and colds. However, only a few of these plants have been screened against SARS-CoV. Natural products hold a prominent role in discovering novel therapeutics to mitigate the current COVID-19 pandemic; however, further investigations regarding in vitro, in vivo, pre-clinical, and clinical phases are still required.

Development of a New Multiplex Real-Time RT-PCR Assay for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Detection

This research describes the development of a new multiplex real-time RT-PCR test for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with primers designed to amplify a 108 bp target on the spike surface glycoprotein (S gene) and a hydrolysis TaqMan probe designed to specifically detect SARS-CoV-2. The limit of detection (LOD) and clinical performance of this new assay were evaluated. A LOD study with inactivated virus exhibited performance equal to the modified CDC assay, with a final LOD of 1301 ± 13 genome equivalents/mL for the Northwell Health Laboratories laboratory-developed test (NWHL LDT) versus 1249 ± 14 genome equivalents/mL for the modified CDC assay. In addition, a clinical evaluation with 270 nasopharyngeal swab specimens exhibited 98.5% positive percent agreement and 99.3% negative percent agreement compared with the modified CDC assay. The NWHL LDT multiplex design allows testing of 91 patients per plate, versus a maximum of 29 patients per plate on the modified CDC assay, providing the benefit of testing significantly more patients per run and saving reagents, during a time when both of these parameters are critical. The results show that the NWHL LDT multiplex assay performs as well as the modified CDC assay but is more efficient and cost-effective and can be used as a diagnostic assay and for epidemiologic surveillance and clinical management of SARS-CoV-2.

Using Open-Source Intelligence to Detect Early Signals of COVID-19 in China: Descriptive Study

Background

The coronavirus disease (COVID-19) outbreak in China was first reported to the World Health Organization (WHO) on December 31, 2019, and the first cases were officially identified around December 8, 2019. Although the origin of COVID-19 has not been confirmed, approximately half of the early cases were linked to a seafood market in Wuhan. However, the first two documented patients did not visit the seafood market. News reports, social media, and informal sources may provide information about outbreaks prior to formal notification.

Objective

The aim of this study was to identify early signals of pneumonia or severe acute respiratory illness (SARI) in China prior to official recognition of the COVID-19 outbreak in December 2019 using open-source data.

Methods

To capture early reports, we searched an open source epidemic observatory, EpiWatch, for SARI or pneumonia-related illnesses in China from October 1, 2019. The searches were conducted using Google and the Chinese search engine Baidu.

Results

There was an increase in reports following the official notification of COVID-19 to the WHO on December 31, 2019, and a report that appeared on December 26, 2019 was retracted. A report of severe pneumonia on November 22, 2019, in Xiangyang was identified, and a potential index patient was retrospectively identified on November 17.

Conclusions

The lack of reports of SARI outbreaks prior to December 31, 2019, with a retracted report on December 26, suggests media censorship, given that formal reports indicate that cases began appearing on December 8. However, the findings also support a relatively recent origin of COVID-19 in November 2019. The case reported on November 22 was transferred to Wuhan approximately one incubation period before the first identified cases on December 8; this case should be further investigated, as only half of the early cases were exposed to the seafood market in Wuhan. Another case of COVID-19 has since been retrospectively identified in Hubei on November 17, 2019, suggesting that the infection was present prior to December.

Deep MLP-CNN Model Using Mixed-Data to Distinguish between COVID-19 and Non-COVID-19 Patients

The limitations and high false-negative rates (30%) of COVID-19 test kits have been a prominent challenge during the 2020 coronavirus pandemic. Manufacturing those kits and performing the tests require extensive resources and time. Recent studies show that radiological images like chest X-rays can offer a more efficient solution and faster initial screening of COVID-19 patients. In this study, we develop a COVID-19 diagnosis model using Multilayer Perceptron and Convolutional Neural Network (MLP-CNN) for mixed-data (numerical/categorical and image data). The model predicts and differentiates between COVID-19 and non-COVID-19 patients, such that early diagnosis of the virus can be initiated, leading to timely isolation and treatments to stop further spread of the disease. We also explore the benefits of using numerical/categorical data in association with chest X-ray images for screening COVID-19 patients considering both balanced and imbalanced datasets. Three different optimization algorithms are used and tested:adaptive learning rate optimization algorithm (Adam), stochastic gradient descent (Sgd), and root mean square propagation (Rmsprop). Preliminary computational results show that, on a balanced dataset, a model trained with Adam can distinguish between COVID-19 and non-COVID-19 patients with a higher accuracy of 96.3%. On the imbalanced dataset, the model trained with Rmsprop outperformed all other models by achieving an accuracy of 95.38%. Additionally, our proposed model outperformed selected existing deep learning models (considering only chest X-ray or CT scan images) by producing an overall average accuracy of 94.6% ± 3.42%.

Update on therapeutic approaches and emerging therapies for SARS-CoV-2 virus

The global pandemic of coronavirus disease 2019 (COVID-19), caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in over 7,273,958 cases with almost over 413,372 deaths worldwide as per the WHO situational report 143 on COVID-19. There are no known treatment regimens with proven efficacy and vaccines thus far, posing an unprecedented challenge to identify effective drugs and vaccines for prevention and treatment. The urgency for its prevention and cure has resulted in an increased number of proposed treatment options. The high rate and volume of emerging clinical trials on therapies for COVID-19 need to be compared and evaluated to provide scientific evidence for effective medical options. Other emerging non-conventional drug discovery techniques such as bioinformatics and cheminformatics, structure-based drug design, network-based methods for prediction of drug-target interactions, artificial intelligence (AI) and machine learning (ML) and phage technique could provide alternative routes to discovering potent Anti-SARS-CoV2 drugs. While drugs are being repurposed and discovered for COVID-19, novel drug delivery systems will be paramount for efficient delivery and avoidance of possible drug resistance. This review describes the proposed drug targets for therapy, and outcomes of clinical trials that have been reported. It also identifies the adopted treatment modalities that are showing promise, and those that have failed as drug candidates. It further highlights various emerging therapies and future strategies for the treatment of COVID-19 and delivery of Anti-SARS-CoV2 drugs.

