RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

Immuno-Inflammatory Characteristics in Low Severity COVID-19 Patients with Digestive Symptoms

AIM

The outbreak of Coronavirus Disease 2019 (COVID-19) has resulted in a global pandemic, with the main manifestations being of respiratory nature, including pneumonia. It is noteworthy that digestive symptoms are also observed in COVID-19 patients. In this article, we describe the immuno-inflammatory characteristics of low severity COVID-19 patients with digestive symptoms.

METHODS

Patients with mild symptoms of COVID-19 were split into three groups based on the patients' symptoms. The first group displayed digestive symptoms only, the second group displayed respiratory symptoms only, and the last group displayed both digestive and respiratory symptoms. Patients were discharged based on negative results of rRT-PCR testing for SARS-CoV-2 from at least two sequential respiratory tract specimens collected ≥24 hours apart. Multiorgan function and immuno-inflammatory characteristics were analyzed for all of the three groups.

RESULTS

Mild liver damage and activation of the immuno-inflammatory system were the most common abnormalities observed in patients with mild COVID-19 symptoms but no significant differences were found (P > 0.05). Patients with digestive symptoms were more likely to have slightly higher and later peak values of inflammatory cytokines during the subsequent course of disease (P < 0.05). In addition, a significant correlation between IL-2 and TNF level was found in the first group which included patients with digestive symptoms only (P < 0.05).

CONCLUSIONS

Patients with mild cases of COVID-19 only displaying digestive symptoms are a special subtype. Patients in this group were more likely to have slightly higher and delayed peak values of inflammatory cytokines during the subsequent course of the disease. Prevention and clinical management of this type should be taken into consideration.

Highly sensitive quantification of plasma SARS-CoV-2 RNA shelds light on its potential clinical value

Background

Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662,000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury or/and multiple organ failure, suggesting a spread of the SARS-CoV-2 in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We herein intended to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAaemia) in hospitalized COVID-19 patients.

Methods

Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild-to-moderate in 17 patients, severe in 16 patients and critical in 26 patients. Plasma SARS-CoV-2 RNAaemia was quantified by droplet digital Crystal Digital PCR™ next-generation technology (Stilla Technologies, Villejuif, France).

Results

Overall, SARS-CoV-2 RNAaemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAaemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (p=0.036). Levels of SARS-CoV-2 RNAaemia were associated with severity (p=0.035). Among nine patients who experienced clinical deterioration during follow-up, eight had positive SARS-CoV-2 RNAaemia at baseline while only one critical patient with undetectable SARS-CoV-2 RNAaemia at the time of analysis died at day 27.

Conclusion

SARS-CoV-2 RNAaemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients

Cancer associates with risk and severe events of COVID-19: A systematic review and meta-analysis

Evidence is mounting to indicate that cancer patients may have more likelihood of having coronavirus disease 2019 (COVID-19) but lack consistency. A robust estimate is urgently needed to convey appropriate information to the society and the public, in the time of ongoing COVID-19 pandemic. We performed a systematic review and meta-analysis through a comprehensive literature search in major databases in English and Chinese, and two investigators conducted publication selection and data extraction independently. A meta-analysis was used to obtain estimates of pooled prevalence of cancer in patients with COVID-19 and determine the association of cancer with severe events, after assessment of potential heterogeneity, publication bias, and correction for the estimates when necessary. Total 38 studies comprising 7094 patients with COVID-9 were included; the pooled prevalence of cancer was estimated at 2.3% (95% confidence limit [CL] [0.018, 0.029]; P < .001) overall and 3.2% (95% CL [0.023, 0.041]; P < .001) in Hubei province; the corresponding estimates were 1.4% and 1.9% after correction for publication bias; cancer was significantly associated with the events of severe cases (odds ratio [OR] = 2.20, 95% CL [1.53, 3.17]; P < .001) and death (OR = 2.97, 95% CL [1.48, 5.96]; P = .002) in patients with COVID-19, there was no significant heterogeneity and a minimal publication bias. We conclude that cancer comorbidity is associated with the risk and severe events of COVID-19; special measures should be taken for individuals with cancer.

Protease Inhibitor Use in COVID-19

The outbreak of a large plaque, novel coronavirus pneumonia (NCP), which also named Coronavirus Disease 2019 (COVID-19) by the WHO, has detrimentally affected the livelihood and health of people in China. During the spread of COVID-19, colleagues who have been working at the frontline have had to face many new challenges in the treatment and prevention of NCP. Therefore, we have provided suggestions for the diagnosis, treatment, and prevention of the novel coronavirus pneumonia in the current epidemic situation based on the latest reports and the experience of doctors treating COVID-19 in our hospital. We recommend lopinavir/ritonavir as the effective drugs for antiviral treatment according to our experience in administering lopinavir/ritonavir to COVID-19 patients and the successful cases of these drugs in treating MERS and SARS, but need more clinical data to prove their efficacy in treating COVID-19.

Current and Perspective Diagnostic Techniques for COVID-19

Since late December 2019, the coronavirus pandemic (COVID-19; previously known as 2019-nCoV) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world. With more than 1,700,000 confirmed cases, the world faces an unprecedented economic, social, and health impact. The early, rapid, sensitive, and accurate diagnosis of viral infection provides rapid responses for public health surveillance, prevention, and control of contagious diffusion. More than 30% of the confirmed cases are asymptomatic, and the high false-negative rate (FNR) of a single assay requires the development of novel diagnostic techniques, combinative approaches, sampling from different locations, and consecutive detection. The recurrence of discharged patients indicates the need for long-term monitoring and tracking. Diagnostic and therapeutic methods are evolving with a deeper understanding of virus pathology and the potential for relapse. In this Review, a comprehensive summary and comparison of different SARS-CoV-2 diagnostic methods are provided for researchers and clinicians to develop appropriate strategies for the timely and effective detection of SARS-CoV-2. The survey of current biosensors and diagnostic devices for viral nucleic acids, proteins, and particles and chest tomography will provide insight into the development of novel perspective techniques for the diagnosis of COVID-19.

Molecular and Serological Assays for SARS-CoV-2: Insights from Genome and Clinical Characteristics

Background

The ongoing outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a challenge for worldwide public health. A reliable laboratory assay is essential both to confirm suspected patients and to exclude patients infected with other respiratory viruses, thereby facilitating the control of global outbreak scenarios.

Content

In this review, we focus on the genomic, transmission and clinical characteristics of SARS-CoV-2, and comprehensively summarize the principles and related details of assays for SARS-CoV-2. We also explore the quality assurance measures for these assays.

Summary

SARS-CoV-2 has some unique gene sequences and specific transmission and clinical features that can inform the conduct of molecular and serological assays in many aspects, including the design of primers, the selection of specimens and testing strategies at different disease stages. Appropriate quality assurance measures for molecular and serological assays are needed to maintain testing proficiency. Because serological assays have the potential to identify later stages of the infection and to confirm highly suspected cases with negative molecular assay results, a combination of these two assays is needed to achieve a reliable capacity to detect SARS-CoV-2.

