Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2015

Estimating the Epidemic Size of Superspreading Coronavirus Outbreaks in Real Time: Quantitative Study

BACKGROUND

Novel coronaviruses have emerged and caused major epidemics and pandemics in the past 2 decades, including SARS-CoV-1, MERS-CoV, and SARS-CoV-2, which led to the current COVID-19 pandemic. These coronaviruses are marked by their potential to produce disproportionally large transmission clusters from superspreading events (SSEs). As prompt action is crucial to contain and mitigate SSEs, real-time epidemic size estimation could characterize the transmission heterogeneity and inform timely implementation of control measures.

OBJECTIVE

This study aimed to estimate the epidemic size of SSEs to inform effective surveillance and rapid mitigation responses.

METHODS

We developed a statistical framework based on back-calculation to estimate the epidemic size of ongoing coronavirus SSEs. We first validated the framework in simulated scenarios with the epidemiological characteristics of SARS, MERS, and COVID-19 SSEs. As case studies, we retrospectively applied the framework to the Amoy Gardens SARS outbreak in Hong Kong in 2003, a series of nosocomial MERS outbreaks in South Korea in 2015, and 2 COVID-19 outbreaks originating from restaurants in Hong Kong in 2020.

RESULTS

The accuracy and precision of the estimation of epidemic size of SSEs improved with longer observation time; larger SSE size; and more accurate prior information about the epidemiological characteristics, such as the distribution of the incubation period and the distribution of the onset-to-confirmation delay. By retrospectively applying the framework, we found that the 95% credible interval of the estimates contained the true epidemic size after 37% of cases were reported in the Amoy Garden SARS SSE in Hong Kong, 41% to 62% of cases were observed in the 3 nosocomial MERS SSEs in South Korea, and 76% to 86% of cases were confirmed in the 2 COVID-19 SSEs in Hong Kong.

CONCLUSIONS

Our framework can be readily integrated into coronavirus surveillance systems to enhance situation awareness of ongoing SSEs.

Multidrug-resistant organisms may be associated with bed allocation and utilization efficiency in healthcare institutions, based on national monitoring data from China (2014-2020)

Analyzing the influence of the bed allocation and utilization efficiency in healthcare institutions on the isolation proportion of Multidrug-resistant organisms (MDROs) to provide data to support prevention and control of MDROs. In this study, the provincial panel data from 2014 to 2020 in China on health resource indicators, including the number of beds per 1,000 population, hospital bed utilization rate, and average hospital stay from 2014 to 2020 in China were used to analyze the relationship between bed allocation or utilization efficiency and MDROs by the panel data quantile regression model. It was shown that the number of beds per 1,000 population had a negative effect on the isolation proportion of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecalis, vancomycin-resistant Enterococcus faecium, penicillin-resistant Streptococcus pneumoniae, methicillin-resistant coagulase-negative Staphylococcus, and cefotaxime or ceftriaxone resistant Escherichia coli (regression coefficient < 0, P < 0.05). The utilization rate of hospital bed had a positive effect on the isolation proportion of methicillin-resistant Staphylococcus aureus, methicillin-resistant coagulase-negative Staphylococcus, vancomycin-resistant Enterococcus faecium, penicillin-resistant Streptococcus pneumoniae, cefotaxime or ceftriaxone resistant Escherichia coli, carbapenem-resistant Escherichia coli, cefotaxime or ceftriaxone resistant Klebsiella pneumoniae, carbapenem-resistant Klebsiella pneumoniae, carbapenem-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii (regression coefficient > 0, P < 0.05). The average hospital stay had a positive effect on the isolation proportion for several antibiotic-resistant organisms, including methicillin-resistant Staphylococcus aureus, methicillin-resistant coagulase-negative Staphylococcus, vancomycin-resistant Enterococcus faecalis, vancomycin-resistant Enterococcus faecium, penicillin-resistant Streptococcus pneumoniae, cefotaxime or ceftriaxone resistant Escherichia coli, carbapenem-resistant Escherichia coli, quinolone-resistant Escherichia coli, cefotaxime or ceftriaxone resistant Klebsiella pneumoniae, carbapenem-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii (regression coefficient > 0, P < 0.05). Bed allocation and utilization efficiency in healthcare institutions may affect the isolation proportion of MDROs in varying degrees.

Nonface-to-Face Visitation to Restrict Patient Visits for Infection Control: Integrative Review

BACKGROUND

In the COVID-19 pandemic, a visit restriction policy for patients has been implemented in medical institutions worldwide and visits are being made using alternative communication technologies. This shift has also required the use of platforms to prevent negative consequences of these restrictions.

OBJECTIVE

The purpose of this review was to comprehensively explore nonface-to-face visits as an alternative during infection prevention and to synthesize the scientific evidence of their benefits and disadvantages.

METHODS

A comprehensive search was conducted via the PubMed, Embase, CINAHL, Cochrane, and Web of Science electronic databases; unpublished trials in the clinical trials register ClinicalTrials.gov; and Virginia Henderson International Nursing Library up to September 10, 2021. The search query was developed according to the guidelines of the Peer Review of Electronic Search Strategies and included keywords on the topics of telemedicine and visitation restrictions. The inclusion criteria were a nonface-to-face modality using telemedicine with family in a hospital setting, experimental and observational studies, and articles written in English. The exclusion criteria were inaccessible in full text, not related to patient or family involvement, mainly focused on the study protocol, or only discussing the pros and cons of telemedicine.

RESULTS

Overall, patients' families experienced emotional distress due to restrictions on face-to-face visits. Nonface-to-face virtual visits compensating for these restrictions had a positive effect on reducing the risk of infection to the patient and the family. This further encouraged psychological and physical recovery and decreased psychological distress. However, nonface-to-face virtual technology could not replace the existence of actual families, and technical problems with networks and devices are reported as limitations.

CONCLUSIONS

Ensuring the availability of technology and educating on the same in alignment with the characteristics of patients and their families, nonface-to-face virtual visits need to show more potential as an effective patient-centered treatment strategy based on more research and advanced practice.

The burden and dynamics of hospital-acquired SARS-CoV-2 in England

Hospital-based transmission had a dominant role in Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) epidemics1,2, but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England, we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 inpatients acquired SARS-CoV-2 in hospitals (1% to 2% of all hospital admissions in this period). Analysis of time series data provided evidence that patients who themselves acquired SARS-CoV-2 infection in hospital were the main sources of transmission to other patients. Increased transmission to inpatients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognized scale of hospital transmission, have direct implications for targeting of hospital control measures and highlight the need to design hospitals better equipped to limit the transmission of future high-consequence pathogens.

Impact of proactive and reactive vaccination strategies for health-care workers against MERS-CoV: a mathematical modelling study

BACKGROUND

Several vaccine candidates are in development against MERS-CoV, which remains a major public health concern. In anticipation of available MERS-CoV vaccines, we examine strategies for their optimal deployment among health-care workers.

METHODS

Using data from the 2013-14 Saudi Arabia epidemic, we use a counterfactual analysis on inferred transmission trees (who-infected-whom analysis) to assess the potential impact of vaccination campaigns targeting health-care workers, as quantified by the proportion of cases or deaths averted. We investigate the conditions under which proactive campaigns (ie vaccinating in anticipation of the next outbreak) would outperform reactive campaigns (ie vaccinating in response to an unfolding outbreak), considering vaccine efficacy, duration of vaccine protection, effectiveness of animal reservoir control measures, wait (time between vaccination and next outbreak, for proactive campaigns), reaction time (for reactive campaigns), and spatial level (hospital, regional, or national, for reactive campaigns). We also examine the relative efficiency (cases averted per thousand doses) of different strategies.