Space-Time Variation and Spatial Differentiation of COVID-19 Confirmed Cases in Hubei Province Based on Extended GWR

Clarifying the regional transmission mechanism of COVID-19 has practical significance for effective protection. Taking 103 county-level regions of Hubei Province as an example, and taking the fastest-spreading stage of COVID-19, which lasted from 29 January 2020, to 29 February 2020, as the research period, we systematically analyzed the population migration, spatio-temporal variation pattern of COVID-19, with emphasis on the spatio-temporal differences and scale effects of related factors by using the daily sliding, time-ordered data analysis method, combined with extended geographically weighted regression (GWR). The results state that: Population migration plays a two-way role in COVID-19 variation. The emigrants’ and immigrants’ population of Wuhan city accounted for 3.70% and 73.05% of the total migrants’ population respectively; the restriction measures were not only effective in controlling the emigrants, but also effective in preventing immigrants. COVID-19 has significant spatial autocorrelation, and spatio-temporal differentiation has an effect on COVID-19. Different factors have different degrees of effect on COVID-19, and similar factors show different scale effects. Generally, the pattern of spatial differentiation is a transitional pattern of parallel bands from east to west, and also an epitaxial radiation pattern centered in the Wuhan 1 + 8 urban circle. This paper is helpful to understand the spatio-temporal evolution of COVID-19 in Hubei Province, so as to provide a reference for similar epidemic prevention.

Knowledge, attitudes, practices of/towards COVID 19 preventive measures and symptoms: A cross-sectional study during the exponential rise of the outbreak in Cameroon

Severe Acute Respiratory Syndrome Coronavirus 2 (COVID 19) has plagued the world with about 7,8 million confirmed cases and over 430,000 deaths as of June 13th, 2020. The knowledge, attitude, and practices (KAP) people hold towards this new disease could play a major role in the way they accept measures put in place to curb its spread and their willingness to seek and adhere to care. We sought to understand if: a) demographic variables of Cameroonian residents could influence KAP and symptomatology, and b) KAP could influence the risk of having COVID19.A cross-sectional KAP/symptomatology online survey was conducted between April 20 to May 20. All analyses were performed using SPSS version 23. Of all respondents (1006), 53.1% were female, 26.6% were students, 26.9% interacted face to face and 62.8% were residents in Yaoundé with a median age of 33. The overall high score was 84.19% for knowledge, 69% for attitude, and 60.8% for practice towards COVID 19. Age > 20 years was associated with a high knowledge of COVID 19. Women had lower practice scores compared to men (OR = 0.72; 95%CI 0.56-0.92). 41 respondents had ≥3 symptoms and only 9 (22.95%) of them had called 1510 (emergency number). There was no significant difference between KAP and symptomatology. The presence of ≥ 3 symptoms in 4% of respondents (with 56% of them having co-morbidities) supports the current trend in the number of confirmed cases (8681) in Cameroon. The continuous increase in the number of cases and the overall good KAP warrants further investigation to assess the effectiveness of the measures put in place to curb the spread of the disease. Sensitization is paramount to preclude negative health-seeking behaviors and encourage positive preventive and therapeutic practices, for fear of an increase in mortality.

Coronavirus Disease-2019 (COVID-19): An Updated Review

The current outbreak of novel Coronavirus Disease-2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major pandemic situation and a catastrophe for humans. COVID-19 is a severe infectious disease particularly of the respiratory system characterized by fatal complications such as severe acute respiratory distress syndrome (SARS), pneumonia, cardiac arrhythmia, kidney failure/ multiple organ failure and even death. Since its discovery, the SARS-CoV-2 has spread across 213 countries or territories, causing more than 8.5 million people with a rising death toll over 5.5 million people (as of June 2020, WHO). In fact, the current looming crisis of COVID-19 has become an increasingly serious concern to public health. It has affected lives of millions of people with severe impact on health systems and economies globally. Since there are no specific drugs and/or vaccines available so far, combating COVID-19 remains to be a major challenging task. Therefore, development of potential and effective treatment regimens (prophylactic/therapeutic) is urgently required which could resolve the issue. In this review, we summarize the current knowledge about the coronavirus, disease epidemiology, clinical manifestations and risk factors, replication of the virus, pathophysiology and host immune responses of SARS-CoV-2 infection. The therapeutic interventions and prophylactic measures along with precautionary measures are the frontline approaches that could be undertaken in order to control and prevent the spread of the deadly and highly contagious COVID-19 are also detailed herein.