COVID-19 Therapeutic Options Under Investigation

Since its emergence in China in December 2019, COVID-19 has quickly spread around the globe causing a pandemic. Vaccination or the development of herd immunity seems the only way to slow down the spread of the virus; however, both are not achievable in the near future. Therefore, effective treatments to mitigate the burden of this pandemic and reduce mortality rates are urgently needed. Preclinical and clinical studies of potential antiviral and immunomodulatory compounds and molecules to identify safe and efficacious therapeutics for COVID-19 are ongoing. Two compounds, remdesivir, and dexamethasone have been so far shown to reduce COVID-19-associated death. Here, we provide a review of the potential therapeutic agents being considered for the treatment and management of COVID-19 patients.

Interest of the thoracic scanner in the diagnosis of COVID-19: study of 35 cases in the Republic of Guinea

Introduction

the aim of this work is to evaluate the contribution of thoracic computed tomography (CT) in the diagnosis of COVID-19 in Guinea.

Methods

this was a retrospective study with data recorded over a 2 Month period. Records of patients who tested positive on chest CT without contrast injection on admission were included in this study. Not included are those who did or did not perform a chest CT scan after confirmation of the diagnosis by RT-PCR. The data were collected under the direction of the National Health Security Agency (ANSS) and analysed using STATA/SE version 11.2 software.

Results

all patients tested performed a chest CT scan without contrast injection while awaiting the RT-PCR test result. Eighty percent (80%) of patients had lesions characteristic of COVID-19 viral pneumonia on chest CT. The reverse transcriptase PCR (RT-PCR) test was later positive in 33 patients (94.28%) and negative in 2 (5.71%).

Conclusion

it is noted from this study that chest computed tomography is a critical tool in the rapid diagnosis of COVID-19 infection. Its systematization in all patients suspected in our dispute, would facilitate diagnosis while waiting for confirmation by RT-PCR and would limit the loss of cases.

Effects of Internet Hospital Consultations on Psychological Burdens and Disease Knowledge During the Early Outbreak of COVID-19 in China: Cross-Sectional Survey Study

Background

Coronavirus disease (COVID-19) has become a global threat to human health. Internet hospitals have emerged as a critical technology to bring epidemic-related web-based services and medical support to the public. However, only a few very recent scientific literature reports have explored the effects of internet hospitals on psychological burden and disease knowledge in major public health emergencies such as the COVID-19 pandemic.

Objective

The aim of this study was to explore the role of internet hospitals in relieving psychological burden and increasing disease knowledge during the early outbreak of the COVID-19 pandemic.

Methods

This survey was conducted from January 26 to February 1, 2020, during the early outbreak of COVID-19 in China. The platform used for the consultation was the WeChat public account of our hospital. To participate in the study, the patient was required to answer a list of questions to exclude the possibility of COVID-19 infection and confirm their willingness to participate voluntarily. Next, the participant was directed to complete the self-report questionnaire. After the internet consultation, the participant was directed to complete the self-report questionnaire again. The questionnaire included sections on general information, the General Health Questionnaire-28 (GHQ-28), and the participant’s worries, disease knowledge, and need for hospital treatment.

Results

The total number of internet consultations was 4120. The consultation topics mainly included respiratory symptoms such as cough, expectoration, and fever (2489/4120, 60.4%) and disease knowledge, anxiety, and fear (1023/4120, 24.8%). A total of 1530 people filled out the questionnaires before and after the internet consultation. Of these people, 1398/1530 (91.4%) experienced psychological stress before the internet consultation, which significantly decreased after consultation (260/1530, 17.0%) (χ²₁=1704.8, P<.001). There was no significant difference in the number of people who expressed concern about the COVID-19 pandemic before and after the internet consultation (χ²₁=0.7, P=.43). However, the degree of concern after the internet consultation was significantly alleviated (t₂₆₉₉=90.638, P<.001). The main worries before and after consultation were the dangers posed by the disease and the risk of infection of family members. The scores of the self-assessment risk after the internet consultation were significantly lower than those before consultation (t₃₀₅₈=95.694, P<.001). After the consultation, the participants’ knowledge of the symptoms, transmission routes, and preventive measures of COVID-19 was significantly higher than before the consultation (t₃₀₅₈=–106.105, –80.456, and –152.605, respectively; all P<.001). The hospital treatment need score after the internet consultation decreased from 3.3 (SD 1.2) to 1.6 (SD 0.8), and the difference was statistically significant (t₃₀₅₈=45.765, P<.001).

Conclusions

During the early outbreak of COVID-19, internet hospitals could help relieve psychological burdens and increase disease awareness through timely and rapid spread of knowledge regarding COVID-19 prevention and control. Internet hospitals should be an important aspect of a new medical model in public health emergency systems.

Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2

Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of the novel coronavirus SARS-CoV-2. Herein, we identified two potent inhibitors of human DHODH, S312 and S416, with favorable drug-likeness and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus, Zika virus, Ebola virus, and particularly against SARS-CoV-2. Notably, S416 is reported to be the most potent inhibitor so far with an EC₅₀ of 17 nmol/L and an SI value of 10,505.88 in infected cells. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knock-out cells. This work demonstrates that both S312/S416 and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-regulation may have clinical potentials to cure SARS-CoV-2 or other RNA viruses circulating worldwide, no matter such viruses are mutated or not.

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.

Multiplex detection and dynamics of IgG antibodies to SARS-CoV2 and the highly pathogenic human coronaviruses SARS-CoV and MERS-CoV

BACKGROUND

Knowledge of the COVID-19 epidemic extent and the level of herd immunity is urgently needed to help manage this pandemic.

METHODS

We used a panel of 167 samples (77 pre-epidemic and 90 COVID-19 seroconverters) and SARS-CoV1, SARS-CoV2 and MERS-CoV Spike and/or Nucleopcapsid (NC) proteins to develop a high throughput multiplex screening assay to detect IgG antibodies in human plasma. Assay performances were determined by ROC curves analysis. A subset of the COVID-19+ samples (n = 36) were also tested by a commercial NC-based ELISA test and the results compared with those of the novel assay.

RESULTS

On samples collected ≥14 days after symptoms onset, the accuracy of the assay is 100 % (95 % CI: 100-100) for the Spike antigen and 99.9 % (95 % CI:99.7-100) for NC. By logistic regression, we estimated that 50 % of the patients have seroconverted at 5.7 ± 1.6; 5.7 ± 1.8 and 7.9 ± 1.0 days after symptoms onset against Spike, NC or both antigens, respectively and all have seroconverted two weeks after symptoms onset. IgG titration in a subset of samples showed that early phase samples present lower IgG titers than those from later phase. IgG to SARS-CoV2 NC cross-reacted at 100 % with SARS-CoV1 NC. Twenty-nine of the 36 (80.5 %) samples tested were positive by the commercial ELISA while 31/36 (86.1 %) were positive by the novel assay.

CONCLUSIONS

Our assay is highly sensitive and specific for the detection of IgG antibodies to SARS-CoV2 proteins, suitable for high throughput epidemiological surveys. The novel assay is more sensitive than a commercial ELISA.