FINDINGS

The spatial scale of reactive campaigns is crucial. Proactive campaigns outperform campaigns that vaccinate health-care workers in response to outbreaks at their hospital, unless vaccine efficacy has waned significantly. However, reactive campaigns at the regional or national levels consistently outperform proactive campaigns, regardless of vaccine efficacy. When considering the number of cases averted per vaccine dose administered, the rank order is reversed: hospital-level reactive campaigns are most efficient, followed by regional-level reactive campaigns, with national-level and proactive campaigns being least efficient. If the number of cases required to trigger reactive vaccination increases, the performance of hospital-level campaigns is greatly reduced; the impact of regional-level campaigns is variable, but that of national-level campaigns is preserved unless triggers have high thresholds.

INTERPRETATION

Substantial reduction of MERS-CoV morbidity and mortality is possible when vaccinating only health-care workers, underlining the need for countries at risk of outbreaks to stockpile vaccines when available.

FUNDING

UK Medical Research Council, UK National Institute for Health Research, UK Research and Innovation, UK Academy of Medical Sciences, The Novo Nordisk Foundation, The Schmidt Foundation, and Investissement d'Avenir France.

Safety and Immunogenicity of the ChAdOx1, MVA-MERS-S, and GLS-5300 DNA MERS-CoV Vaccines

Background

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a pathogen associated with an acute respiratory infection that has a high mortality rate in humans. It was first identified in June of 2012 in the Arabian Peninsula. The success of the COVID-19 vaccines has shown that it is possible to take advantage of medical and scientific advances to produce safe and effective vaccines for coronaviruses. This study aimed to examine the safety and immunogenicity of MERS-CoV vaccines.

Methods

The research method Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) was used as the guideline for this study. RevMan 5.4 software was used to perform a meta-analysis of the included studies. The safety was assessed by recording adverse events following vaccination, and the immunogenicity was assessed by using seroconversion.

Results

The study included five randomized controlled trials that met the inclusion criteria after screening. The studies had 173 participants and were performed in four countries. The vaccines examined were the ChAdOx1 MERS vaccine, MVA-MERS-S vaccine, and GLS-5300 DNA MERS-CoV vaccine. The meta-analysis showed no significant differences in local adverse effects (all local adverse effects and pain) or systemic adverse effects (all systemic adverse effects, fatigue, and headache) among participants in groups receiving a high-dose vaccine or a low-dose vaccine. There were, however, higher levels of seroconversion in high-dose groups than in low-dose groups (OR 0.16 [CI 0.06, 0.42, p = 0.0002]).

Conclusion

The findings showed that high doses of current MERS-CoV vaccine candidates conferred better immunogenicity than low doses and that there were no differences in the safety of the vaccines.

The effect of variation of individual infectiousness on SARS-CoV-2 transmission in households

Quantifying variation of individual infectiousness is critical to inform disease control. Previous studies reported substantial heterogeneity in transmission of many infectious diseases including SARS-CoV-2. However, those results are difficult to interpret since the number of contacts is rarely considered in such approaches. Here, we analyze data from 17 SARS-CoV-2 household transmission studies conducted in periods dominated by ancestral strains, in which the number of contacts was known. By fitting individual-based household transmission models to these data, accounting for number of contacts and baseline transmission probabilities, the pooled estimate suggests that the 20% most infectious cases have 3.1-fold (95% confidence interval: 2.2- to 4.2-fold) higher infectiousness than average cases, which is consistent with the observed heterogeneity in viral shedding. Household data can inform the estimation of transmission heterogeneity, which is important for epidemic management.

Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans

Emerging infectious diseases of zoonotic origin are an ever-increasing public health risk and economic burden. The factors that determine if and when an animal virus is able to spill over into the human population with sufficient success to achieve ongoing transmission in humans are complex and dynamic. We are currently unable to fully predict which pathogens may appear in humans, where and with what impact. In this review, we highlight current knowledge of the key host–pathogen interactions known to influence zoonotic spillover potential and transmission in humans, with a particular focus on two important human viruses of zoonotic origin, the Nipah virus and the Ebola virus. Namely, key factors determining spillover potential include cellular and tissue tropism, as well as the virulence and pathogenic characteristics of the pathogen and the capacity of the pathogen to adapt and evolve within a novel host environment. We also detail our emerging understanding of the importance of steric hindrance of host cell factors by viral proteins using a “flytrap”-type mechanism of protein amyloidogenesis that could be crucial in developing future antiviral therapies against emerging pathogens. Finally, we discuss strategies to prepare for and to reduce the frequency of zoonotic spillover occurrences in order to minimize the risk of new outbreaks.

Transmission of COVID-19 in Nightlife, Household, and Health Care Settings in Tokyo, Japan, in 2020

IMPORTANCE

There have been few studies on the heterogeneous interconnection of COVID-19 outbreaks occurring in different social settings using robust, surveillance epidemiological data.

OBJECTIVES

To describe the characteristics of COVID-19 transmission within different social settings and to evaluate settings associated with onward transmission to other settings.

DESIGN, SETTING, AND PARTICIPANTS

This is a case series study of laboratory-confirmed COVID-19 cases in Tokyo between January 23 and December 5, 2020, when vaccination was not yet implemented. Using epidemiological investigation data collected by public health centers, epidemiological links were identified and classified into 7 transmission settings: imported, nightlife, dining, workplace, household, health care, and other.

MAIN OUTCOMES AND MEASURES

The number of cases per setting and the likelihood of generating onward transmissions were compared between different transmission settings.

RESULTS

Of the 44 054 confirmed COVID-19 cases in this study, 25 241 (57.3%) were among male patients, and the median (IQR) age of patients was 36 (26-52) years. Transmission settings were identified in 13 122 cases, including 6768 household, 2733 health care, and 1174 nightlife cases. More than 6600 transmission settings were detected, and nightlife (72 of 380 [18.9%]; P < .001) and health care (119 [36.2%]; P < .001) settings were more likely to involve 5 or more cases than dining, workplace, household, and other settings. Nightlife cases appeared in the earlier phase of the epidemic, while household and health care cases appeared later. After adjustment for transmission setting, sex, age group, presence of symptoms, and wave, household and health care cases were less likely to generate onward transmission compared with nightlife cases (household: adjusted odds ratio, 0.03; 95% CI, 0.02-0.05; health care: adjusted odds ratio, 0.57; 95% CI, 0.41-0.79). Household settings were associated with intergenerational transmission, while nonhousehold settings mainly comprised transmission between the same age group. Among 30 932 cases without identified transmission settings, cases with a history of visiting nightlife establishments were more likely to generate onward transmission to nonhousehold settings (adjusted odds ratio, 5.30 [95% CI, 4.64-6.05]; P < .001) than those without such history.

CONCLUSIONS AND RELEVANCE

In this case series study, COVID-19 cases identified in nightlife settings were associated with a higher likelihood of spreading COVID-19 than household and health care cases. Surveillance and interventions targeting nightlife settings should be prioritized to disrupt COVID-19 transmission, especially in the early stage of an epidemic.

A Review of the Currently Available Antibody Therapy for the Treatment of Coronavirus Disease 2019 (COVID-19)

Monoclonal antibodies are a promising treatment for COVID-19. However, the emergence of SARS-CoV-2 variants raised concerns about these therapies' efficacy and long-term viability. Studies reported several antibodies, that received authorization for COVID-19 treatment, are not effective against new variants or subvariants of SARS-CoV-2, hence their distribution has to be paused. Here, the authors reviewed the status of the currently available monoclonal antibodies for COVID-19 treatment, their potential as a therapeutic agent, and the challenges ahead. To address these issues, the authors presented general information on SARS-CoV-2 and how monoclonal antibodies work against SARS-CoV-2. The authors then focus on the antibodies that have been deployed for COVID-19 treatment and their current status, as well as the evidence supporting their potential as an early intervention against COVID-19. Lastly, the authors discussed some leading obstacles that hinder the development and administration of monoclonal antibodies for the treatment of COVID-19.