The microbial coinfection in COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel β-coronavirus, is the main pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19). SARS-CoV-2 infects much more people, especially the elder population, around the world than other coronavirus, such as SARS-CoV and MERS-CoV, which is challenging current global public health system. Beyond the pathogenesis of SARS-CoV-2, microbial coinfection plays an important role in the occurrence and development of SARS-CoV-2 infection by raising the difficulties of diagnosis, treatment, prognosis of COVID-19, and even increasing the disease symptom and mortality. We summarize the coinfection of virus, bacteria and fungi with SARS-CoV-2, their effects on COVID-19, the reasons of coinfection, and the diagnosis to emphasize the importance of microbial coinfection in COVID-19. KEY POINTS: • Microbial coinfection is a nonnegligible factor in COVID-19. • Microbial coinfection exacerbates the processes of the occurrence, development and prognosis of COVID-19, and the difficulties of clinical diagnosis and treatment. • Different virus, bacteria, and fungi contributed to the coinfection with SARS-CoV-2.

Potential therapeutic targets for combating SARS-CoV-2: Drug repurposing, clinical trials and recent advancements

The present pandemic of SARS-CoV-2 has been a tough task for the whole world to deal with. With the absence of specific drugs or vaccines against SARS-CoV-2, the situation is very difficult to control. Apart from the absence of specific therapies, the lack of knowledge about potential therapeutic targets and individual perception is adding to the complications. The present review describes the novel SARS-CoV-2 structure, surface proteins, asymptomatic and symptomatic transmission in addition to the genotype and phenotype of SARS-CoV-2 along with genetic strains and similarity between SARS, MERS and SARS-CoV-2. Therapeutic strategies such as inhibition of the endocytic pathway and suppressing RNA polymerase activity by metal ions, which could be quite beneficial for controlling COVID-19, are outlined. The drug repurposing for SARS-CoV-2 is discussed in detail along with therapeutic classes such as antivirals, antibiotics, and amino quinolones and their probable role in suppressing SARS-CoV-2 with reference to case studies. The ongoing clinical trials both with respect to drug repurposing and vaccines are summarized along with a brief description. The recent advancements and future perspective of ongoing research for therapy and detection of SARS-CoV-2 are provided. The review, in brief, summarizes epidemiology, therapy and the current scenario for combating SARS-CoV-2.

Preparedness of personal protective equipment and implementation of new CPR strategies for patients with out-of-hospital cardiac arrest in the COVID-19 era

BACKGROUND

In February and March 2020, healthcare providers and citizens in Daegu, South Korea, experienced the onslaught of a large-scale community epidemic of COVID-19. This had a profound impact on patients who experienced out-of-hospital cardiac arrest (OHCA).

METHODS

We conducted a retrospective observational study of 171 OHCA patients based on the multicenter WinCOVID registry. Demographic and clinical characteristics, overall survival, COVID-19 related data, as well as personal protective equipment (PPE) and resuscitation techniques used during the COVID-19 outbreak were evaluated and compared with outcomes from a 2018 historical cohort (n ​= ​158).

RESULTS

Among the interventions, high-level PPE was introduced and standard cardiopulmonary resuscitation was changed to chest compressions using mechanical devices. All OHCA patients were treated as confirmed or suspicious for COVID-19 regardless of symptoms. Furthermore, complete or partial closures of emergency centers and the number of medical personnel requiring self-isolation decreased in response to the introduction of isolated resuscitation units. However, the adjusted odds ratio and 95% confidence intervals for survival discharge and favorable neurologic outcome were 0.51 (0.25-0.97) and 0.45 (0.21-1.07) compared with those in the 2018 historical cohort.

CONCLUSIONS

Responses to the COVID-19 pandemic included changes to current PPE strategies and introduction of isolated resuscitation units; the latter intervention reduced the number of unexpected closures and quarantines of emergency resources early on during the COVID-19 outbreak. Given the possibility of future outbreaks, we need to have revised resuscitation strategies and the capacity to commandeer emergency resources for OHCA patients.

Could herbal medicine (Soshihotang) be a new treatment option for COVID-19?: a narrative review

BACKGROUND

While the world struggles under the coronavirus disease 2019 (COVID-19) pandemic, a variety of antiviral agents and symptomatic treatments are being administered to patients and urgent clinical trials are underway. Under these circumstances, it is important to explore various possibilities for the treatment of COVID-19 including herbal medicines. Among various herbal medicines, Soshihotang (SSHT, Xiao Chai Hu Tang in Chinese) has been prescribed to treat various viral diseases and is used in combination with other herbal medicines depending on the patient's symptoms.

METHODS

For conducting the present review, we searched electronic databases focusing on the antiviral effect of SSHT in experimental and clinical study until April 2020. The search keywords included SSHT, constituents of SSHT, and antiviral effect. We also searched for materials related to topic directly from websites and published books. Based on these search results, we summarized the results of the included materials in the form of a narrative review.

RESULTS

In a number of recent clinical studies, treatment with SSHT improved the infection status of the respiratory and hepatobiliary systems, and experimental studies demonstrated the antiviral effect of SSHT and its components. Furthermore, SSHT are being used in China-where COVID-19 outbreak first took place-and offer a new option to treat COVID-19.

CONCLUSION

Based on the present evidences, it is believed that SSHT is likely to be a new therapeutic option for COVID-19. Conducting further studies might provide improved understanding regarding the use of SSHT in treating COVID-19.