COVID-19 diagnostic testing: Technology perspective

The corona virus disease 2019 (COVID-19) is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 18 million people were infected with a total of 0.7 million deaths in ∼188 countries. Controlling the spread of SARS-CoV-2 is therefore inherently dependent on identifying and isolating infected individuals, especially since COVID-19 can result in little to no symptoms. Here, we provide a comprehensive review of the different primary technologies used to test for COVID-19 infection, discuss the advantages and disadvantages of each technology, and highlight the studies that have employed them. We also describe technologies that have the potential to accelerate SARS-CoV-2 detection in the future, including digital PCR, CRISPR, and microarray. Finally, remaining challenges in COVID-19 diagnostic testing are discussed, including (a) the lack of universal standards for diagnostic testing; (b) the identification of appropriate sample collection site(s); (c) the difficulty in performing large population screening; and (d) the limited understanding of SARS-COV-2 viral invasion, replication, and transmission.

Where are we with understanding of COVID-19?

Coronavirus disease 2019 caused by SARS-CoV-2 originated from China and spread across every corner of the world. The scientific interest on COVID-19 increased after WHO declared it a pandemic in the early February of 2020. In fact, this pandemic has had a worldwide impact on economy, health, and lifestyle like no other in the last 100 years. SARS-CoV-2 belongs to Coronaviridae family and causes the deadliest clinical manifestations when compared to other viruses in the family. COVID-19 is an emerging zoonotic disease that has resulted in over 383,000 deaths around the world. Scientists are scrambling for ideas to develop treatment and prevention strategies to thwart the disease condition. In this review, we have attempted to summarize the latest information on the virus, disease, prevention, and treatment strategies. The future looks promising.

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

The new coronavirus SARS-CoV-2, the cause of COVID-19, has become a public health emergency of global concern. Like the SARS and influenza pandemics, there have been a large number of cases coinfected with other viruses, fungi, and bacteria, some of which originate from the oral cavity. Capnocytophaga, Veillonella, and other oral opportunistic pathogens were found in the BALF of the COVID-19 patients by mNGS. Risk factors such as poor oral hygiene, cough, increased inhalation under normal or abnormal conditions, and mechanical ventilation provide a pathway for oral microorganisms to enter the lower respiratory tract and thus cause respiratory disease. Lung hypoxia, typical symptoms of COVID-19, would favor the growth of anaerobes and facultative anaerobes originating from the oral microbiota. SARS-CoV-2 may aggravate lung disease by interacting with the lung or oral microbiota via mechanisms involving changes in cytokines, T cell responses, and the effects of host conditions such as aging and the oral microbiome changes due to systemic diseases. Because the oral microbiome is closely associated with SARS-CoV-2 co-infections in the lungs, effective oral health care measures are necessary to reduce these infections, especially in severe COVID-19 patients. We hope this review will draw attention from both the scientific and clinical communities on the role of the oral microbiome in the current global pandemic.

Is There an Association Between COVID-19 Mortality and the Renin-Angiotensin System? A Call for Epidemiologic Investigations

Mortality from coronavirus disease 2019 (COVID-19) is strongly associated with cardiovascular disease, diabetes, and hypertension. These disorders share underlying pathophysiology related to the renin-angiotensin system (RAS) that may be clinically insightful. In particular, activity of the angiotensin-converting enzyme 2 (ACE2) is dysregulated in cardiovascular disease, and this enzyme is used by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to initiate the infection. Cardiovascular disease and pharmacologic RAS inhibition both increase ACE2 levels, which may increase the virulence of SARS-CoV-2 within the lung and heart. Conversely, mechanistic evidence from related coronaviruses suggests that SARS-CoV-2 infection may downregulate ACE2, leading to toxic overaccumulation of angiotensin II that induces acute respiratory distress syndrome and fulminant myocarditis. RAS inhibition could mitigate this effect. With conflicting mechanistic evidence, we propose key clinical research priorities necessary to clarify the role of RAS inhibition in COVID-19 mortality that could be rapidly addressed by the international research community.

Clinical Characteristics of Imported Cases of Coronavirus Disease 2019 (COVID-19) in Jiangsu Province: A Multicenter Descriptive Study

BACKGROUND

We aimed to report the clinical characteristics of imported cases of coronavirus disease 2019 (COVID-19) in Jiangsu Province.

METHODS

We retrospectively investigated the clinical, imaging, and laboratory characteristics of confirmed cases of COVID-19 with World Health Organization interim guidance in 3 grade IIIA hospitals of Jiangsu from 22 January to 14 February 2020. Real-time RT-PCR was used to detect the new coronavirus in respiratory samples.

RESULTS

Of the 80 patients infected with COVID-19, 41 were female, with a median age of 46.1 years. Except for 3 severe patients, the rest of the 77 patients exhibited mild or moderate symptoms. Nine patients were unconfirmed until a third nucleic acid test; 38 cases had a history of chronic diseases. The main clinical manifestations of the patients were fever and cough, which accounted for 63 (78.75%) and 51 (63.75%) cases, respectively. Only 3 patients (3.75%) showed liver dysfunction. Imaging examination showed that 55 patients (68.75%) showed abnormal density shadow and 25 cases (31.25%) had no abnormal density shadow in the parenchyma of both lungs. Currently, 21 cases have been discharged from the hospital, and no patient died. The average length of stay for discharged patients was 8 days.

CONCLUSIONS

Compared with the cases in Wuhan, the cases in Jiangsu exhibited mild or moderate symptoms and no obvious gender susceptibility. The proportion of patients having liver dysfunction and abnormal CT imaging was relatively lower than that in Wuhan. Notably, infected patients may be falsely excluded based on 2 consecutively negative respiratory pathogenic nucleic acid test results.

A systematic review and meta-analysis of the efficacy and safety of arbidol in the treatment of coronavirus disease 2019

BACKGROUND

Coronavirus disease 2019 (COVID-19) is highly contagious, and the epidemic has spread to hundreds of countries around the world, and seriously threatens the life safety of people around the world. Arbidol is an antiviral drug with high potential against COVID-19, but evidence of effectiveness and safety is lacking. The systematic review protocol aims to formulate a research plan that can evaluate the efficacy and safety of arbidol for COVID-19.

METHODS

The retrieval time will be from the database establishment to June 2020. The retrieval database will include the Cochrane Library, PubMed, Embase, OVID, CNKI, Wanfang, VIP, CBM, etc. The primary outcome will be clinical efficacy, and the secondary results will be accompanying symptoms, time for the temperature to return to normal, time of novel coronavirus nucleic acid turning negative, blood sample test, Computed Tomography examination, length of hospitalization, adverse reactions, and adverse events. RevManV.5.3 software will be used for meta-analysis, and fixed effects model, random-effects model, subgroup analysis, and descriptive analysis will be adopted according to the heterogeneity of the research results.

RESULTS

To provide the latest evidence of clinical efficacy and safety of arbidol in the treatment of COVID-19.

CONCLUSION

Our study will provide the latest evidence analysis of the efficacy and safety of arbidol for COVID-19, to provide evidence-based medicine for the prevention and control of this epidemic.

REGISTRATION DETAILS

PROSPERO CRD42020189203.