Monitoring real-time transmission heterogeneity from incidence data

The transmission heterogeneity of an epidemic is associated with a complex mixture of host, pathogen and environmental factors. And it may indicate superspreading events to reduce the efficiency of population-level control measures and to sustain the epidemic over a larger scale and a longer duration. Methods have been proposed to identify significant transmission heterogeneity in historic epidemics based on several data sources, such as contact history, viral genomes and spatial information, which may not be available, and more importantly ignore the temporal trend of transmission heterogeneity. Here we attempted to establish a convenient method to estimate real-time heterogeneity over an epidemic. Within the branching process framework, we introduced an instant-individualheterogenous infectiousness model to jointly characterize the variation in infectiousness both between individuals and among different times. With this model, we could simultaneously estimate the transmission heterogeneity and the reproduction number from incidence time series. We validated the model with data of both simulated and real outbreaks. Our estimates of the overall and real-time heterogeneities of the six epidemics were consistent with those presented in the literature. Additionally, our model is robust to the ubiquitous bias of under-reporting and misspecification of serial interval. By analyzing recent data from South Africa, we found evidence that the Omicron might be of more significant transmission heterogeneity than Delta. Our model based on incidence data was proved to be reliable in estimating the real-time transmission heterogeneity.

Changes in Emergency Department Case Severity and Length of Stay before and after COVID-19 Outbreak in Korea

Severe patients visited regional emergency centers more frequently during the COVID-19 period, and disposition status warranting admission to the intensive care unit or resulting in death was more common during the COVID-19 period. This study was conducted to compare the characteristics and severity of patients, and emergency department length of stay before and after the COVID-19 outbreak. Subjects were 75,409 patients who visited the regional emergency medical center from 1 February 2019 to 19 January 2020 and from 1 February 2020 to 19 January 2021. Data was analyzed using the SPSS/WIN 22.0 program. The significance level was p < 0.05. The chi-square test and t-test were used for variables, and Cramer V was used for correlation. We found that the total number of patients visiting the emergency room decreased by 37.6% after COVID-19, but emergency department length of stay among severely ill patients increased by 203.7%. Additionally, the utilization rate of 119 ambulances and relatively more severe patients increased by 9.0% and by 2.1%. More studies about emergency department designs and operational programs should be conducted for better action not only during regular periods but also during periods of pandemic.

Mathematical Analysis of a COVID-19 Epidemic Model by Using Data Driven Epidemiological Parameters of Diseases Spread in India

This paper attempts to describe the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) via an epidemic model. This virus has dissimilar effects in different countries. The number of new active coronavirus cases is increasing gradually across the globe. India is now in the second stage of COVID-19 spreading, it will be an epidemic very quickly if proper protection is not undertaken based on the database of the transmission of the disease. This paper is using the current data of COVID-19 for the mathematical modeling and its dynamical analysis. We bring in a new representation to appraise and manage the outbreak of infectious disease COVID-19 through SEQIR pandemic model, which is based on the supposition that the infected but undetected by testing individuals are send to quarantine during the incubation period. During the incubation period if any individual be infected by COVID-19, then that confirmed infected individuals are isolated and the necessary treatments are arranged so that they cannot taint the other residents in the community. Dynamics of the SEQIR model is presented by basic reproduction number R ₀ and the comprehensive stability analysis. Numerical results are depicted through apt graphical appearances using the data of five states and India.

Mathematical Analysis of a COVID-19 Epidemic Model by Using Data Driven Epidemiological Parameters of Diseases Spread in India

This paper attempts to describe the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) via an epidemic model. This virus has dissimilar effects in different countries. The number of new active coronavirus cases is increasing gradually across the globe. India is now in the second stage of COVID-19 spreading, it will be an epidemic very quickly if proper protection is not undertaken based on the database of the transmission of the disease. This paper is using the current data of COVID-19 for the mathematical modeling and its dynamical analysis. We bring in a new representation to appraise and manage the outbreak of infectious disease COVID-19 through SEQIR pandemic model, which is based on the supposition that the infected but undetected by testing individuals are send to quarantine during the incubation period. During the incubation period if any individual be infected by COVID-19, then that confirmed infected individuals are isolated and the necessary treatments are arranged so that they cannot taint the other residents in the community. Dynamics of the SEQIR model is presented by basic reproduction number R 0 and the comprehensive stability analysis. Numerical results are depicted through apt graphical appearances using the data of five states and India.

Coronavirus disease vulnerability map using a geographic information system (GIS) from 16 April to 16 May 2020

In recent months, the world has been affected by the infectious coronavirus disease and Iran is one of the most affected countries. The Iranian government's health facilities for an urgent investigation of all provinces do not exist simultaneously. There is no management tool to identify the vulnerabilities of Iranian provinces in prioritizing health services. The aim of this study was to prepare a coronavirus vulnerability map of Iranian provinces using geographic information system (GIS) to monitor the disease. For this purpose, four criteria affecting coronavirus, including population density, percentage of older people, temperature, and humidity, were prepared in the GIS. A multiscale geographically weighted regression (MGWR) model was used to determine the vulnerability of coronavirus in Iran. An adaptive neuro-fuzzy inference system (ANFIS) model was used to predict vulnerability in the next two months. Results indicated that, population density and older people have a more significant impact on coronavirus in Iran. Based on MGWR models, Tehran, Mazandaran, Gilan, and Alborz provinces were more vulnerable to coronavirus in February and March. The ANFIS model findings showed that West Azerbaijan, Zanjan, Fars, Yazd, Semnan, Sistan and Baluchistan, and Tehran provinces were more vulnerable in April and May.

Why do some coronaviruses become pandemic threats when others do not?

Despite multiple spillover events and short chains of transmission on at least 4 continents, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has never triggered a pandemic. By contrast, its relative, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has, despite apparently little, if any, previous circulation in humans. Resolving the unsolved mystery of the failure of MERS-CoV to trigger a pandemic could help inform how we understand the pandemic potential of pathogens, and probing it underscores a need for a more holistic understanding of the ways in which viral genetic changes scale up to population-level transmission.

Middle East respiratory syndrome coronavirus (MERS-CoV) infection: Analyses of risk factors and literature review of knowledge, attitude and practices

The study aimed to explore the risk factors for MERS-CoV infection and systematic review of knowledge, attitudes and practices (KAP) with regard to MERS-CoV among the health care workers (HCWs) and the general population. The World Health Organization's MERS-CoV line list (January 2013-January 2020) of the Kingdom of Saudi Arabia (KSA) was analysed. A Poisson regression model was used to calculate the univariate relative risk of outcomes to each potential risk factor, p-values and 95% confidence intervals. An electronic literature search was conducted to assess knowledge, attitudes and practices of the HCWs and general population of the KSA, with regards to transmission of the infection, risk factors and preventative measures. The line list analysis shows that age, gender, comorbidity, exposure to camels and camel milk consumption were associated with an increased risk of fatality; however, year-wise analysis did not show any decline. Over the years, the mean durations between the symptom onset and hospitalization; the hospitalization and laboratory confirmation have reduced. The review of literature shows that the health care workers and the general population had inadequate knowledge about MERS-CoV, lacked motivation and were disconnected from the health authorities. The WHO line list provides information on risk factors for MERS-CoV, KAP analysis helps to know the potential underlying factors. The literature review shows that continuous education for HCWs and increasing public awareness can help effectively manage future MERS-CoV.

Changes in mortality rate of the general population during the COVID-19 pandemic: an interrupted time series study in Korea

Background

Unlike other countries, South Korea did not implement a large-scale lockdown or closure of businesses to manage the coronavirus disease 2019 (COVID-19) pandemic, but relied on changes in population behaviours and early isolation and treatment of patients. It is important to evaluate the effectiveness of such alternative strategies on the mortality of the general population.