COVID-19 pathways for brain and heart injury in comorbidity patients: A role of medical imaging and artificial intelligence-based COVID severity classification: A review

Artificial intelligence (AI) has penetrated the field of medicine, particularly the field of radiology. Since its emergence, the highly virulent coronavirus disease 2019 (COVID-19) has infected over 10 million people, leading to over 500,000 deaths as of July 1st, 2020. Since the outbreak began, almost 28,000 articles about COVID-19 have been published (https://pubmed.ncbi.nlm.nih.gov); however, few have explored the role of imaging and artificial intelligence in COVID-19 patients-specifically, those with comorbidities. This paper begins by presenting the four pathways that can lead to heart and brain injuries following a COVID-19 infection. Our survey also offers insights into the role that imaging can play in the treatment of comorbid patients, based on probabilities derived from COVID-19 symptom statistics. Such symptoms include myocardial injury, hypoxia, plaque rupture, arrhythmias, venous thromboembolism, coronary thrombosis, encephalitis, ischemia, inflammation, and lung injury. At its core, this study considers the role of image-based AI, which can be used to characterize the tissues of a COVID-19 patient and classify the severity of their infection. Image-based AI is more important than ever as the pandemic surges and countries worldwide grapple with limited medical resources for detection and diagnosis.

Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization

We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM (Jupyter notebook), https://github.com/EESI/ncov_ism (command line tool) and via an interactive website at https://covid19-ism.coe.drexel.edu/.

Risk factors associated with occurrence of COVID-19 among household persons exposed to patients with confirmed COVID-19 in Qingdao Municipal, China

Tracing and isolation of close contacts is used to control outbreaks of coronavirus disease 2019 (COVID-19) in China. However, risk factors associated with the occurrence of COVID-19 among close contacts have not been well described. A total of 106 household contacts were included in this study, of whom 19 developed into COVID-19 cases, and the secondary attack rate was 17.9%. Multivariable analysis showed that increasing risk of occurrence of COVID-19 among household contacts was associated with female index patients (adjusted hazard ratio [aHR] = 3.84, 95% CI = 1.07-13.78), critical disease index patients (aHR = 7.58, 95% CI = 1.66-34.66), effective contact duration with index patients > 2 days (aHR = 4.21, 95% CI = 1.29-13.73), and effective contact duration > 11 days (aHR = 17.88, 95% CI = 3.26-98.01). The sex and disease severity of index patients with COVID-19 and longer effective contact duration with patients with confirmed COVID-19 could help epidemiologists to identify potential COVID-19 cases among household contacts at an early stage.

Characterization of accessory genes in coronavirus genomes

BACKGROUND

The Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of the coronavirus (CoV) family. CoV genomes code for a ORF1a / ORF1ab polyprotein and four structural proteins widely studied as major drug targets. The genomes also contain a variable number of open reading frames (ORFs) coding for accessory proteins that are not essential for virus replication, but appear to have a role in pathogenesis. The accessory proteins have been less well characterized and are difficult to predict by classical bioinformatics methods.

METHODS

We propose a computational tool GOFIX to characterize potential ORFs in virus genomes. In particular, ORF coding potential is estimated by searching for enrichment in motifs of the X circular code, that is known to be over-represented in the reading frames of viral genes.

RESULTS

We applied GOFIX to study the SARS-CoV-2 and related genomes including SARS-CoV and SARS-like viruses from bat, civet and pangolin hosts, focusing on the accessory proteins. Our analysis provides evidence supporting the presence of overlapping ORFs 7b, 9b and 9c in all the genomes and thus helps to resolve some differences in current genome annotations. In contrast, we predict that ORF3b is not functional in all genomes. Novel putative ORFs were also predicted, including a truncated form of the ORF10 previously identified in SARS-CoV-2 and a little known ORF overlapping the Spike protein in Civet-CoV and SARS-CoV.

CONCLUSIONS

Our findings contribute to characterizing sequence properties of accessory genes of SARS coronaviruses, and especially the newly acquired genes making use of overlapping reading frames.

Coronaviruses pandemics: Can neutralizing antibodies help?

For the first time in Homo sapiens history, possibly, most of human activities is stopped by coronavirus disease 2019 (COVID-19). Nearly eight billion people of this world are facing a great challenge, maybe not "to be or not to be" yet, but unpredictable. What happens to other major pandemics in the past, and how human beings went through these hurdles? The human body is equipped with the immune system that can recognize, respond and fight against pathogens such as viruses. Following the innate response, immune system processes the adaptive response by which each pathogen is encoded and recorded in memory system. The humoral reaction containing cytokines and antibodies is expected to activate when the pathogens come back. Exploiting this nature of body protection, neutralizing antibodies have been investigated. Learning from past, in parallel to SARS-CoV-2, other coronaviruses SARS-CoV and MERS-CoV who caused previous pandemics, are recalled in this review. We here propose insights of origin and characteristics and perspective for the future of antibodies development.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and coronavirus disease 19 (COVID-19) - anatomic pathology perspective on current knowledge

BACKGROUND

The world is currently witnessing a major devastating pandemic of Coronavirus disease-2019 (COVID-19). This disease is caused by a novel coronavirus named Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). It primarily affects the respiratory tract and particularly the lungs. The virus enters the cell by attaching its spike-like surface projections to the angiotensin-converting enzyme-2 (ACE-2) expressed in various tissues. Though the majority of symptomatic patients have mild flu-like symptoms, a significant minority develop severe lung injury with acute respiratory distress syndrome (ARDS), leading to considerable morbidity and mortality. Elderly patients with previous cardiovascular comorbidities are particularly susceptible to severe clinical manifestations. BODY: Currently, our limited knowledge of the pathologic findings is based on post-mortem biopsies, a few limited autopsies, and very few complete autopsies. From these reports, we know that the virus can be found in various organs but the most striking tissue damage involves the lungs resulting almost always in diffuse alveolar damage with interstitial edema, capillary congestion, and occasional interstitial lymphocytosis, causing hypoxia, multiorgan failure, and death. A few pathology studies have also reported intravascular microthrombi and pulmonary thrombembolism. Although the clinical presentation of this disease is fairly well characterized, knowledge of the pathologic aspects remains comparatively limited.