SARS-CoV, MERS-CoV, SARS-CoV-2 Comparison of Three Emerging Coronaviruses

: In December 2019, in Wuhan, China began the outbreak of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemic. As a result of rapid spread, it turned into a pandemic announced by WHO on March 11, 2020. SARS-CoV-2 is an etiological factor of a new disease called COVID-19. The virus is transmitted mainly through the droplet route. In most cases, it causes mild symptoms such as fever, dry cough, weakness, and muscle pain; less common symptoms include sore throat, runny nose, diarrhea, and chills. However, among people with impaired immunity and comorbidities, as well as among older people, it leads to life-threatening complications in the form of acute respiratory distress syndrome (ARDS), sepsis, and septic shock. Moreover, SARS-CoV-2 is the third highly pathogenic in humans and easily spreading coronavirus after the virus of a severe acute respiratory syndrome (SARS) in 2002 - 2003 and virus of the Middle East respiratory syndrome (MERS) in 2012. This review summarizes current information on the emergence, origin, diversity, and common characteristics, as well as the epidemiology of the above three highly contagious coronaviruses.

Reverse-Transcription Recombinase-Aided Amplification Assay for Rapid Detection of the 2019 Novel Coronavirus (SARS-CoV-2)

A novel coronavirus (SARS-CoV-2) was recently identified in patients with acute respiratory disease and spread quickly worldwide. A specific and rapid diagnostic method is important for early identification. The reverse-transcription recombinase-aided amplification (RT-RAA) assay is a rapid detection method for several pathogens. Assays were performed within 5-15 min as a one-step single tube reaction at 39 °C. In this study, we established two RT-RAA assays for the S and orf1ab gene of SARS-CoV-2 using clinical specimens for validation. The analytical sensitivity of the RT-RAA assay was 10 copies for the S and one copy for the orf1ab gene per reaction. Cross-reactions were not observed with any of the other respiratory pathogens. A 100% agreement between the RT-RAA and real-time PCR assays was accomplished after testing 120 respiratory specimens. These results demonstrate that the proposed RT-RAA assay will be beneficial as it is a faster, more sensitive, and more specific tool for the detection of SARS-CoV-2.

Current strategies against COVID-19

Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently was declared a pandemic by world health organization (WHO) Due to sudden outbreaks, currently, no completely effective vaccine or drug is clinically approved. Several therapeutic strategies can be envisaged to prevent further mortality and morbidity. Based on the past contribution of traditional Chinese medicines (TCM) and immune-based therapies as a treatment option in crucial pathogen outbreaks, we aimed to summarize potential therapeutic strategies that could be helpful to stop further spread of SARS-CoV-2 by effecting its structural components or modulation of immune responses. Several TCM with or without modification could be effective against the structural protein, enzymes, and nucleic acid should be tested from available libraries or to identify their immune-stimulatory activities to enhance several antiviral biological agents for effective elimination of SARS-CoV-2 from the host. TCM is not only effective in the direct inhibition of virus attachment and internalization in a cell but can also prevent their replication and can also help to boost up host immune response. Immune-modulatory effects of TCMs may lead to new medications and can guide us for the scientific validity of drug development. Besides, we also summarized the effective therapies in clinical for controlling inflammation. This review will be not only helpful for the current situation of COVID-19, but can also play a major role in such epidemics in the future.

Debatable points of using angiotensin-converting enzyme inhibitors and angiotensin receptor antagonists in patients with COVID-19

The COVID-19 pandemic is a serious threat to global health. The infection mechanism is the binding of SARS-CoV-2 to angiotensin-converting enzyme 2 (ACE2) and internalization of the complex by the host cell. ACE inhibitors/angiotensin receptor antagonists (ARA) are known to increase ACE2 expression and are recommended for the treatment of many cardiovascular diseases (CVD). Thus, it has been suggested that treatment with renin-angiotensin-aldosterone system blockers (RAAS) increases the viral load and the risk of severe acute respiratory distress syndrome. However, ACE2 also converts angiotensin II into substances with cardioprotective effects. In addition, there is no evidence that RAAS inhibitors increase the severity of COVID-19 infection, while the risks of withdrawal of ACE inhibitors/ARA in patients with CVD are proven. There is also no evidence to support the idea that the administration of ACE inhibitors/ARA promotes the coronavirus’s penetration by increasing the ACE2 expression. According to the guidelines of the Russian Society of Cardiology and the consensus statements of international cardiology societies, it is necessary to continue taking RAAS inhibitors in high-risk patients with COVID-19. This review provides an analysis of foreign articles revealing the pathophysiological pathways and recommendations for using ACE inhibitors/ARA in patients with CVD and COVID-19 infection.

Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report

Background

Urinary tract infection (UTI) caused by various pathogenic microorganisms is ubiquitous in the parts of the urinary system such as kidney, ureter, bladder, and urethra. Currently, clinical detection of UTI is mainly focused on urine culture; however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate, especially in patients who have used antibiotics. Generally, treatment for UTI relies on empirical medication rather than pathogen diagnosis, which leads to the inappropriate use of antimicrobial agents and a significant increase in resistant strains. Comparatively, metagenomic next-generation sequencing (mNGS) is capable of overcoming the disadvantages of clinical culture, and identifying pathogens for further treatment.

Case presentation

A 33-year-old male patient was admitted to hospital with a high fever and chills. None of his autoimmune disease or thyroid function related indicators were positive, and he had no risk of endocarditis. His white blood cell count, C-reactive protein, procalcitonin, interleukin 6, and neutrophil proportion were markedly elevated. He was initially diagnosed as having an infection of unknown etiology. Since empirical treatment of Sulperazon and Metronidazole did not relieve his symptoms, both the blood and urine specimens were examined using traditional culture, serological testing, and mNGS assay. Traditional culture and serological testing produced negative results, while the mNGS assay revealed the presence of a potential pathogen, Enterococcus faecalis, in the urine specimen, which was further confirmed by both Sanger sequencing and qPCR analysis. A CT scan of the patient’s whole abdomen showed stones in the right kidney. Once targeted antibiotic therapy was administered, the patient recovered quickly.

Conclusions

Our case illustrated that mNGS, as a novel culture-independent approach, demonstrated the capability of rapid, sensitive, and accurate pathogen identification. Furthermore, this technology provides strong support for guiding clinicians to determine appropriate treatment.

Mechanism of inflammatory response in associated comorbidities in COVID-19

BACKGROUND AND AIMS

The outbreak of the new coronavirus, SARS-CoV-2, causes a respiratory disease and individuals with pre-existing cardiometabolic disorders display worse prognosis through the infection course. The aim of this minireview is to present epidemiological data related to metabolic comorbidities in association with the SARS-CoV-2.

METHODS

This is a narrative mini-review with Pubmed search until April 23, 2020 using the keywords COVID-19, SARS-CoV-2, treatment of coronavirus and following terms: diabetes mellitus, obesity, arterial hypertension, ACE-inhibitors, cytokine storm, immune response and vitamin D.