Methods

Mortality and monthly population data from 2013 to 2020 were obtained. A quasi-Poisson regression model adjusting for age structure, seasonality and time was used to evaluate whether underlying trends for monthly mortality rate have changed with the pandemic. Stratification analyses based on sex and location of deaths (inside vs outside of medical facilities) were conducted.

Results

The risk estimates showed no changes in non-accidental mortality during the COVID-19 pandemic [relative risk (RR) (95% confidence interval, 95% CI), slope change: 1.00 (1.00, 1.01), step change: 0.99 (0.97, 1.01)] compared with those before the pandemic. In cause-specific analysis, there was an abrupt and sustained decrease in the mortality rate of respiratory diseases [RR (95% CI), step change: 0.81 (0.77, 0.84)]. In the analysis of deaths by location, an increase in non-accidental mortality [RR (95% CI), slope change: 1.01 (1.01, 1.02), step change: 1.16 (1.11, 1.22)] and several cause-specific mortalities was observed outside of medical facilities.

Conclusions

The non-accidental mortality rate in South Korea for the first year of the pandemic followed the historical trends. However, there was a decrease in mortality associated with respiratory diseases, and an increase in mortality occurring outside of medical facilities. The findings may be attributed to changes in public behaviours, and availability of medical resources during the pandemic.

The urgency of wider adoption of one health approach for the prevention of a future pandemic

Recurring outbreaks of emerging and re-emerging zoonoses serve as a reminder that the health of humans, animals, and the environment are interconnected. Therefore, multisectoral, transdisciplinary, and collaborative approaches are required at local, regional, and global levels to tackle the ever-increasing zoonotic threat. The ongoing pandemic of COVID-19 zoonosis has been posing tremendous threats to global human health and economies. The devastation caused by the COVID-19 pandemic teaches us to adopt a "One Health Approach (OHA)" to tackle a possible future pandemic through a concerted effort of the global scientific community, human health professionals, public health experts, veterinarians and policymakers through open science and open data sharing practices. The OHA is an integrated, holistic, collaborative, multisectoral, and transdisciplinary approach to tackle potential pandemic zoonotic diseases. It includes expanding scientific inquiry into zoonotic infections; monitoring, and regulating traditional food markets, transforming existing food systems, and incentivizing animal husbandry and legal wildlife trade to adopt effective zoonotic control measures. To adopt an OHA globally, research and academic institutions, governments and non-government sectors at the local, regional, and international levels must work together. This review aimed to provide an overview of the major pandemics in human history including the COVID-19, anthropogenic drivers of zoonoses, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) reverse zoonoses, the concept of OHA and how an OHA could be utilized to prevent future pandemic threats to the human-animal-ecosystem interfaces. In addition, this review article discusses the strategic framework of OHA and possible challenges to implement OHA in practice to prevent any future pandemics. The practices of open data sharing, open science, and international collaboration should be included in the OHA to prevent and/or rapidly tackle any health emergencies in the future.

The substitution spectra of coronavirus genomes

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has triggered an unprecedented international effort to sequence complete viral genomes. We leveraged this wealth of information to characterize the substitution spectrum of SARS-CoV-2 and to compare it with those of other human and animal coronaviruses. We show that, once nucleotide composition is taken into account, human and most animal coronaviruses display a mutation spectrum dominated by C to U and G to U substitutions, a feature that is not shared by other positive-sense RNA viruses. However, the proportions of C to U and G to U substitutions tend to decrease as divergence increases, suggesting that, whatever their origin, a proportion of these changes is subsequently eliminated by purifying selection. Analysis of the sequence context of C to U substitutions showed little evidence of apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-mediated editing and such contexts were similar for SARS-CoV-2 and Middle East respiratory syndrome coronavirus sampled from different hosts, despite different repertoires of APOBEC3 proteins in distinct species. Conversely, we found evidence that C to U and G to U changes affect CpG dinucleotides at a frequency higher than expected. Whereas this suggests ongoing selective reduction of CpGs, this effect alone cannot account for the substitution spectra. Finally, we show that, during the first months of SARS-CoV-2 pandemic spread, the frequency of both G to U and C to U substitutions increased. Our data suggest that the substitution spectrum of SARS-CoV-2 is determined by an interplay of factors, including intrinsic biases of the replication process, avoidance of CpG dinucleotides and other constraints exerted by the new host.

Bio-safety and bio-security: A major global concern for ongoing COVID-19 pandemic

Besides its impacts on governance, economics, human culture, geostrategic partnership and environment, globalization greatly exerted control over science and security policies. Biosecurity is the critical job of efforts, policy and preparation to protect health of human, animal and environmental against any biological threats. With the transition into a global village, the possibility of biosecurity breaches has significantly increased. The COVID-19 pandemic is an example of an infringement on biosecurity that has posed a serious threat to the world. Since the first report on the recognition of COVID-19, a number of governments have taken preventive measures, like; lockdown, screening and early detection of suspected and implementing the required response to protect the loss of life and economy. Unfortunately, some of these measures have only recently been taken in some countries, which have contributed significantly to an increased morbidity and loss of life on a daily basis. In this article, the biological risks affecting human, animal and environmental conditions, biosafety violations and preventive measures have been discussed in order to reduce the outbreak and impacts of a pandemic like COVID-19.

A Review of SARS-CoV2: Compared With SARS-CoV and MERS-CoV

The outbreak of coronavirus disease 2019 (COVID-19) has been spreading rapidly in China and the Chinese government took a series of policies to control the epidemic. Studies found that severe COVID-19 is characterized by pneumonia, lymphopenia, exhausted lymphocytes and a cytokine storm. Studies have showen that SARS-CoV2 has significant genomic similarity to the severe acute respiratory syndrome (SARS-CoV), which was a pandemic in 2002. More importantly, some diligent measures were used to limit its spread according to the evidence of hospital spread. Therefore, the Public Health Emergency of International Concern (PHEIC) has been established by the World Health Organization (WHO) with strategic objectives for public health to curtail its impact on global health and economy. The purpose of this paper is to review the transmission patterns of the three pneumonia: SARS-CoV2, SARS-CoV, and MERS-CoV. We compare the new characteristics of COVID-19 with those of SARS-CoV and MERS-CoV.

Within Host Dynamics of SARS-CoV-2 in Humans: Modeling Immune Responses and Antiviral Treatments

In December 2019, a newly discovered SARS-CoV-2 virus was emerged from China and propagated worldwide as a pandemic, resulting in about 3–5% mortality. Mathematical models can provide useful scientific insights about transmission patterns and targets for drug development. In this study, we propose a within-host mathematical model of SARS-CoV-2 infection considering innate and adaptive immune responses. We analyze the equilibrium points of the proposed model and obtain an expression of the basic reproduction number. We then numerically show the existence of a transcritical bifurcation. The proposed model is calibrated to real viral load data of two COVID-19 patients. Using the estimated parameters, we perform global sensitivity analysis with respect to the peak of viral load. Finally, we study the efficacy of antiviral drugs and vaccination on the dynamics of SARS-CoV-2 infection. Results suggest that blocking the virus production from infected cells can be an effective target for antiviral drug development. Finally, it is found that vaccination is more effective intervention as compared to the antiviral treatments.

Stochastic model of the transmission dynamics of COVID-19 pandemic

In this paper, we formulate an SVITR deterministic model and extend it to a stochastic model by introducing intensity of stochastic factors and Brownian motion. Our basic qualitative analysis of both models includes the positivity of the solution, invariant region, disease-free equilibrium point, basic reproduction number, local and global stability of disease-free equilibrium point, endemic equilibrium point, and sensitivity. We obtain the stochastic reproduction number and local stability by using twice differentiable Itô's formula. We prove the global stability of the disease-free equilibrium point by using a Lyapunov function. We determine the sensitivity of the effect of each parameter on basic reproduction number of the model by using a normalized sensitivity index formula. On the other hand, we demonstrate numerical simulation results of deterministic and stochastic models of COVID-19 by using Maple 18 and MATLAB software. Our simulation results indicate that reducing the contact between infected and susceptible individuals and improvement of treatment play a vital role in COVID-19 pandemic control.

