Lethal zoonotic coronavirus infections of humans - comparative phylogenetics, epidemiology, transmission, and clinical features of coronavirus disease 2019, The Middle East respiratory syndrome and severe acute respiratory syndrome.

PURPOSE OF REVIEW: Severe acute respiratory syndrome-coronaviruses-2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), emerged as a new zoonotic pathogen of humans at the end of 2019 and rapidly developed into a global pandemic. Over 106 million COVID-19 cases including 2.3 million deaths have been reported to the WHO as of February 9, 2021. This review examines the epidemiology, transmission, clinical features, and phylogenetics of three lethal zoonotic coronavirus infections of humans: SARS-CoV-1, SARS-CoV-2, and The Middle East respiratory syndrome coronavirus (MERS-COV). RECENT FINDINGS: Bats appear to be the common natural source of SARS-like CoV including SARS-CoV-1 but their role in SARS-CoV-2 and MERS-CoV remains unclear. Civet cats and dromedary camels are the intermediary animal sources for SARS-CoV-1 and MERS-CoV infection, respectively whereas that of SARS-CoV-2 remains unclear. SARS-CoV-2 viral loads peak early on days 2-4 of symptom onset and thus high transmission occurs in the community, and asymptomatic and presymptomatic transmission occurs commonly. Nosocomial outbreaks are hallmarks of SARS-CoV-1 and MERS-CoV infections whereas these are less common in COVID-19. Several COVID-19 vaccines are now available. SUMMARY: Of the three lethal zoonotic coronavirus infections of humans, SARS-CoV-2 has caused a devastating global pandemic with over a million deaths. The emergence of genetic variants, such as D614G, N501Y (variants 1 and 2), has led to an increase in transmissibility and raises concern about the possibility of re-infection and impaired vaccine response. Continued global surveillance is essential for both SARS-CoV-2 and MERS-CoV, to monitor changing epidemiology due to viral variants.

Assessment of the quality of systematic reviews on COVID-19: A comparative study of previous coronavirus outbreaks.

Several systematic reviews (SRs) have been conducted on the COVID-19 outbreak, which together with the SRs on previous coronavirus outbreaks, form important sources of evidence for clinical decision and policy making. Here, we investigated the methodological quality of SRs on COVID-19, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Online searches were performed to obtain SRs on COVID-19, SARS, and MERS. The methodological quality of the included SRs was assessed using the AMSTAR-2 tool. Descriptive statistics were used to present the data. In total, of 49 SRs that were finally included in our study, 17, 16, and 16 SRs were specifically on COVID-19, MERS, and SARS, respectively. The growth rate of SRs on COVID-19 was the highest (4.54/month) presently. Of the included SRs, 6, 12, and 31 SRs were of moderate, low, and critically low quality, respectively. SRs on SARS showed the optimum quality among the SRs on the three diseases. Subgroup analyses showed that the SR topic (P < .001), the involvement of a methodologist (P < .001), and funding support (P = .046) were significantly associated with the methodological quality of the SR. According to the adherence scores, adherence to AMSTAR-2 items sequentially decreased in SRs on SARS, MERS, and COVID-19. The methodological quality of most SRs on coronavirus outbreaks is unsatisfactory, and those on COVID-19 have higher risks of poor quality, despite the rapid actions taken to conduct SRs. The quality of SRs should be improved in the future. Readers must exercise caution in accepting and using the results of these SRs.

Rapid assessment of regional SARS-CoV-2 community transmission through a convenience sample of healthcare workers, the Netherlands, March 2020.

To rapidly assess possible community transmission in Noord-Brabant, the Netherlands, healthcare workers (HCW) with mild respiratory complaints and without epidemiological link (contact with confirmed case or visited areas with active circulation) were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Within 2 days, 1,097 HCW in nine hospitals were tested; 45 (4.1%) were positive. Of six hospitals with positive HCW, two accounted for 38 positive HCW. The results informed local and national risk management.

The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: what lessons have we learned?

OBJECTIVES: To provide an overview of the three major deadly coronaviruses and identify areas for improvement of future preparedness plans, as well as provide a critical assessment of the risk factors and actionable items for stopping their spread, utilizing lessons learned from the first two deadly coronavirus outbreaks, as well as initial reports from the current novel coronavirus (COVID-19) epidemic in Wuhan, China. METHODS: Utilizing the Centers for Disease Control and Prevention (CDC, USA) website, and a comprehensive review of PubMed literature, we obtained information regarding clinical signs and symptoms, treatment and diagnosis, transmission methods, protection methods and risk factors for Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS) and COVID-19. Comparisons between the viruses were made. RESULTS: Inadequate risk assessment regarding the urgency of the situation, and limited reporting on the virus within China has, in part, led to the rapid spread of COVID-19 throughout mainland China and into proximal and distant countries. Compared with SARS and MERS, COVID-19 has spread more rapidly, due in part to increased globalization and the focus of the epidemic. Wuhan, China is a large hub connecting the North, South, East and West of China via railways and a major international airport. The availability of connecting flights, the timing of the outbreak during the Chinese (Lunar) New Year, and the massive rail transit hub located in Wuhan has enabled the virus to perforate throughout China, and eventually, globally. CONCLUSIONS: We conclude that we did not learn from the two prior epidemics of coronavirus and were ill-prepared to deal with the challenges the COVID-19 epidemic has posed. Future research should attempt to address the uses and implications of internet of things (IoT) technologies for mapping the spread of infection.