RESULTS

Studies indicate that obese individuals are more likely to develop infections, and that adipose tissue serves as a pathogen reservoir. In diabetic individuals higher rate of inflammatory processes is seen due to constant glucose recognition by C type lectin receptors. Hypertensive individuals, usually grouped with other conditions, are treated with drugs to reduce blood pressure mostly through ACEi and ARB, that leads to increased ACE2 expression, used by SARS-CoV-2 for human's cell entry. Until now, the studies have shown that individuals with those conditions and affected by COVID-19 present an uncontrolled release of pro-inflammatory cytokines and an unbalanced immune response, leading to the cytokine storm phenomenon. Vitamin D is highlighted as a potential therapeutic target, because in addition to acting on the immune system, it plays an important role in the control of cardiometabolic diseases.

CONCLUSION

Currently, since there is no proven and effective antiviral therapy for SARS-CoV-2, the efforts should focus on controlling inflammatory response and reduce the risks of associated complications.

Serological immunochromatographic approach in diagnosis with SARS-CoV-2 infected COVID-19 patients

An outbreak of new coronavirus SARS-CoV-2 was occurred in Wuhan, China and rapidly spread to other cities and nations. The standard diagnostic approach that widely adopted in the clinic is nucleic acid detection by real-time RT-PCR. However, the false-negative rate of the technique is unneglectable and serological methods are urgently warranted. Here, we presented the colloidal gold-based immunochromatographic (ICG) strip targeting viral IgM or IgG antibody and compared it with real-time RT-PCR. The sensitivity of ICG assay with IgM and IgG combinatorial detection in nucleic acid confirmed cases were 11.1%, 92.9% and 96.8% at the early stage (1-7 days after onset), intermediate stage (8-14 days after onset), and late stage (more than 15 days), respectively. The ICG detection capacity in nucleic acid-negative suspected cases was 43.6%. In addition, the concordance of whole blood samples and plasma showed Cohen's kappa value of 0.93, which represented the almost perfect agreement between two types of samples. In conclusion, serological ICG strip assay in detecting SARS-CoV-2 infection is both sensitive and consistent, which is considered as an excellent supplementary approach in clinical application.

Sensitivity in Detection of Antibodies to Nucleocapsid and Spike Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 in Patients With Coronavirus Disease 2019

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), is associated with respiratory-related disease and death. Assays to detect virus-specific antibodies are important to understand the prevalence of infection and the course of the immune response.

METHODS

Quantitative measurements of plasma or serum antibodies to the nucleocapsid and spike proteins were analyzed using luciferase immunoprecipitation system assays in 100 cross-sectional or longitudinal samples from patients with SARS-CoV-2 infection. A subset of samples was tested both with and without heat inactivation.

RESULTS

At >14 days after symptom onset, antibodies against SARS-CoV-2 nucleocapsid protein showed 100% sensitivity and 100% specificity, whereas antibodies to spike protein were detected with 91% sensitivity and 100% specificity. Neither antibody levels nor the rate of seropositivity were significantly reduced by heat inactivation of samples. Analysis of daily samples from 6 patients with COVID-19 showed anti-nucleocapsid and spike protein antibodies appearing between days 8 and 14 after initial symptoms. Immunocompromised patients generally had a delayed antibody response to SARS-CoV-2, compared with immunocompetent patients.

CONCLUSIONS

Antibody to the nucleocapsid protein of SARS-CoV-2 is more sensitive than spike protein antibody for detecting early infection. Analyzing heat-inactivated samples with a luciferase immunoprecipitation system assay is a safe and sensitive method for detecting SARS-CoV-2 antibodies.

A simple method for detection of a novel coronavirus (SARS-CoV-2) using one-step RT-PCR followed by restriction fragment length polymorphism

A novel coronavirus associated with acute respiratory disease (named SARS-CoV-2) is recently identified in Wuhan city, China, spread rapidly worldwide. Early identification of this novel coronavirus by molecular tools is critical for surveillance and control of the epidemic outbreak. We aimed to establish a simple method for the detection of SARS-CoV-2 in differentiating with SARS-CoV. Primers of our in-house reverse transcription polymerase chain reaction (RT-PCR) assays were designed to target conserved regions of the RdRP gene and E gene, selected restriction enzymes EcoRI, Tsp45I, and AluI to distinguish between SARS-CoV-2 and SARS-CoV. In this report, a 396-bp fragment of the RdRp gene and 345-bp fragment of the E gene were amplified by one-step RT-PCR. Enzyme Tsp45I cuts the RdRP-amplified product of SARS-CoV-2 generating three fragments of 45, 154, and 197 bp, but it did not cut the amplicon of SARS-CoV. In contrast, the amplified product of SARS-CoV was digested with EcoRI producing two fragments of 76 and 320 bp, whereas the amplicon of SARS-CoV-2 was undigested by Tsp45I help to distinguish clearly SARS-CoV-2 from SARS-CoV on gel electrophoresis. In addition, AluI cut the amplicon of the E gene of SARS-CoV-2 generating two fragments of 248 and 97 bp without cutting to SARS-CoV. The accuracy of the assay was confirmed by sequencing and phylogenetic analysis. When evaluated on clinical samples showed a high sensitivity of 95%, specificity of our assay was 100% and clinical performance for detection of SARS-CoV-2 in comparison with other reference assays. In conclusion, in the present study, we successfully developed a simple method for molecular detection of SARS-CoV-2 in differentiating with SARS-CoV.

The value of urine biochemical parameters in the prediction of the severity of coronavirus disease 2019

Background Among patients with coronavirus disease 2019 (COVID-19), the cases of a significant proportion of patients are severe. A viral nucleic acid test is used for the diagnosis of COVID-19, and some hematological indicators have been used in the auxiliary diagnosis and identification of the severity of COVID-19. Regarding body fluid samples, except for being used for nucleic acid testing, the relationship between COVID-19 and routine body fluid parameters is not known. Our aim was to investigate the value of urine biochemical parameters in the prediction of the severity of COVID-19. Methods A total of 119 patients with COVID-19 were enrolled at Renmin Hospital of Wuhan University. According to the severity of COVID-19, the patients were divided into three groups (moderate 67, severe 42 and critical 10), and 45 healthy persons were enrolled in the same period as healthy controls. The relationship between the results of urine biochemical parameters and the severity of COVID-19 was analyzed. Results The positive rates of urine occult blood (BLOOD) and proteinuria (PRO) were higher in COVID-19 patients than in healthy controls (p < 0.05); the urine specific gravity (SG) value was lower in patients than in healthy controls (p < 0.05), and the urine potential of hydrogen (pH) value was higher in patients than in healthy controls (p < 0.01). The positive rates of urine glucose (GLU-U) and PRO in the severe and critical groups were higher than those in the moderate group (p < 0.01 and p < 0.05, respectively); other biochemical parameters of urine were not associated with the severity of COVID-19. Conclusions Some urine biochemical parameters are different between patients with severe acute respiratory syndrome (SARS)-CoV-2 and healthy controls, and GLU-U and PRO may be helpful for the differentiation of COVID-19 severity.

A COVID-19 case report from asymptomatic contact: implication for contact isolation and incubation management

Background

As of 2 March, 2020, at least 80 151 coronavirus disease 2019 (COVID-19) cases were reported in China. Most of the patients had a history of visiting Hubei Province or contacting with people who had ever stayed in or passed by Hubei Province or were exposed to symptoms. Some patients got infected through only asymptomatic contact. This study aimed to report the epidemic features and lab identification of a patient confirmed with COVID-19 infection through only asymptomatic contact.