CONCLUSION

In this review, we discuss clinical, pathologic, and genomic features of COVID-19, review current hypotheses regarding the pathogenesis, and briefly discuss the clinical characteristics. We also compare the salient features of COVID-19 with other coronavirus-related illnesses that have posed significant public health issues in the past, including SARS and the Middle East Respiratory Syndrome (MERS).

[Use of point-of-care technologies for the management of the COVID-19 pandemic in Colombia]

OBJECTIVE

To propose a health care model that integrates point-of-care technologies and artificial intelligence for the management of the COVID-19 pandemic.

METHODS

A theoretical model was used in which one million people accessed the mobile application CoronApp-Colombia, which collects personal data, signs, symptoms and epidemiological links compatible with COVID-19. With the information from the app artificial intelligence techniques (data science) were applied in a virtual situation room.

RESULTS

Users compatible with COVID-19 were prioritized and subjected to a rapid diagnostic test for anti-SARS-CoV-2 antibodies. Screening with the rapid diagnostic test would allow detection of sero-reactive individuals, for whom diagnostic confirmation would be carried out using molecular biology (PCR). Information from positive cases confirmed by PCR would be re-screened using artificial intelligence and spatial statistical techniques to identify geographical foci of infection. These foci could be actively searched for contacts with positive index cases and the diagnostic route would be followed again using the rapid diagnostic test and PCR.

CONCLUSION

This model may be useful for countries in the region with weak or absent technological platforms for PCR diagnosis to maximize existing resources, estimate the epidemiological burden of COVID-19 (infection, morbidity, mortality and lethality) and implement containment, mitigation and control plans according to their needs.

A comprehensive review of COVID-19 characteristics

In December 2019, a novel coronavirus, named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or (2019-nCoV) with unknown origin spread in Hubei province of China. The epidemic disease caused by SARS-CoV-2 called coronavirus disease-19 (COVID-19). The presence of COVID-19 was manifested by several symptoms, ranging from asymptomatic/mild symptoms to severe illness and death. The viral infection expanded internationally and WHO announced a Public Health Emergency of International Concern. To quickly diagnose and control such a highly infectious disease, suspicious individuals were isolated and diagnostic/treatment procedures were developed through patients' epidemiological and clinical data. Early in the COVID-19 outbreak, WHO invited hundreds of researchers from around the world to develop a rapid quality diagnosis, treatment and vaccines, but so far no specific antiviral treatment or vaccine has been approved by the FDA. At present, COVID-19 is managed by available antiviral drugs to improve the symptoms, and in severe cases, supportive care including oxygen and mechanical ventilation is used for infected patients. However, due to the worldwide spread of the virus, COVID-19 has become a serious concern in the medical community. According to the current data of WHO, the number of infected and dead cases has increased to 8,708,008 and 461,715, respectively (Dec 2019 -June 2020). Given the high mortality rate and economic damage to various communities to date, great efforts must be made to produce successful drugs and vaccines against 2019-nCoV infection. For this reason, first of all, the characteristics of the virus, its pathogenicity, and its infectious pathways must be well known. Thus, the main purpose of this review is to provide an overview of this epidemic disease based on the current evidence.

Emerging Human Coronavirus Infections (SARS, MERS, and COVID-19): Where They Are Leading Us

Coronavirus infections are responsible for mild, moderate, and severe infections in birds and mammals. These were first isolated in humans as causal microorganisms responsible for common cold. The 2002-2003 SARS epidemic caused by SARS-CoV and 2012 MERS epidemic (64 countries affected) caused by MERS-CoV showed their acute and fatal side. These two CoV infections killed thousands of patients infected worldwide. However, WHO has still reported the MERS case in December 2019 in middle-eastern country (Saudi Arabia), indicating the MERS epidemic has not ended completely yet. Although we have not yet understood completely these two CoV epidemics, a third most dangerous and severe CoV infection has been originated in the Wuhan city, Hubei district of China in December 2019. This CoV infection called COVID-19 or SARS-CoV2 infection has now spread to 210 countries and territories around the world. COVID-19 has now been declared a pandemic by the World Health Organization (WHO). It has infected more than 16.69 million people with more than 663,540 deaths across the world. Thus the current manuscript aims to describe all three (SARS, MERS, and COVID-19) in terms of their causal organisms (SARS-CoV, MERS-CoV, and SARS-CoV2), similarities and differences in their clinical symptoms, outcomes, immunology, and immunopathogenesis, and possible future therapeutic approaches.

Reopening of dental clinics during SARS-CoV-2 pandemic: an evidence-based review of literature for clinical interventions

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes serious acute respiratory diseases including pneumonia and bronchitis with approximately 2.3% fatality occurrence.

Main body

This study argues the main concepts that need to be considered for the gradual reopening of dental offices include treatment planning approaches, fundamental elements needed to prevent transmission of SARS-CoV-2 virus in dental healthcare settings, personal protection equipment (PPE) for dental health care providers, environmental measures, adjunctive measures, and rapid point of care tests in dental offices.

Conclusion

This article seeks to provide an overview of existing scientific evidence to suggest a guideline for reopening dental offices.