Stochastic two-group models with transmission dependent on host infectivity or susceptibility.

Stochastic epidemic models with two groups are formulated and applied to emerging and re-emerging infectious diseases. In recent emerging diseases, disease spread has been attributed to superspreaders, highly infectious individuals that infect a large number of susceptible individuals. In some re-emerging infectious diseases, disease spread is attributed to waning immunity in susceptible hosts. We apply a continuous-time Markov chain (CTMC) model to study disease emergence or re-emergence from different groups, where the transmission rates depend on either the infectious host or the susceptible host. Multitype branching processes approximate the dynamics of the CTMC model near the disease-free equilibrium and are used to estimate the probability of a minor or a major epidemic. It is shown that the probability of a major epidemic is greater if initiated by an individual from the superspreader group or by an individual from the highly susceptible group. The models are applied to Severe Acute Respiratory Syndrome and measles.

Review of economic evaluations of mask and respirator use for protection against respiratory infection transmission.

BACKGROUND: There has been increasing debate surrounding mask and respirator interventions to control respiratory infection transmission in both healthcare and community settings. As decision makers are considering the recommendations they should evaluate how to provide the most efficient protection strategies with minimum costs. The aim of this review is to identify and evaluate the existing economic evaluation literature in this area and to offer advice on how future evaluations on this topic should be conducted. METHODS: We searched the Scopus database for all literature on economic evaluation of mask or respirator use to control respiratory infection transmission. Reference lists from the identified studies were also manually searched. Seven studies met our inclusion criteria from the initial 806 studies identified by the search strategy and our manual search. RESULTS: Five studies considered interventions for seasonal and/or pandemic influenza, with one also considering SARS (Severe Acute Respiratory Syndrome). The other two studies focussed on tuberculosis transmission control interventions. The settings and methodologies of the studies varied greatly. No low-middle income settings were identified. Only one of the reviewed studies cited clinical evidence to inform their mask/respirator intervention effectiveness parameters. Mask and respirator interventions were generally reported by the study authors to be cost saving or cost-effective when compared to no intervention or other control measures, however the evaluations had important limitations. CONCLUSIONS: Given the large cost differential between masks and respirators, there is a need for more comprehensive economic evaluations to compare the relative costs and benefits of these interventions in situations and settings where alternative options are potentially applicable. There are at present insufficient well conducted cost-effectiveness studies to inform decision-makers on the value for money of alternative mask/respirator options.

How change of public transportation usage reveals fear of the SARS virus in a city.

The outbreaks of the severe acute respiratory syndrome (SARS) epidemic in 2003 resulted in unprecedented impacts on people's daily life. One of the most significant impacts to people is the fear of contacting the SARS virus while engaging daily routine activity. Here we use data from daily underground ridership in Taipei City and daily reported new SARS cases in Taiwan to model the dynamics of the public fear of the SARS virus during the wax and wane of the SARS period. We found that for each reported new SARS case there is an immediate loss of about 1200 underground ridership (the fresh fear). These daily loss rates dissipate to the following days with an e-folding time of about 28 days, reflecting the public perception on the risk of contacting SARS virus when traveling with the underground system (the residual fear). About 50% of daily ridership was lost during the peak of the 2003 SARS period, compared with the loss of 80% daily ridership during the closure of the underground system after Typhoon Nari, the loss of 50-70% ridership due to the closure of the governmental offices and schools during typhoon periods, and the loss of 60% daily ridership during Chinese New Year holidays.

Temporal variability and social heterogeneity in disease transmission: the case of SARS in Hong Kong.