Case presentation

A 44-year-old man, who lived in Nanchang, Jiangxi Province, China until 6 March 2020, suffered from cough on 27 January 2020. Fever symptoms appeared on 28 January, with a maximum temperature of 38.8 °C, accompanied by cough, sore throat, headache, fatigue, muscle ache, joint ache, and other symptoms. The symptoms continued until he was hospitalized on 30 January. Coronavirus conventional polymerase chain reaction assay was positive for the throat swab sample. The patient, along with his wife and son, drove from Nanchang to back to Honghu City, Hubei Province, on 23 January 2020. After staying with his parents and brother’s family for 3 days, the patient drove back to Nanchang and arrived on 25 January. On the way back home, they stopped by Tongshan service area, Hubei Province, without any close contact with other people. After arriving home in Nanchang City, Jiangxi Province, none of them left their residence. In addition, his parents stayed at home for 20 days with his younger brother’s family before they got back. His younger brother and one of his brother’s children visited Wuhan on 5 January and came home on 6 January 2020.

Conclusions

This report suggested that, in the early phase of COVID-19 pneumonia, routine screening could miss patients who were virus carriers. Highlighting travel history is of paramount importance for the early detection and isolation of severe acute respiratory syndrome coronavirus 2 cases.

High-coverage SARS-CoV-2 genome sequences acquired by target capture sequencing

In this study, we designed a set of SARS‐CoV‐2 enrichment probes to increase the capacity for sequence‐based virus detection and obtain the comprehensive genome sequence at the same time. This universal SARS‐CoV‐2 enrichment probe set contains 502 120 nt single‐stranded DNA biotin‐labeled probes designed based on all available SARS‐CoV‐2 viral sequences and it can be used to enrich for SARS‐CoV‐2 sequences without prior knowledge of type or subtype. Following the CDC health and safety guidelines, marked enrichment was demonstrated in a virus strain sample from cell culture, three nasopharyngeal swab samples (cycle threshold [C_t] values: 32.36, 36.72, and 38.44) from patients diagnosed with COVID‐19 (positive control) and four throat swab samples from patients without COVID‐19 (negative controls), respectively. Moreover, based on these high‐quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication and its phylogenetic relationship with other selected high‐quality samples from the Genome Variation Map. Therefore, this universal SARS‐CoV‐2 enrichment probe system can capture and enrich SARS‐CoV‐2 viral sequences selectively and effectively in different samples, especially clinical swab samples with a relatively low concentration of viral particles.

Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID-19

Objectives: Development and validation of a single-step and accurate reverse transcriptase loop-mediated isothermal amplification technique (RT-LAMP) for rapid identification of SARS-CoV-2 relative to commercial quantitative reverse transcriptase real-time PCR (qRT-PCR) assays to allow prompt initiation of proper medical care and containment of virus spread.

Methods: Primers showing optimal in-silico features were subjected to analytical sensitivity and specificity to assess the limit of detection (LOD) and cross-reaction with closely- and distantly-related viral species, and clinically prominent bacterial and fungal species. In order to evaluate the clinical utility, our RT-LAMP was subjected to a large number of clinical samples, including 213 negative and 47 positive patients, relative to two commercial quantitative RT-PCR assays.

Results: The analytical specificity and sensitivity of our assay was 100% and 500 copies/ml when serial dilution was performed in both water and sputum. Subjecting our RT-LAMP assay to clinical samples showed a high degree of specificity (99.5%), sensitivity (91.4%), positive predictive value (97.7%), and negative predictive value (98.1%) when used relative to qRT-PCR. Our RT-LAMP assay was two times faster than qRT-PCR and is storable at room temperature. A suspected case that later became positive tested positive using both our RT-LAMP and the two qRT-PCR assays, which shows the capability of our assay for screening purposes.

Conclusions: We present a rapid RT-LAMP assay that could extend the capacity of laboratories to process two times more clinical samples relative to qRT-PCR and potentially could be used for high-throughput screening purposes when demand is increasing at critical situations.

ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens

Quantitative real time PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load specimens and the limitations of RT-PCR, significant numbers of false negative reports are inevitable, which results in failure to timely diagnose, cut off transmission, and assess discharge criteria. To improve this situation, an optimized droplet digital PCR (ddPCR) was used for detection of SARS-CoV-2, which showed that the limit of detection of ddPCR is significantly lower than that of RT-PCR. We further explored the feasibility of ddPCR to detect SARS-CoV-2 RNA from 77 patients, and compared with RT-PCR in terms of the diagnostic accuracy based on the results of follow-up survey. 26 patients of COVID-19 with negative RT-PCR reports were reported as positive by ddPCR. The sensitivity, specificity, PPV, NPV, negative likelihood ratio (NLR) and accuracy were improved from 40% (95% CI: 27–55%), 100% (95% CI: 54–100%), 100%, 16% (95% CI: 13–19%), 0.6 (95% CI: 0.48–0.75) and 47% (95% CI: 33–60%) for RT-PCR to 94% (95% CI: 83–99%), 100% (95% CI: 48–100%), 100%, 63% (95% CI: 36–83%), 0.06 (95% CI: 0.02–0.18), and 95% (95% CI: 84–99%) for ddPCR, respectively. Moreover, 6/14 (42.9%) convalescents were detected as positive by ddPCR at 5–12 days post discharge. Overall, ddPCR shows superiority for clinical diagnosis of SARS-CoV-2 to reduce the false negative reports, which could be a powerful complement to the RT-PCR.

COVID-19: molecular diagnostics overview

The last day of 2019 delivered the first report to the World Health Organization (WHO) about a group of cases of pneumonia of unknown etiology in Wuhan, China. Subsequent investigations identified the new comer, a novel coronavirus related to severe acute respiratory syndrome coronavirus (SARS-CoV) and thus was termed as SARS-CoV-2. Being very contagious, the new virus led the era of “COVID-19” which is the acronym of “coronavirus disease 2019,” evoking an imminent threat to global health security with unprecedented devastating challenges to human kind. In this article, we provide a molecular overview on the SARS-CoV-2 virus and summarize tremendous efforts that have been made to develop a rapid confirmatory diagnostic test for COVID-19. The diagnostic performances of the available tests are analyzed based on the best current information from the early research.

Clinical Perspective on 2019 Novel Coronavirus Pneumonia: A Systematic Review of Published Case Reports

The ongoing pandemic of 2019 novel coronavirus (2019-nCoV), which originated from Wuhan, China, has led to 68,279 deaths due to 2019-nCoV pneumonia as of May 5, 2020. We conducted a systematic review and included 16 case reports to summarize the transmission and pathology of 2019-nCoV, and clinical presentation, laboratory and imaging findings, and treatment in 2019-nCoV pneumonia. The disease is mild in most people; in some, it may progress to severe pneumonia with acute respiratory distress syndrome (ARDS). Patients with mild illness usually recover at home, with supportive care and isolation in accordance with guidelines. Patients who have moderate to severe pneumonia are usually monitored in the hospital. Although there is no definitive treatment for 2019-nCoV pneumonia so far, some antiviral drugs have shown promising results. The use of lopinavir/ritonavir and remdesivir was associated with significant clinical improvement in severe pneumonia. Nonetheless, we need more randomized clinical trials (RCTs) and treatment guidelines for developing effective management of the 2019-nCoV and improve patient outcomes by reducing mortality in high-risk patients. We also need more clinical trials and management guidelines for the effective management of 2019-nCoV pneumonia.