A narrative literature review on traditional medicine options for treatment of corona virus disease 2019 (COVID-19)

Coronavirus disease 2019 (COVID-19) as a life-threatening disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is accounted as global public health concern. Treatment of COVID-19 is primarily supportive and the role of antiviral agents is yet to be established. However, there are no specific anti-COVID-19 drugs and vaccine until now. This review focuses on traditional medicine such as medicinal plant extracts as promising approaches against COVID-19. Chinese, Indian and Iranian traditional medicine, suggests some herbs for prevention, treatment and rehabilitation of the diseases including COVID-19. Although, inhibition of viral replication is considered as general mechanism of herbal extracts, however some studies demonstrated that traditional herbal extracts can interact with key viral proteins which are associated with virus virulence. Chinese, Indian and Iranian traditional medicine, suggests some herbs for prevention, treatment and rehabilitation of the diseases including COVID-19. However the beneficial effects of these traditional medicines and their clinical trials remained to be known. Herein, we reviewed the latest updates on traditional medicines proposed for treatment of COVID-19.

COVID-19 cardiovascular epidemiology, cellular pathogenesis, clinical manifestations and management

Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. These cardiovascular effects are worse in patients who have pre-existing cardiac conditions such as coronary artery disease, hypertension, diabetes mellitus, and coagulation abnormalities. Other predisposing risk factors include advanced age, immunocompromised state, and underlying systemic inflammatory conditions. Here we review the cellular pathophysiology, clinical manifestations and treatment modalities of the cardiac manifestations seen in patients with COVID-19.

Effects of air pollutants on the transmission and severity of respiratory viral infections

Particulate matter, sulfur dioxide, nitrogen oxides, ozone, carbon monoxide, volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs) are among the outdoor air pollutants that are major factors in diseases, causing especially adverse respiratory effects in humans. On the other hand, the role of respiratory viruses in the pathogenesis of severe respiratory infections is an issue of great importance. The present literature review was aimed at assessing the potential effects of air pollutants on the transmission and severity of respiratory viral infections. We have reviewed the scientific literature regarding the association of outdoor air pollution and respiratory viruses on respiratory diseases. Evidence supports a clear association between air concentrations of some pollutants and human respiratory viruses interacting to adversely affect the respiratory system. Given the undoubted importance and topicality of the subject, we have paid special attention to the association between air pollutants and the transmission and severity of the effects caused by the coronavirus named SARS-CoV-2, which causes the COVID-19. Although to date, and by obvious reasons, the number of studies on this issue are still scarce, most results indicate that chronic exposure to air pollutants delays/complicates recovery of patients of COVID-19 and leads to more severe and lethal forms of this disease. This deserves immediate and in-depth experimental investigations.

Clinical characteristics of patients with COVID-19 presenting with gastrointestinal symptoms as initial symptoms: Retrospective case series

BACKGROUND

A large number of pneumonia cases due to coronavirus disease 2019 (COVID-19) have been first reported in China. Meanwhile, the virus is sweeping all around the world and has infected millions of people. Fever and pulmonary symptoms have been noticed as major and early signs of infection, whereas gastrointestinal symptoms were also observed in a significant portion of patients. The clinical investigation of disease onset was underestimated, especially due to the neglection of cases presenting with gastrointestinal symptoms.

AIM

To characterize the clinical features of coronavirus-infected patients with gastrointestinal symptoms as initial symptoms.

METHODS

This is a retrospective, single-center case series of the general consecutive hospitalized patients with confirmed COVID-19 at Wuhan Union Hospital from February 2, 2020 to February 13, 2020. According to their initial symptoms, these patients were classified into two groups. Patients in group one presented with pulmonary symptoms (PS) as initial symptoms, and group two presented with gastrointestinal symptoms (GS). Epidemiological, demographic, clinical, laboratory, and treatment data were collected for analysis.

RESULTS

Among the 50 patients recruited, no patient has been admitted to intensive care units, and no patient died during the study. The duration of hospitalization was longer in the GS group than in the PS group (12.13 ± 2.44 vs 10.00 ± 2.13, P < 0.01). All of the 50 patients exhibited decreased lymphocytes. However, lymphocytes in the GS group were significantly lower compared to those in the PS group (0.94 ± 0.06 vs 1.04 ± 0.15, P < 0.01). Procalcitonin and hs-CRP were both significantly higher in the GS group than in the PS group. Accordingly, the duration of viral shedding was significantly longer in the GS group compared to the PS group (10.22 ± 1.93 vs 8.15 ± 1.87, P < 0.01).

CONCLUSION

COVID-19 patients presenting with gastrointestinal symptoms as initial symptoms need more days of viral shedding and hospitalization than the patients presenting with pulmonary symptoms.

Quantifying early COVID-19 outbreak transmission in South Africa and exploring vaccine efficacy scenarios

The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83-3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44-99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72-69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76-80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.

Pharmacy services at a temporary COVID-19 hospital in Wuhan, China

In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

COVID-19: A Review on Diagnosis, Treatment, and Prophylaxis

Coronavirus 2 (CoV) Severe Acute Respiratory Syndrome (SARS-CoV2) is causing a highly infectious pandemic pneumonia. Coronaviruses are positive sense single-stranded RNA viruses that infect several animal species, causing symptoms that range from those similar to the common cold to severe respiratory syndrome. The Angiotensin Converting Enzyme 2 (ACE2) is the SARS-CoV2 functional receptor. Measures are currently undertaken worldwide to control the infection to avoid disruption of the social and economic equilibrium, especially in countries with poor healthcare resources. In a guarded optimistic view, we hope that the undertaken preventive and treatment measures will at least contribute to contain viral diffusion, attenuate activity, or even eliminate SARS-CoV2. In this review, we discuss emerging perspectives for prevention/treatment of COVID-19 infection. In addition to vaccines under development, passive immunization is an open opportunity since patients develop neutralizing antibodies. A full spectrum of potential drugs for COVID-19 infections could in turn affect virus binding or enzymatic activities involved in viral replication and transcription. Furthermore, clinical trials are currently evaluating the safety and efficacy of anti-inflammatory drugs, such as tocilizumab. Bioinformatics may allow characterization of specific CD8+ and CD4+ T cell responses; thus, CoV2 T cells' frequency can be correlated with the disease severity and outcome. Combinatorial antibody phage display may be empowered to identify the immune repertoire of CoV2-specific neutralizing antibodies.