The extent to which self-adopted or intervention-related changes in behaviors affect the course of epidemics remains a key issue for outbreak control. This study attempted to quantify the effect of such changes on the risk of infection in different settings, i.e., the community and hospitals. The 2002-2003 severe acute respiratory syndrome (SARS) outbreak in Hong Kong, where 27% of cases were healthcare workers, was used as an example. A stochastic compartmental SEIR (susceptible-exposed-infectious-removed) model was used: the population was split into healthcare workers, hospitalized people and general population. Super spreading events (SSEs) were taken into account in the model. The temporal evolutions of the daily effective contact rates in the community and hospitals were modeled with smooth functions. Data augmentation techniques and Markov chain Monte Carlo (MCMC) methods were applied to estimate SARS epidemiological parameters. In particular, estimates of daily reproduction numbers were provided for each subpopulation. The average duration of the SARS infectious period was estimated to be 9.3 days (+/-0.3 days). The model was able to disentangle the impact of the two SSEs from background transmission rates. The effective contact rates, which were estimated on a daily basis, decreased with time, reaching zero inside hospitals. This observation suggests that public health measures and possible changes in individual behaviors effectively reduced transmission, especially in hospitals. The temporal patterns of reproduction numbers were similar for healthcare workers and the general population, indicating that on average, an infectious healthcare worker did not infect more people than any other infectious person. We provide a general method to estimate time dependence of parameters in structured epidemic models, which enables investigation of the impact of control measures and behavioral changes in different settings.

Bayesian analysis of severe acute respiratory syndrome: the 2003 Hong Kong epidemic.

This paper analyzes data arising from a Severe Acute Respiratory Syndrome (SARS) epidemic in Hong Kong in 2003 involving 1755 cases. A discrete time stochastic model that uses a back-projection approach is proposed. Markov Chain Monte Carlo (MCMC) methods are developed for estimation of model parameters. The algorithm is further extended to integrate numerically over unobserved variables of the model. Applying the method to SARS data from Hong Kong, a value of 3.88 with a posterior standard deviation of 0.09 was estimated for the basic reproduction number. An estimate of the transmission parameter at the beginning of the epidemic was also obtained as 0.149 with a posterior standard deviation of 0.003. A reduction in the transmission parameter during the course of the epidemic forced the effective reproduction number to cross the threshold value of one, seven days after control interventions were introduced. At the end of the epidemic, the effective reproduction number was as low as 0.001 suggesting that the epidemic was brought under control by the intervention measures introduced.

Homelessness and the response to emerging infectious disease outbreaks: lessons from SARS.

During the 2003 severe acute respiratory syndrome (SARS) outbreak in Toronto, the potential introduction of SARS into the homeless population was a serious concern. Although no homeless individual in Toronto contracted SARS, the outbreak highlighted the need to develop an outbreak preparedness plan that accounts for unique issues related to homeless people. We conducted key informant interviews with homeless service providers and public health officials (n = 17) and identified challenges specific to the homeless population in the areas of communication, infection control, isolation and quarantine, and resource allocation. Planning for future outbreaks should take into account the need to (1) develop systems that enable rapid two-way communication between public health officials and homeless service providers, (2) ensure that homeless service providers have access to infection control supplies and staff training, (3) prepare for possible homeless shelter closures due to staff shortages or high attack rates among clients, and (4) plan for where and how clinically ill homeless individuals will be isolated and treated. The Toronto SARS experience provided insights that are relevant to response planning for future outbreaks in cities with substantial numbers of homeless individuals.

Predicting case numbers during infectious disease outbreaks when some cases are undiagnosed.

We describe a method for calculating 95 per cent bounds for the current number of hidden cases and the future number of diagnosed cases during an outbreak of an infectious disease. A Bayesian Markov chain Monte Carlo approach is used to fit a model of infectious disease transmission that takes account of undiagnosed cases. Assessing this method on simulated data, we find that it provides conservative 95 per cent bounds for the number of undiagnosed cases and future case numbers, and that these bounds are robust to modifications in the assumptions generating the simulated data. Moreover, the method provides a good estimate of the initial reproduction number, and the reproduction number in the latter stages of the outbreak. Applying the approach to SARS data from Hong Kong, Singapore, Taiwan and Canada, the bounds on future diagnosed cases are found to be reliable, and the bounds on hidden cases suggests that there were few hidden cases remaining at the end of the outbreaks in each region. We estimate that the initial reproduction numbers lay between 1.5 and 3, and the reproduction numbers in the later stages of the outbreak lay between 0.36 and 0.6.

A loophole in international quarantine procedures disclosed during the SARS crisis.

This study describes a loophole in the international quarantine system during the recent Asian severe acute respiratory syndrome (SARS) outbreak. Specifically, that of travelers disguising symptoms of respiratory tract infection at international airports, in order to board aircraft to return to their home countries-notwithstanding the infection risks this involves to others. High medical fees for treatment to non-residents in epidemic areas were found to be the main cause for this behaviour. This phenomenon revealed a loophole in the control mechanisms of international quarantine procedures, letting travelers carrying a highly contagious virus slip by undetected and causing possible multi-country outbreaks of communicable diseases. Clinical evidence collected from medical records at medical centers can highlight this oversight.

Estimating in real time the efficacy of measures to control emerging communicable diseases.