Elevated serum aspartate aminotransferase level identifies patients with coronavirus disease 2019 and predicts the length of hospital stay

BACKGROUND

Coronavirus disease 2019 (COVID-19) has become a worldwide public health emergency. This study aimed to investigate the clinical significance of liver blood tests in COVID-19 patients.

METHODS

The analysis included clinical data of 23 patients with suspected COVID-19 and 66 patients with confirmed COVID-19 from January 25 to February 20, 2020. The relationship between liver blood test results, liver condition (HBsAb positive, HBcAb positive, and fatty liver disease), and duration of hospital stay among COVID-19 patients was analyzed.

RESULTS

The median hospital stay of COVID-19 patients was 6 days. Serum albumin (Alb) level was lower in patients with COVID-19 confirmed on admission than in patients with suspected COVID-19 (40.08 g/L vs 42.50 g/L, P = .016), while the level of aspartate aminotransferase (AST) was higher (23 U/L vs 18 U/L, P = .005). Abnormal results of liver blood tests in patients with COVID-19 included increased levels of alanine transaminase (ALT) (21.2%, 14 patients), AST (15.2%, 10 patients), and gamma-glutamyl transpeptidase (GGT) (22.7%, 15 patients). After 5-10 days of treatment, levels of Alb and AST in COVID-19 patients were significantly decreased (P < .001 and P = .027, respectively). Abnormal levels of Alb and AST in patients with COVID-19 were not associated with the liver condition (all P > .05). In addition, only levels of AST were positively correlated with the duration of hospital stay (r = .334, P = .007).

CONCLUSION

Abnormal results of the liver blood test were found in COVID-19 patients. The COVID-19 patients on admission with the higher levels of AST might have longer hospital stays.

Digestive Symptoms in COVID-19 Patients With Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes

OBJECTIVES

Coronavirus disease 2019 (COVID-19) most commonly presents with respiratory symptoms, including cough, shortness of breath, and sore throat. However, digestive symptoms also occur in patients with COVID-19 and are often described in outpatients with less severe disease. In this study, we sought to describe the clinical characteristics of COVID-19 patients with digestive symptoms and mild disease severity.

METHODS

We identified COVID-19 patients with mild disease and one or more digestive symptoms (diarrhea, nausea, and vomiting), with or without respiratory symptoms, and compared them with a group presenting solely with respiratory symptoms. We followed up patients clinically until they tested negative for COVID-19 on at least 2 sequential respiratory tract specimens collected ≥24 hours apart. We then compared the clinical features between those with digestive symptoms and those with respiratory symptoms.

RESULTS

There were 206 patients with low severity COVID-19, including 48 presenting with a digestive symptom alone, 69 with both digestive and respiratory symptoms, and 89 with respiratory symptoms alone. Between the 2 groups with digestive symptoms, 67 presented with diarrhea, of whom 19.4% experienced diarrhea as the first symptom in their illness course. The diarrhea lasted from 1 to 14 days, with an average duration of 5.4 ± 3.1 days and a frequency of 4.3 ± 2.2 bowel movements per day. Concurrent fever was found in 62.4% of patients with a digestive symptom. Patients with digestive symptoms presented for care later than those with respiratory symptoms (16.0 ± 7.7 vs 11.6 ± 5.1 days, P < 0.001). Nevertheless, patients with digestive symptoms had a longer duration between symptom onset and viral clearance (P < 0.001) and were more likely to be fecal virus positive (73.3% vs 14.3%, P = 0.033) than those with respiratory symptoms.

DISCUSSION

We describe a unique subgroup of COVID-19 patients with mild disease severity marked by the presence of digestive symptoms. These patients are more likely to test positive for viral RNA in stool, to have a longer delay before viral clearance, and to experience delayed diagnosis compared with patients with only respiratory symptoms.

Coronavirus Disease 2019 (COVID-19) pandemic, lessons to be learned!

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported as a worldwide emergency. Due to the extensiveness of spread and death, it has been declared as a pandemic. This review focused on the current pandemic situation and understanding the prevention and control strategies of COVID-19. Data presented here was by April 3, 2020. A total of 1,016,399 cases of COVID-19 with 53,238 deaths was reported from 204 countries and territories including two international conveyances over the world. After China, most of the new cases were from Europe, particularly Italy acting as the source of importation to many of the other countries around the world. China has obtained success by ascribing control strategies against COVID-19. The implementation of China's strategy, as well as the development of a vaccine, may control the pandemic of COVID-19. Further robust studies are required for a clear understanding of transmission parameters, prevention, and control strategies of SARS-CoV-2. This review paper describes the nature of COVID-19 and the possible ways for the effective controlling of the COVID-19 or similar viral diseases that may come in the future.

The epidemiology and clinical information about COVID-19

In December 2019, pneumonia of unknown cause occurred in Wuhan, Hubei Province, China. On 7 January 2020, a novel coronavirus, named as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was identified in the throat swab sample of one patient. The World Health Organization (WHO) announced the epidemic disease caused by SARS-CoV-2 as coronavirus disease 2019 (COVID-19). Currently, COVID-19 has spread widely around the world, affecting more than seventy countries. China, with a huge burden of this disease, has taken strong measures to control the spread and improve the curative rate of COVID-19. In this review, we summarized the epidemiological characteristics, clinical features, diagnosis, treatment, and prognosis of COVID-19. A comprehensive understanding will help to control the disease.

Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2

The COVID-19 outbreak has become a global health risk, and understanding the response of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host deaminases is an innate restriction process to counter virus infection, but it is not yet known whether this process operates against coronaviruses. Here, we analyze RNA sequences from bronchoalveolar lavage fluids obtained from coronavirus-infected patients. We identify nucleotide changes that may be signatures of RNA editing: adenosine-to-inosine changes from ADAR deaminases and cytosine-to-uracil changes from APOBEC deaminases. Mutational analysis of genomes from different strains of Coronaviridae from human hosts reveals mutational patterns consistent with those observed in the transcriptomic data. However, the reduced ADAR signature in these data raises the possibility that ADARs might be more effective than APOBECs in restricting viral propagation. Our results thus suggest that both APOBECs and ADARs are involved in coronavirus genome editing, a process that may shape the fate of both virus and patient.

The epidemiology and clinical information about COVID-19

In December 2019, pneumonia of unknown cause occurred in Wuhan, Hubei Province, China. On 7 January 2020, a novel coronavirus, named as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was identified in the throat swab sample of one patient. The World Health Organization (WHO) announced the epidemic disease caused by SARS-CoV-2 as coronavirus disease 2019 (COVID-19). Currently, COVID-19 has spread widely around the world, affecting more than seventy countries. China, with a huge burden of this disease, has taken strong measures to control the spread and improve the curative rate of COVID-19. In this review, we summarized the epidemiological characteristics, clinical features, diagnosis, treatment, and prognosis of COVID-19. A comprehensive understanding will help to control the disease.

Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID-19) implicate special control measures

By 27 February 2020, the outbreak of coronavirus disease 2019 (COVID-19) caused 82 623 confirmed cases and 2858 deaths globally, more than severe acute respiratory syndrome (SARS) (8273 cases, 775 deaths) and Middle East respiratory syndrome (MERS) (1139 cases, 431 deaths) caused in 2003 and 2013, respectively. COVID-19 has spread to 46 countries internationally. Total fatality rate of COVID-19 is estimated at 3.46% by far based on published data from the Chinese Center for Disease Control and Prevention (China CDC). Average incubation period of COVID-19 is around 6.4 days, ranges from 0 to 24 days. The basic reproductive number (R0 ) of COVID-19 ranges from 2 to 3.5 at the early phase regardless of different prediction models, which is higher than SARS and MERS. A study from China CDC showed majority of patients (80.9%) were considered asymptomatic or mild pneumonia but released large amounts of viruses at the early phase of infection, which posed enormous challenges for containing the spread of COVID-19. Nosocomial transmission was another severe problem. A total of 3019 health workers were infected by 12 February 2020, which accounted for 3.83% of total number of infections, and extremely burdened the health system, especially in Wuhan. Limited epidemiological and clinical data suggest that the disease spectrum of COVID-19 may differ from SARS or MERS. We summarize latest literatures on genetic, epidemiological, and clinical features of COVID-19 in comparison to SARS and MERS and emphasize special measures on diagnosis and potential interventions. This review will improve our understanding of the unique features of COVID-19 and enhance our control measures in the future.

Primer design for quantitative real-time PCR for the emerging Coronavirus SARS-CoV-2

In December 2019, a new coronavirus disease (COVID-19) outbreak occurred in Wuhan, China. Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which is the seventh coronavirus known to infect humans, is highly contagious and has rapidly expanded worldwide since its discovery. Quantitative nucleic acid testing has become the gold standard for diagnosis and guiding clinical decisions regarding the use of antiviral therapy. However, the RT-qPCR assays targeting SARS-CoV-2 have a number of challenges, especially in terms of primer design. Primers are the pivotal components of a RT-qPCR assay. Once virus mutation and recombination occur, it is difficult to effectively diagnose viral infection by existing RT-qPCR primers. Some primers and probes have also been made available on the WHO website for reference. However, no previous review has systematically compared the previously reported primers and probes and described how to design new primers in the event of a new coronavirus infection. This review focuses on how primers and probes can be designed methodically and rationally, and how the sensitivity and specificity of the detection process can be improved. This brief review will be useful for the accurate diagnosis and timely treatment of the new coronavirus pneumonia.

Investigation of Turkish dentists' clinical attitudes and behaviors towards the COVID-19 pandemic: a survey study

Currently, the whole world is under the threat of the COVID-19 pandemic, and dentists are at high risk. The aim of this study was to investigate what kind of precautions Turkish dentists take in dental clinics during the COVID-19 pandemic. The study population consisted of dentists in Turkey. An online questionnaire (23 questions-57 items) was sent to a sample of Turkish dentists from March 16 to March 20, 2020. The questionnaire comprised a series of questions about dentists' demographic characteristics, their concerns, and the measures taken in dental clinics against COVID-19. This study included a total of 1,958 Turkish dentists. A total of 1,274 (65.1%) were general dentists, and 684 (34.9%) were specialists. Five hundred twenty-two (26.7%) dentists attended an informational meeting on COVID-19. Of these dentists, 69.8% were aware of COVID-19 according to their self-assessed knowledge scores. More than 90% of the dentists were concerned about themselves and their families. Only 12% of the dentists wore an N95 mask. Although Turkish dentists took some precautionary measures, they did not take enough precautions to protect themselves, the dental staff, and other patients from COVID-19. As the number of COVID-19 cases increased, the measures taken slightly increased in dental clinics as well. Dentists are strongly recommended to take maximum precautions in the clinical setting. The guidelines about the COVID-19 pandemic should be sent to all dentists by the regional and national dental associations.

Laboratory Diagnosis of COVID-19: Current Issues and Challenges

The COVID-19 outbreak has had a major impact on clinical microbiology laboratories in the past several months. This commentary covers current issues and challenges for the laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the preanalytical stage, collecting the proper respiratory tract specimen at the right time from the right anatomic site is essential for a prompt and accurate molecular diagnosis of COVID-19. Appropriate measures are required to keep laboratory staff safe while producing reliable test results.

The COVID-19 outbreak has had a major impact on clinical microbiology laboratories in the past several months. This commentary covers current issues and challenges for the laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the preanalytical stage, collecting the proper respiratory tract specimen at the right time from the right anatomic site is essential for a prompt and accurate molecular diagnosis of COVID-19. Appropriate measures are required to keep laboratory staff safe while producing reliable test results. In the analytic stage, real-time reverse transcription-PCR (RT-PCR) assays remain the molecular test of choice for the etiologic diagnosis of SARS-CoV-2 infection while antibody-based techniques are being introduced as supplemental tools. In the postanalytical stage, testing results should be carefully interpreted using both molecular and serological findings. Finally, random-access, integrated devices available at the point of care with scalable capacities will facilitate the rapid and accurate diagnosis and monitoring of SARS-CoV-2 infections and greatly assist in the control of this outbreak.

Considering the Effects of Microbiome and Diet on SARS-CoV-2 Infection: Nanotechnology Roles

The impact of dietary patterns and the commensal microbiome on susceptibility to and severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has been largely ignored to date. In this Perspective, we present a rationale for an urgent need to investigate this possible impact and therapeutic options for COVID-19 based on dietary and microbiome modifications. The mitigating role of nanotechnology with relation to the impact of SARS-CoV-2 virus is highlighted.

Coronavirus Disease 2019 (COVID-19) in Neonates and Children From China: A Review

At the end of 2019, a novel coronavirus began to spread in Wuhan, Hubei Province, China. The confirmed cases increased nationwide rapidly, in part due to the increased population mobility during the Chinese Lunar New Year festival. The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Soon, transmission from person to person was confirmed and the virus spread to many other countries. To date, many cases have been reported in the pediatric age group, most of which were from China. The management and treatment strategies have also been improved, which we believe would be helpful to pediatric series in other countries as well. However, the characteristics of neonatal and childhood infection still have not been evaluated in detail. This review summarizes the current understanding of SARS-CoV-2 infection in neonates and children from January 24 to May 1, as an experience from China.

Clinical interventions for severe and critical COVID-19: what are the options

The coronavirus disease 2019 (COVID-19) has been ongoing outbreak and declared as a global public health emergency by the World Health Organization. Severe and critical COVID-19 has high fatality rate due to complications like acute respiratory distress syndrome, acute respiratory failure or multiple organ failure. So far, there have been mounting research on the epidemiological and clinical characteristics of COVID-19. However, the information regarding treatment of severe and critical COVID-19 is limited. The current study reviewed published evidence of clinical interventions of severe and critical COVID-19, aiming to provide an up-to-date reference for further clinical treatment.