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

Analyzing host transcriptional changes in response to SARS-CoV-2 infection will help delineate biological processes underlying viral pathogenesis. Comparison of expression profiles of lung cell lines A549 (infected with either SARS-CoV-2 (with ACE2 expression)) or Influenza A virus (IAV)) and Calu3 (infected with SARS-CoV-2 or MERS-CoV) revealed upregulation of the antiviral interferon signaling in all three viral infections. However, perturbations in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2 infected cells. Validation of findings from cell line data revealed perturbations in autophagy and mitochondrial processes in the infected human nasopharyngeal samples. Specifically, downregulation of mTOR expression, mitochondrial ribosomal, mitochondrial complex I, and lysosome acidification genes were concurrently observed in both infected cell lines and human datasets. Furthermore, SARS-CoV-2 infection impedes autophagic flux by upregulating GSK3B in lung cell lines, or by downregulating autophagy genes, SNAP29 and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Additionally, downregulation of MTFP1 (in cell lines) or SOCS6 (in human samples) results in hyperfused mitochondria and impede proper interferon response. Coexpression networks analysis identifies correlated clusters of genes annotated to inflammation and mitochondrial processes that are misregulated in SARS-CoV-2 infected cells. Finally, comparison of age stratified human gene expression data revealed impaired upregulation of chemokines, interferon stimulated and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2 infection.

Multiple sclerosis and COVID-19

This paper reviews currently available data on the novel coronavirus and clinical features of COVID-19, followed by a detailed section on possible modifications of immunomodulatory therapy in multiple sclerosis patients with COVID-19, based on what we know so far. There are discussed: (i) The COVID-19 disease (Epidemiological background SARS-CoV-1 coronavirus; Autoimmune response to COVID-19; Asymptomatic course; SARS-CoV-2 test; COVID-19 symptoms), (ii) Treatment of COVID-19 (Experimental plasma treatment; Antiviral therapy; Antimalarial treatment scheme; Biological treatment; Corticosteroid treatment; Symptomatic treatment; Vaccine preparation) and (iii) Multiple sclerosis and SARS-CoV-2 infection (Epidemiological recommendation).

Efficacy of integrative Traditional Chinese and Western medicine for the treatment of patients infected with 2019 novel coronavirus (COVID-19): A protocol for systematic review and meta analysis

BACKGROUND

No specific anti-virus drugs or vaccines have been available for the treatment of COVID-19. Integrative traditional Chinese and western medicine has been proposed as a therapeutic option with substantial applications in China. This protocol is proposed for a systematic review and meta-analysis that aims to evaluate the efficacy of integrative traditional Chinese and western medicine treatment on patients with COVID-19.

METHODS

Ten databases including PubMed, EMBASE, Cochrane Library, CIHAHL, Web of Science, Chinese National Knowledge Infrastructure (CNKI), Chinese Scientific Journals Database (VIP), Wanfang database, China Biomedical Literature Database (CBM) and Chinese Biomedical Literature Service System (SinoMed) will be searched. All published randomized controlled trials, clinical controlled trials, case-control, and case series that meet the pre-specified eligibility criteria will be included. Primary outcome measures include mortality, clinical recovery rate, duration of fever, progression rate from mild or moderate to severe, improvement of symptoms, biomarkers of laboratory examination and changes in computed tomography. Secondary outcomes include dosage of hormonotherapy, incidence and severity of adverse events and quality of life. Study selection, data extraction and assessment of bias risk will be conducted by 2 reviewers independently. RevMan software (V.5.3.5) will be used to perform data synthesis. Subgroup and sensitivity analysis will be performed when necessary. The strength of evidence will be assessed by the GRADE system.

RESULTS

This study will provide a well-reported and high-quality synthesis on the efficacy of integrative traditional Chinese and western medicine treatment on patients with COVID-19.

CONCLUSION

This systematic review protocol will be helpful for providing evidence of whether integrative traditional Chinese and western medicine treatment is an effective therapeutic approach for patients with COVID-19.

ETHICS AND DISSEMINATION

Ethical approval is unnecessary as no individual patient or privacy data is collected. The results of this study will be disseminated in a peer-reviewed scientific journal and/or conference presentation.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42020167205.

Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2

Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.

Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.