Association of HLA class I and II genes with Middle East respiratory syndrome coronavirus infection in Koreans

Introduction

Middle East Respiratory Syndrome (MERS) caused by MERS‐coronavirus (CoV) is a lower respiratory tract disease characterized by a high mortality rate. MERS‐CoV spread from Saudi Arabia to other countries, including South Korea. Dysfunction of the human leukocyte antigen (HLA) system has many effects due to genetic complexity and its role in the adaptive immune response. We investigated the association of HLA class I and II alleles with MERS‐CoV in 32 patients with MERS.

Methods

HLA‐A, ‐B, ‐C, ‐DRB1, ‐DQB1, and ‐DPB1 were genotyped by polymerase chain reaction sequence‐based typing.

Results

HLA‐DQB1*03:02 are significantly associated with moderate/mild cases of MERS‐CoV. Other alleles are no statistical significance.

Conclusions

Treatment strategies based on current research on the HLA gene and MERS‐CoV will provide potential therapeutic targets.

Early reports of epidemiological parameters of the COVID-19 pandemic

Background

The emergence of a new pathogen requires a rapid assessment of its transmissibility, to inform appropriate public health interventions.

Methods

The peer-reviewed literature published between 1 January and 30 April 2020 on COVID-19 in PubMed was searched. Estimates of the incubation period, serial interval and reproduction number for COVID-19 were obtained and compared.

Results

A total of 86 studies met the inclusion criteria. Of these, 33 estimated the mean incubation period (4–7 days) and 15 included estimates of the serial interval (mean 4–8 days; median length 4–5 days). Fifty-two studies estimated the reproduction number. Although reproduction number estimates ranged from 0.3 to 14.8, in 33 studies (63%), they fell between 2 and 3.

Discussion

Studies calculating the incubation period and effective reproduction number were published from the beginning of the pandemic until the end of the study period (30 April 2020); however, most of the studies calculating the serial interval were published in April 2020. The calculated incubation period was similar over the study period and in different settings, whereas estimates of the serial interval and effective reproduction number were setting-specific. Estimates of the serial interval were shorter at the end of the study period as increasing evidence of pre-symptomatic transmission was documented and as jurisdictions enacted outbreak control measures. Estimates of the effective reproduction number varied with the setting and the underlying model assumptions. Early analysis of epidemic parameters provides vital information to inform the outbreak response.

Short-term predictions and prevention strategies for COVID-19: A model-based study

An outbreak of respiratory disease caused by a novel coronavirus is ongoing from December 2019. As of December 14, 2020, it has caused an epidemic outbreak with more than 73 million confirmed infections and above 1.5 million reported deaths worldwide. During this period of an epidemic when human-to-human transmission is established and reported cases of coronavirus disease 2019 (COVID-19) are rising worldwide, investigation of control strategies and forecasting are necessary for health care planning. In this study, we propose and analyze a compartmental epidemic model of COVID-19 to predict and control the outbreak. The basic reproduction number and the control reproduction number are calculated analytically. A detailed stability analysis of the model is performed to observe the dynamics of the system. We calibrated the proposed model to fit daily data from the United Kingdom (UK) where the situation is still alarming. Our findings suggest that independent self-sustaining human-to-human spread ( R 0 > 1 , R c > 1 ) is already present. Short-term predictions show that the decreasing trend of new COVID-19 cases is well captured by the model. Further, we found that effective management of quarantined individuals is more effective than management of isolated individuals to reduce the disease burden. Thus, if limited resources are available, then investing on the quarantined individuals will be more fruitful in terms of reduction of cases.

Caring for Cancer Patients during Corona Pandemic-(COVID-19)-A Narrative Review

Background Coronavirus disease 2019, the third pandemic of 21st century which has brought the whole world under panic, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a zoonotic beta coronavirus sharing phylogenetic, genomic similarities with SARS virus and Middle East Respiratory Syndrome virus. Specific Concerns Cancer patients are at double the risk than normal patients since these patients are at immunocompromised state. WHO guidelines advice the patients to plan only emergency hospital visits only till the pandemic persists. Should meet patient/visitors in a well-ventilated room or outdoors and maintain at least 2 m distance between the visitor/patients. It also encourages the patient to refill the prescribed medications in well advance and to stay physically active, if possible. Discussion The World Health Organizations' isolate, trace, test, treat policy needs to be followed to protect these high-risk patients from this global pandemic.].

A generalizable data assembly algorithm for infectious disease outbreaks

During infectious disease outbreaks, health agencies often share text-based information about cases and deaths. This information is rarely machine-readable, thus creating challenges for outbreak researchers. Here, we introduce a generalizable data assembly algorithm that automatically curates text-based, outbreak-related information and demonstrate its performance across 3 outbreaks. After developing an algorithm with regular expressions, we automatically curated data from health agencies via 3 information sources: formal reports, email newsletters, and Twitter. A validation data set was also curated manually for each outbreak, and an implementation process was presented for application to future outbreaks. When compared against the validation data sets, the overall cumulative missingness and misidentification of the algorithmically curated data were ≤2% and ≤1%, respectively, for all 3 outbreaks. Within the context of outbreak research, our work successfully addresses the need for generalizable tools that can transform text-based information into machine-readable data across varied information sources and infectious diseases.

Meta-analysis and comprehensive study of coronavirus outbreaks: SARS, MERS and COVID-19

BACKGROUND

Zoonotic coronaviruses have caused several endemic and pandemic situations around the world. SARS caused the first epidemic alert at the beginning of this century, followed by MERS. COVID-19 appeared to be highly contagious, with human-to-human transmission by aerosol droplets, and reached nearly all countries around the world. A plethora of studies were performed, with reports being published within a short period of time by scientists and medical physicians. It has been difficult to find the relevant data to create an overview of the situation according to studies from accumulated findings and reports. In the present study we aimed to perform a comprehensive study in the context of the case fatality ratios (CFRs) of three major human Coronavirus outbreaks which occurred during the first twenty years of 21st century.

METHODS

In this study, we performed meta-analyses on SARS, MERS and COVID-19 outbreak events from publicly available records. Study analyses were performed with the help of highly reputable scientific databases such as PubMed, WOS and Scopus to evaluate and present current knowledge on zoonotic coronavirus outbreaks, starting from 2000 to the end of 2020.

RESULTS

A total of 250,194 research studies and records were identified with specific keywords and synonyms for the three viruses in order to cover all publications. In the end, 41 records were selected and included after applying several exclusion and inclusion criteria on identified datasets. SARS was found to have a nearly 11% case fatality ratio (CFR), which means the estimated number of deaths as a proportion of confirmed positive cases; Taiwan was the country most affected by the SARS outbreak based on the CFR analysis. MERS had CFRs of 35.8 and 26 in Saudi Arabia during the 2012 and 2015 outbreaks, respectively. COVID-19 resulted in a 2.2 CFR globally, and the USA reported the highest mortality ratio in the world in the end of first year of COVID-19 pandemic.

CONCLUSION

Some members of the Coronaviridae family can cause highly contagious and devastating infections among humans. Within the last two decades, the whole world has witnessed several deadly emerging infectious diseases, which are most commonly zoonotic in nature. We conclude that pre-existing immunity during the early stages of a pandemic might be important, but case control and management strategies should be improved to decrease CFRs. Finally, we have addressed several concerns in relation to outbreak events in this study.