Controlling an emerging communicable disease requires prompt adoption of measures such as quarantine. Assessment of the efficacy of these measures must be rapid as well. In this paper, the authors present a framework to monitor the efficacy of control measures in real time. Bayesian estimation of the reproduction number R (mean number of cases generated by a single infectious person) during an outbreak allows them to judge rapidly whether the epidemic is under control (R < 1). Only counts and time of onset of symptoms, plus tracing information from a subset of cases, are required. Markov chain Monte Carlo and Monte Carlo sampling are used to infer the temporal pattern of R up to the last observation. The operating characteristics of the method are investigated in a simulation study of severe acute respiratory syndrome-like outbreaks. In this particular setting, control measures lacking efficacy (R > or = 1.1) could be detected after 2 weeks in at least 70% of the epidemics, with less than a 5% probability of a wrong conclusion. When control measures are efficacious (R = 0.5), this situation may be evidenced in 68% of the epidemics after 2 weeks and 92% of the epidemics after 3 weeks, with less than a 5% probability of a wrong conclusion.

Research gaps in protecting healthcare workers from SARS and other respiratory pathogens: an interdisciplinary, multi-stakeholder, evidence-based approach.

OBJECTIVE: To identify priorities for further research in protecting healthcare workers (HCWs) from severe acute respiratory syndrome (SARS) and other respiratory pathogens by summarizing the basic science of infectious bioaerosols and the efficacy of facial protective equipment; the organizational, environmental, and individual factors that influence the success of infection control and occupational health programs; and factors identified by HCWs as important. METHOD: An extensive literature review was conducted and 15 focus groups held, mostly with frontline HCWs in Toronto. Critical gaps in knowledge were identified and prioritized. RESULTS: Highest priority was given to organizational factors that create a climate of safety. Other priority areas included understanding aerosolization risks and practical measures to control bioaerosols at the source. CONCLUSIONS: Further research is warranted to improve safety climate in health care and, specifically, to provide greater protection against respiratory pathogens.

[Preventive measures suggested to protect health workers from the risk due to a potential exposure to SARS agents]. / Misure di prevenzione e protezione per la potenziale esposizione all'agente biologico responsabile della SARS in ambiente ospedaliero.

The Authors describe the personal and environmental preventive measures suggested to protect health workers from the risks due to a potential exposure to SARS agents. The Authors stress the need that workers are allowed to wear individual protective disposable complying with technical regulations in order to be assured the best protection.

[Preparatory guidelines for local health services on how to respond to new cases of severe acute respiratory syndrome (SARS)]. / Guía para preparar a los servicios locales de salud ante la aparición de casos de síndrome respiratorio agudo grave (SARS).

The Centers for Disease Control and Prevention (CDC) of the United States of America recently issued a set of guidelines on how different community health services should prepare for and respond to the reemergence of severe acute respiratory syndrome (SARS). This document summarizes the recommendations of the CDC for basic health services. Disease surveillance in communities and hospitals should be performed in light of existing information on risk factors, particularly those related to geographic dissemination patterns and to documented transmission of SARS-CoV, the coronavirus that causes SARS. As long as no cases of person-to-person disease transmission are reported anywhere in the world, efforts should be aimed at early detection and notification of cases and of groups of people who are in contact with one another and who have severe respiratory infections of undetermined cause, such as pneumonia, which could signal the reemergence of SARS. If cases of transmission of SARS-CoV have been reported, the aim should be to immediately identify and notify any cases detected in order to take appropriate diagnostic and therapeutic measures and to facilitate outbreak control. The reach of surveillance and reporting activities in specific communities should depend on how widely the disease has spread, both in the community and in local health services. Physicians and public health workers should be familiar with ways to detect SARS cases early, as well as with existing norms for reporting any cases detected.

Infection control measures for operative procedures in severe acute respiratory syndrome-related patients.

BACKGROUND: Singapore reported its first case of Severe Acute Respiratory Syndrome (SARS) in early March 2003 and was placed on the World Health Organization's list of SARS-affected countries on March 15, 2003. During the outbreak, Tan Tock Seng Hospital was designated as the national SARS hospital in Singapore to manage all known SARS patients. Stringent infection control measures were introduced to protect healthcare workers and control intrahospital transmission of SARS. Work-flow processes for surgery were extensively modified. METHODS: The authors describe the development of infection control measures, the conduct of surgical procedures, and the management of high-risk procedures during the SARS outbreak. RESULTS: Forty-one operative procedures, including 15 high-risk procedures (surgical tracheostomy), were performed on SARS-related patients. One hundred twenty-four healthcare workers had direct contact with SARS patients during these procedures. There was no transmission of SARS within the operating room complex. CONCLUSIONS: Staff personal protection, patient risk categorization, and reorganization of operating room workflow processes formed the key elements for the containment of SARS transmission. Lessons learned during this outbreak will help in the planning and execution of infection control measures, should another outbreak occur.