A data-driven hypothesis on the epigenetic dysregulation of host metabolism by SARS coronaviral infection: Potential implications for the SARS-CoV-2 modus operandi

COVID-19, the disease caused by the novel SARS-CoV-2, a betacoronavirus structurally similar to SARS-CoV. Based on both structural and syndromic similarities with SARS-CoV, a hypothesis is formed on SARS-CoV-2 potential to affect the host's metabolism as part of its lifecycle. This hypothesis is evaluated by (a) exploratory analysis of SARS-CoV/human transcriptomic interaction data and gene set enrichment analysis (b) a confirmatory, focused review of the literature based on the findings by (a). A STRING Viruses (available search for human - SARS-CoV (NCBI taxonomy Id: 9606 vs. NCBI taxonomy Id: 694009) genomic interactions reveals ten human proteins, interacting with SARS-CoV: SGTA, FGL2, SPECC1, STAT3, PHB, BCL2L1, PPP1CA, CAV1, JUN, XPO1. Gene set enrichment analyses (GSEA) with STRING on this network revealed their role as a putative protein - protein interaction network (PPI; Enrichment p-value = 0.0296) mediating, viral parasitism, interleukin as well as insulin signaling, diabetes and triglyceride catabolism. In the literature, SARS-CoV has been known to cause de novo diabetes by ACE2-dependent uptake on pancreatic isle cells, and furthermore dysregulate lipid autophagy in favor of the viral lifecycle. Conversely, currently there are only non-causative, observational evidence of worse outcomes for COVID-19 patients with comorbid diabetes or hyperglycemia. No study has reported on the lipid profiles of COVID-19 patients; however, lipid-targeting molecules have been proposed as agents against SARS-CoV-2. Future studies, reporting on lipid and glucose metabolism of COVID-19 patients could help elucidate the disease's seculae and aid drug design.

Can wearing face masks in public affect transmission route and viral load in COVID-19?

The mandatory face mask wearing was implemented in the Czech Republic and Slovakia shortly after the COVID-19 outbreak in Central Europe. So far, the number of COVID-19-associated deaths per 100,000 individuals is far lower in these countries as compared with other neighbouring or close countries. The use of face masks in public may not protect the general public from contracting the virus, however, presumptively decreases the viral load and contributes to a favourable clinical outcome in COVID-19 disease. A certain time is required for antigen-specific T cells and B cells to fully develop. Obligatory face mask wearing in public favours the virus transmission through oral mucosa and/or conjunctival epithelium, which enables the adaptive immune responses to evolve. In the case of inhalation of high loads of SARS-CoV-2, the time for the development of fully protective adaptive immune responses seems to be insufficient. Then, a less specific and more damaging innate immune response prevails.

Risiken und Chancen von Immuntherapien in Zeiten der Coronavirus-2019-Pandemie

Immuntherapien stellen die essenzielle Grundlage der Behandlung von neuroinflammatorischen Erkrankungen dar. In Zeiten der Coronavirus-2019 (COVID-19)-Pandemie ergibt sich im klinischen Alltag jedoch zunehmend die Frage, ob eine Immuntherapie bei neurologischen Patienten aufgrund des potenziellen Infektionsrisikos eingeleitet, intensiviert, pausiert oder gar beendet werden sollte. Unsicherheit besteht v. a. deshalb, weil verschiedene nationale und internationale Fachgesellschaften diesbezüglich unterschiedliche Empfehlungen veröffentlichten. In diesem Artikel soll ein Überblick über die Wirkmechanismen von Immuntherapien und den daraus abzuleitenden Infektionsrisiken in Bezug auf COVID-19 (durch den Coronavirus verursachte Erkrankung) gegeben werden. Potenzielle Chancen und vorteilhafte Effekte einzelner Substrate in der Akuttherapie von COVID-19 werden diskutiert.

Immunosuppressive agents for dermatological indications in the ongoing COVID-19 pandemic: Rationalizing use and clinical applicability

The ongoing COVID-19 epidemic has brought to the fore many concerns related to use of immunosuppressive agents (ISAs) in dermatology. While it is unclear whether the patients on ISAs for skin conditions are more prone to develop COVID-19, and what impact the ISA may have on the clinical outcome if a patient does get infected, rationalizations based on the specific immune effects of each drug, and existing literature on incidence of various infections with each, are possible. In this review, we provide the readers with practically useful insights into these aspects, related to the conventional ISAs, and briefly mention the clinical outcome data available on related scenarios from other patient groups so far. In the end, we have attempted to provide some clinically useful points regarding practical use of each dermatologically relevant conventional ISA in the current scenario.

Obesity ‑ a risk factor for increased COVID‑19 prevalence, severity and lethality (Review)

Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are a group of viruses that cause infections in the human respiratory tract, which can be characterized clinically from mild to fatal. The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is the virus responsible. The global spread of COVID‑19 can be described as the worst pandemic in humanity in the last century. To date, COVID‑19 has infected more than 3,000,000 people worldwide and killed more than 200,000 people. All age groups can be infected from the virus, but more serious symptoms that can possibly result in death are observed in older people and those with underlying medical conditions such as cardiovascular and pulmonary disease. Novel data report more severe symptoms and even a negative prognosis for the obese patients. A growing body of evidence connects obesity with COVID‑19 and a number of mechanisms from immune system activity attenuation to chronic inflammation are implicated. Lipid peroxidation creates reactive lipid aldehydes which in a patient with metabolic disorder and COVID‑19 will affect its prognosis. Finally, pregnancy‑associated obesity needs to be studied further in connection to COVID‑19 as this infection could pose high risk both to pregnant women and the fetus.

COVID-19 in Singapore and Malaysia: Rising to the Challenges of Orthopaedic Practice in an Evolving Pandemic

With the increasing number of COVID-19 cases and related deaths worldwide, we decided to share the development of this condition in Singapore and Malaysia. First few cases were diagnosed in the two countries at the end of January 2020, and the numbers have surged to thousands by end of March 2020. We will focus on strategies adopted by the government and also the Orthopaedic community of the two countries up till the beginning of April 2020. We hope that by sharing of relevant information and knowledge on how we are managing the COVID-19 condition, we can help other communities, and health care workers to more effectively overcome this pandemic.