Investigating the Effective Factors of Using Personal Protective Equipment from the Perspective of Nurses Caring for COVID-19 Patients: A Cross-Sectional Study

Considering the importance of appropriate personal protective equipment (PPE) for preventing COVID-19 transmission, the aim of this study was to investigate the factors affecting the use of PPE from the perspective of the nurses caring for COVID-19 patients. This descriptive cross-sectional study surveyed 240 nurses working in the central COVID-19 hospitals of Arak, Iran. Nurses were enrolled in the study by a convenience sampling method. The data collection tool was a validated questionnaire. Data were analyzed by SPSS 16 software using descriptive statistics, analysis of variance (ANOVA), and independent sample t-test. Environmental (4.24 ± 0.45), personal (4.16 ± 0.42), and organizational (4.04 ± 0.50) factors all contribute significantly to nursing attitudes about PPE use (p < 0.05). The average score, combining all identified factors, was 4.15 ± 0.31. The most influential factor contributing to appropriate use of PPE was environmental, while the least impactful parameters were related to rules and regulations. Environmental factors have the greatest impact on the use of PPE from the perspective of the nurses caring for patients with COVID-19. Managers and healthcare organizations should provide appropriate and adequate PPE to nurses, educate them on proper use, and monitor the process to resolve barriers.

Impact of Coronavirus Disease 2019 Pandemic on Crowding: A Call to Action for Effective Solutions to “Access Block”

Introduction

Healthcare patterns change during disease outbreaks and pandemics. Identification of modified patterns is important for future preparedness and response. Emergency department (ED) crowding can occur because of the volume of patients waiting to be seen, which results in delays in patient assessment or treatment and impediments to leaving the ED once treatment is complete. Therefore, ED crowding has become a growing problem worldwide and represents a serious barrier to healthcare operations.

Methods

This observational study was based on a retrospective review of the epidemiologic and clinical records of patients who presented to the Foundation IRCCS Policlinic San Matteo in Pavia, Italy, during the coronavirus disease 2019 (COVID-19) outbreak (February 21–May 1, 2020, pandemic group). The methods involved an estimation of the changes in epidemiologic and clinical data from the annual baseline data after the start of the COVID-19 pandemic.

Results

We identified reduced ED visits (180 per day in the control period vs 96 per day in the pandemic period; P < 0.001) during the COVID-19 pandemic, irrespective of age and gender, especially for low-acuity conditions. However, patients who did present to the ED were more likely to be hemodynamically unstable, exhibit abnormal vital signs, and more frequently required high-intensity care and hospitalization. During the pandemic, ED crowding dramatically increased primarily because of an increased number of visits by patients with high-acuity conditions, changes in patient management that prolonged length of stay, and increased rates of boarding, which led to the inability of patients to gain access to appropriate hospital beds within a reasonable amount of time. During the pandemic, all crowding output indices increased, especially the rates of boarding (36% vs 57%; P < 0.001), “access block” (24% vs 47%; P < 0.001), mean boarding time (640 vs 1,150 minutes [min]; P 0.001), mean “access block” time (718 vs 1,223 min; P < 0.001), and “access block” total time (650,379 vs 1,359,172 min; P < 0.001).

Conclusion

Crowding in the ED during the COVID-19 pandemic was due to the inability to access hospital beds. Therefore, solutions to this lack of access are required to prevent a recurrence of crowding due to a new viral wave or epidemic.

Animal models of SARS-CoV-2 transmission

SARS-CoV-2 emerged in China as a zoonotic virus in December 2019. The virus proved to be human-to-human transmissible and its global spread resulted in the ongoing COVID-19 pandemic, associated with high morbidity and mortality. Vaccines were developed at an unprecedented speed and proved to be efficacious in preventing disease, but it remains to be determined if vaccines are able to interrupt transmission. Moreover, virus variants of concern continue to emerge that appear more transmissible and/or less sensitive to virus-specific immune responses. Here, we briefly review the role of animal models in assessing prophylactic and therapeutic options to interrupt SARS-CoV-2 transmission.

Protective population behavior change in outbreaks of emerging infectious disease

BACKGROUND

During outbreaks of emerging and re-emerging infections, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible population are paramount, particularly isolation and hospitalization. Ebola virus disease (EVD), Severe Acute Respiratory Syndrome (SARS), and Middle East Respiratory Syndrome (MERS) are zoonotic viruses that have caused significant recent outbreaks with sustained human-to-human transmission.

METHODS

This investigation quantified changing mean removal rates (MRR) and days from symptom onset to hospitalization (DSOH) of infected individuals from the population in seven different outbreaks of EVD, SARS, and MERS, to test for statistically significant differences in these metrics between outbreaks.

RESULTS

We found that epidemic week and viral serial interval were correlated with the speed with which populations developed and maintained health behaviors in each outbreak.

CONCLUSIONS

These findings highlight intrinsic population-level changes in isolation rates in multiple epidemics of three zoonotic infections with established human-to-human transmission and significant morbidity and mortality. These data are particularly useful for disease modelers seeking to forecast the spread of emerging pathogens.

Risk Assessment for the Transmission of Middle East Respiratory Syndrome Coronavirus (MERS-Cov) on Aircraft: A Systematic Review

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a potentially fatal respiratory disease. Although it is most common in the Arabian Peninsula, it has been exported to 17 countries outside the Middle East, mostly through air travel. The Risk Assessment Guidelines for Infectious Diseases transmitted on Aircraft (RAGIDA) advise authorities on measures to take when an infected individual travelled by air. The aim of this systematic review was to gather all available information on documented MERS-CoV cases that had travelled by air, to update RAGIDA. The databases used were PubMed, Embase, Scopus and Global Index Medicus; Google was searched for grey literature and hand searching was performed on the EU Early Warning and Response System and the WHO Disease Outbreak News. Forty-seven records were identified, describing 21 cases of MERS that had travelled on 31 flights. Contact tracing was performed for 17 cases. Most countries traced passengers sitting in the same row and the two rows in front and behind the case. Only one country decided to trace all passengers and crew. No cases of in-flight transmission were observed; thus, considering the resources it requires, a conservative approach may be appropriate when contact tracing passengers and crew where a case of MERS has travelled by air.

Middle East Respiratory Syndrome (MERS) Virus-Pathophysiological Axis and the Current Treatment Strategies

Middle East respiratory syndrome (MERS) is a lethal respiratory disease with its first case reported back in 2012 (Jeddah, Saudi Arabia). It is a novel, single-stranded, positive-sense RNA beta coronavirus (MERS-CoV) that was isolated from a patient who died from a severe respiratory illness. Later, it was found that this patient was infected with MERS. MERS is endemic to countries in the Middle East regions, such as Saudi Arabia, Jordan, Qatar, Oman, Kuwait and the United Arab Emirates. It has been reported that the MERS virus originated from bats and dromedary camels, the natural hosts of MERS-CoV. The transmission of the virus to humans has been thought to be either direct or indirect. Few camel-to-human transmissions were reported earlier. However, the mode of transmission of how the virus affects humans remains unanswered. Moreover, outbreaks in either family-based or hospital-based settings were observed with high mortality rates, especially in individuals who did not receive proper management or those with underlying comorbidities, such as diabetes and renal failure. Since then, there have been numerous reports hypothesising complications in fatal cases of MERS. Over the years, various diagnostic methods, treatment strategies and preventive measures have been strategised in containing the MERS infection. Evidence from multiple sources implicated that no treatment options and vaccines have been developed in specific, for the direct management of MERS-CoV infection. Nevertheless, there are supportive measures outlined in response to symptom-related management. Health authorities should stress more on infection and prevention control measures, to ensure that MERS remains as a low-level threat to public health.

Review of epidemic, containment strategies, clinical management, and economic evaluation of COVID-19 pandemic

The spread of the emerging pathogen, named as SARS-CoV-2, has led to an unprecedented COVID-19 pandemic since 1918 influenza pandemic. This review first sheds light on the similarity on global transmission, surges of pandemics, and the disparity of prevention between two pandemics. Such a brief comparison also provides an insight into the potential sequelae of COVID-19 based on the inference drawn from the fact that a cascade of successive influenza pandemic occurred after 1918 and also the previous experience on the epidemic of SARS and MERS occurring in 2003 and 2015, respectively. We then propose a systematic framework for elucidating emerging infectious disease (EID) such as COVID-19 with a panorama viewpoint from natural infection and disease process, public health interventions (non-pharmaceutical interventions (NPIs) and vaccine), clinical treatments and therapies (antivirals), until global aspects of health and economic loss, and economic evaluation of interventions with emphasis on mass vaccination. This review not only concisely delves for evidence-based scientific literatures from the origin of outbreak, the spread of SARS-CoV-2 to three surges of pandemic, and NPIs and vaccine uptakes but also provides a new insight into how to apply big data analytics to identify unprecedented discoveries through COVID-19 pandemic scenario embracing from biomedical to economic viewpoints.

Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012-2019

BACKGROUND

The Middle East Respiratory Syndrome-related Coronavirus (MERS-CoV) continues to exist in the Middle East sporadically. Thorough investigations of the evolution of human coronaviruses (HCoVs) are urgently required. In the current study, we studied amplified fragments of ORF1a/b, Spike (S) gene, ORF3/4a, and ORF4b of four human MERS-CoV strains for tracking the evolution of MERS-CoV over time.

METHODS

RNA isolated from nasopharyngeal aspirate, sputum, and tracheal swabs/aspirates from hospitalized patients with suspected MERS-CoV infection were analyzed for amplification of nine variable genomic fragments. Sequence comparisons were done using different bioinformatics tools available.

RESULTS

Several mutations were identified in ORF1a/b, ORF3/4a and ORF4b, with the highest mutation rates in the S gene. Five codons; 4 in ORF1a and 1 in the S gene, were found to be under selective pressure. Characteristic amino acid changes, potentially hosted and year specific were defined across the S protein and in the receptor-binding domain Phylogenetic analysis using S gene sequence revealed clustering of MERS-CoV strains into three main clades, A, B and C with subdivision of with clade B into B1 to B4.

CONCLUSIONS

In conclusion, MERS-CoV appears to continuously evolve. It is recommended that the molecular and pathobiological characteristics of future MERS-CoV strains should be analyzed on regular basis to prevent potential future outbreaks at early phases.

Severe acute respiratory syndrome coronavirus 2 for physicians: Molecular characteristics and host immunity (Review)

Recently, severe acute respiratory syndrome (SARS) coronavirus (CoV) 2 (SARS‑CoV‑2)‑causing CoV disease 2019 (COVID‑19) emerged in China and has become a global pandemic. SARS‑CoV‑2 is a novel CoV originating from β‑CoVs. Major distinctions in the gene sequences between SARS‑CoV and SARS‑CoV‑2 include the spike gene, open reading frame (ORF) 3b and ORF 8. SARS‑CoV‑2 infection is initiated when the virus interacts with angiotensin‑converting enzyme 2 (ACE2) receptors on host cells. Through this mechanism, the virus infects the alveolar, esophageal epithelial, ileum, colon and other cells on which ACE2 is highly expressed, causing damage to target organs. To date, host innate immunity may be the only identified direct factor associated with viral replication. However, increased ACE2 expression may upregulate the viral load indirectly by increasing the baseline level of infectious virus particles. The peak viral load of SARS‑CoV‑2 is estimated to occur ~10 days following fever onset, causing patients in the acute stage to be the primary infection source. However, patients in the recovery stage or with occult infections can also be contagious. The host immune response in patients with COVID‑19 remains to be elucidated. By studying other SARS and Middle East respiratory syndrome coronaviruses, it is hypothesized that patients with COVID‑19 may lack sufficient antiviral T‑cell responses, which consequently present with innate immune response disorders. This may to a certain degree explain why this type of CoV triggers severe inflammatory responses and immune damage and its associated complications.

COVID-19 case management strategies: what are the options for Africa?

The ongoing coronavirus disease 2019 (COVID-19) pandemic has put a strain on health systems globally. Although Africa is the least affected region to date, it has the weakest health systems and an exponential rise in cases as has been observed in other regions, is bound to overwhelm its health systems. Early detection and isolation of suspected and confirmed COVID-19 cases are pivotal to the prevention and control of the pandemic. The World Health Organization (WHO) recommends that all laboratory-confirmed cases should be isolated and treated in a health care facility; however, where this is not possible due to the health system capacity, patients can be isolated in re-purposed facilities or at home. An already very apparent future challenge for Africa is facility-based isolation of COVID-19 cases, given the already limited health infrastructure and health workforce, and the risk of nosocomial transmission. Use of repurposed facilities requires additional resources, including health workers. Home isolation, on the other hand, would be a challenge given the poor housing, overcrowding, inadequate access to water and sanitation, and stigma related to infectious disease that is prevalent in many African societies. Conflict settings on the continent pose an additional challenge to the prevention and control of COVID-19 with the resultant population displacements in overcrowded camps where access to social services is limited. These unique cultural, social, economic and developmental differences on the continent, call for a tailored approach to COVID-19 case management strategies. This article proposes three broad case management strategies based on the transmission scenarios defined by WHO, and the criteria and package of care for each option, for consideration by policy makers and governments in African countries. Moving forward, African countries should generate local evidence to guide the development of realistic home-grown strategies, protocol and equipment for the management of COVID-19 cases on the continent .

Serial interval and incubation period of COVID-19: a systematic review and meta-analysis

BACKGROUND

Understanding the epidemiological parameters that determine the transmission dynamics of COVID-19 is essential for public health intervention. Globally, a number of studies were conducted to estimate the average serial interval and incubation period of COVID-19. Combining findings of existing studies that estimate the average serial interval and incubation period of COVID-19 significantly improves the quality of evidence. Hence, this study aimed to determine the overall average serial interval and incubation period of COVID-19.

METHODS

We followed the PRISMA checklist to present this study. A comprehensive search strategy was carried out from international electronic databases (Google Scholar, PubMed, Science Direct, Web of Science, CINAHL, and Cochrane Library) by two experienced reviewers (MAA and DBK) authors between the 1st of June and the 31st of July 2020. All observational studies either reporting the serial interval or incubation period in persons diagnosed with COVID-19 were included in this study. Heterogeneity across studies was assessed using the I2 and Higgins test. The NOS adapted for cross-sectional studies was used to evaluate the quality of studies. A random effect Meta-analysis was employed to determine the pooled estimate with 95% (CI). Microsoft Excel was used for data extraction and R software was used for analysis.

RESULTS

We combined a total of 23 studies to estimate the overall mean serial interval of COVID-19. The mean serial interval of COVID-19 ranged from 4. 2 to 7.5 days. Our meta-analysis showed that the weighted pooled mean serial interval of COVID-19 was 5.2 (95%CI: 4.9-5.5) days. Additionally, to pool the mean incubation period of COVID-19, we included 14 articles. The mean incubation period of COVID-19 also ranged from 4.8 to 9 days. Accordingly, the weighted pooled mean incubation period of COVID-19 was 6.5 (95%CI: 5.9-7.1) days.

CONCLUSIONS

This systematic review and meta-analysis showed that the weighted pooled mean serial interval and incubation period of COVID-19 were 5.2, and 6.5 days, respectively. In this study, the average serial interval of COVID-19 is shorter than the average incubation period, which suggests that substantial numbers of COVID-19 cases will be attributed to presymptomatic transmission.

The history of the emergence and transmission of human coronaviruses

Human coronaviruses are known respiratory pathogens associated with a range of respiratory illnesses, and there are considerable morbidity and hospitalisation amongst immune-compromised individuals of all age groups. The emergence of a highly pathogenic human coronavirus in China in 2019 has confirmed the long-held opinion that these viruses are important emerging and re-emerging pathogens. In this review article, we trace the discovery and emergence of coronaviruses (CoVs) over time since they were first reported. The review article will enrich our understanding on the host range, diversity and evolution, transmission of human CoVs and the threat posed by these viruses circulating in animal populations but overtime have spilled over to humans because of the increased proximity between humans and animals.

Altered Influenza Vaccination Coverage and Related Factors in Pregnant Women in Korea from 2007 to 2019

BACKGROUND

Pregnant women are at a high-risk of influenza infection. We have previously reported a low influenza vaccination coverage rate (4.0%) in Korea during the 2006-2007 influenza season. We conducted follow-up studies in 2011-2012 and 2018-2019 to observe changes in influenza vaccination coverage.

METHODS

Women who delivered at Inha University Hospital (Incheon, Korea) in 2011-2012 and 2018-2019 were enrolled in the study. We surveyed the rate of influenza vaccination, perception scores, and related factors through telephonic interviews and compared the results from 2011-2012 and 2018-2019 with those from 2006-2007.

RESULTS

The number of survey respondents was 227 in 2006-2007, 152 in 2011-2012, and 171 in 2018-2019. The rate of vaccination coverage increased from 4.0% in 2006-2007 to 42.0% in 2011-2012 and 59.3% in 2018-2019. Perception scores also increased progressively from 3.8 in 2006-2007 to 4.2 in 2011-2012 and 5.1 in 2018-2019. Physician recommendations for influenza vaccination also increased from 4.8% in 2006-2007 to 36.8% in 2011-2012 and 49.7% in 2018-2019. The most common reason for not getting vaccinated was the lack of awareness of influenza vaccination during pregnancy (36.9%). The perception scores and physician recommendation rates were significantly lower for unvaccinated women (3.87 and 8.4%, respectively) than for vaccinated women (5.14 and 69.1%, respectively).

CONCLUSION

The influenza vaccination coverage rate in pregnant women has increased significantly since our study in 2006-2007. However, further improvement in the coverage rate is needed. There is a need for active and comprehensive publicity and education regarding this issue among physicians and pregnant women.

Subcritical Transmission in the Early Stage of COVID-19 in Korea

While the coronavirus disease 2019 (COVID-19) outbreak has been ongoing in Korea since January 2020, there were limited transmissions during the early stages of the outbreak. In the present study, we aimed to provide a statistical characterization of COVID-19 transmissions that led to this small outbreak. We collated the individual data of the first 28 confirmed cases reported from 20 January to 10 February 2020. We estimated key epidemiological parameters such as reporting delay (i.e., time from symptom onset to confirmation), incubation period, and serial interval by fitting probability distributions to the data based on the maximum likelihood estimation. We also estimated the basic reproduction number (R0) using the renewal equation, which allows for the transmissibility to differ between imported and locally transmitted cases. There were 16 imported and 12 locally transmitted cases, and secondary transmissions per case were higher for the imported cases than the locally transmitted cases (nine vs. three cases). The mean reporting delays were estimated to be 6.76 days (95% CI: 4.53, 9.28) and 2.57 days (95% CI: 1.57, 4.23) for imported and locally transmitted cases, respectively. The mean incubation period was estimated to be 5.53 days (95% CI: 3.98, 8.09) and was shorter than the mean serial interval of 6.45 days (95% CI: 4.32, 9.65). The R0 was estimated to be 0.40 (95% CI: 0.16, 0.99), accounting for the local and imported cases. The fewer secondary cases and shorter reporting delays for the locally transmitted cases suggest that contact tracing of imported cases was effective at reducing further transmissions, which helped to keep R0 below one and the overall transmissions small.

MERS-CoV: epidemiology, molecular dynamics, therapeutics, and future challenges

The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.

A SIQ mathematical model on COVID-19 investigating the lockdown effect

This research paper aims at studying the impact of lockdown on the dynamics of novel Corona Virus Disease (COVID-19) emerged in Wuhan city of China in December 2019. Perceiving the pandemic situation throughout the world, Government of India restricted international passenger traffic through land check post (Liang, 2020) and imposed complete lockdown in the country on 24 March 2020. To study the impact of lockdown on disease dynamics we consider a three-dimensional mathematical model using nonlinear ordinary differential equations. The proposed model has been studied using stability theory of nonlinear ordinary differential equations. Basic reproduction ratio is computed and significant parameters responsible to keep basic reproduction ratio less than one are identified. The study reveals that disease vanishes from the system only if complete lockdown is imposed otherwise disease will always persist in the population. However, disease can be kept under control by implementing contact tracing and quarantine measures as well along with lockdown if lockdown is imposed partially.

Product of natural evolution (SARS, MERS, and SARS-CoV-2); deadly diseases, from SARS to SARS-CoV-2

SARS-CoV-2, the virus causing COVID-19, is a single-stranded RNA virus belonging to the order Nidovirales, family Coronaviridae, and subfamily Coronavirinae. SARS-CoV-2 entry to cellsis initiated by the binding of the viral spike protein (S) to its cellular receptor. The roles of S protein in receptor binding and membrane fusion makes it a prominent target for vaccine development. SARS-CoV-2 genome sequence analysis has shown that this virus belongs to the beta-coronavirus genus, which includes Bat SARS-like coronavirus, SARS-CoV and MERS-CoV. A vaccine should induce a balanced immune response to elicit protective immunity. In this review, we compare and contrast these three important CoV diseases and how they inform on vaccine development.

Phytocompounds of Rheum emodi, Thymus serpyllum, and Artemisia annua Inhibit Spike Protein of SARS-CoV-2 Binding to ACE2 Receptor: In Silico Approach

COVID-19, the disease caused by SARS-CoV-2, has been declared as a global pandemic. Traditional medicinal plants have long history to treat viral infections. Our in silico approach suggested that unique phytocompounds such as emodin, thymol and carvacrol, and artemisinin could physically bind SARS-CoV-2 spike glycoproteins (6VXX and 6VYB), SARS-CoV-2 B.1.351 South Africa variant of Spike glycoprotein (7NXA), and even with ACE2 and prevent the SARS-CoV-2 binding to the host ACE2, TMPRSS2 and neutrapilin-1 receptors. Since Chloroquine has been looked as potential therapy against COVID-19, we also compared the binding of chloroquine and artemisinin for its interaction with spike proteins (6VXX, 6VYB) and its variant 7NXA, respectively. Molecular docking study of phytocompounds and SARS-CoV-2 spike protein was performed by using AutoDock/Vina software. Molecular dynamics (MD) simulation was performed for 50ns. Among all the phytocompounds, molecular docking studies revealed lowest binding energy of artemisinin with 6VXX and 6VYB, with E_total -10.5 KJ mol^-1 and -10.3 KJ mol^-1 respectively. Emodin showed the best binding affinity with 6VYB with E_total -8.8 KJ mol^-1and SARS-CoV-2 B.1.351 variant (7NXA) with binding energy of -6.4KJ mol^-1. Emodin showed best interactions with TMPRSS 2 and ACE2 with E_total of -7.1 and -7.3 KJ mol^-1 respectively, whereas artemisinin interacts with TMPRSS 2 and ACE2 with E_total of -6.9 and -7.4 KJ mol^-1 respectively. All the phytocompounds were non-toxic and non-carcinogenic. MD simulation showed that artemisinin has more stable interaction with 6VYB as compared to 6VXX, and hence proposed as potential phytochemical to prevent SARS-CoV-2 interaction with ACE-2 receptor.

GRAPHICAL ABSTRACT

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40495-021-00259-4.