This is an update of an article originally published on 27 January 2020 in InSight+. It is now available here, and at

An outbreak of a novel coronavirus, now formally named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causing coronavirus disease 2019 (COVID-19), emerged in the city of Wuhan in Hubei province in central China in December 2019. The first cases were noted as a cluster of patients with pneumonia who were all linked to a live animal market, and testing found the presence of a previously unknown coronavirus. Coronaviruses are a group of viruses that affect both animals and humans, and several (OC43, 229E, HKU1 and NL63) are a cause of the common cold (here, and here). However, two coronaviruses have previously caused significant outbreaks associated with more severe disease: the SARS coronavirus in 2002–2003 and the Middle East respiratory syndrome coronavirus that emerged in 2012. Chinese authorities and researchers should be commended for their rapid sharing of viral sequences which enabled laboratories worldwide to develop diagnostic tests within weeks of discovery of the pathogen. An Australian laboratory subsequently isolated the virus from a clinical sample (the first to do so outside of China), and rapidly shared this virus with relevant global agencies, further aiding diagnostic, therapeutic and vaccine development efforts.

Information on this new virus and its impact is being updated constantly. We know that SARS-CoV-2 can cause severe disease, although active surveillance of contacts is required to define the milder end of the disease spectrum and to estimate the true hospitalisation and case fatality ratio. The cases reported to date suggest that most are older adults; it is currently unclear whether comorbidities reflect the age group affected or whether they are risk factors for severe disease (here, and here).

Early studies using data before the institution of public health interventions in China suggest that SARS-CoV-2 is as transmissible as SARS coronavirus and probably more transmissible than influenza viruses (here, and here). The timing of infectiousness relative to symptom onset is a particularly important parameter with implications for public health control. While reports suggest that asymptomatic infection and transmission may result from minimally symptomatic cases, the contribution of this to transmission is not yet known. Careful analysis of early data suggests that the mean incubation period is 6 days, with a range of up to 14 days. Reports of multiple health care workers infected by a single patient raises the possibility of highly infective super-spreaders, a feature of previous coronavirus outbreaks. The importance of infection control is also reinforced by a report that 41% of cases in Wuhan were acquired nosocomially (including 40 health care workers and 17 patients).

At the time of writing (18 Feb 2020), there were 15 confirmed cases of COVID-19 in Australia, across four jurisdictions. Globally, cases have been reported in many countries, with rates reflecting travel to mainland China, and a large outbreak reported on a cruise ship. However, it is likely that this will change in the days or weeks ahead. Although absolute case numbers are small in Australia, the public health, political and societal ramifications have already been considerable, ranging from travel restrictions on non-Australians coming from China, the use of offshore and remote quarantine facilities, and disturbing reports of racism against members of our Asian community.

For clinicians, the main considerations are the clinical management of patients with suspected novel coronavirus infection but also systems to facilitate the identification of potential cases and to permit safe assessment and referral as appropriate. The experience with SARS and Middle East respiratory syndrome also reinforces the need for health services (both internationally and within Australia) to promptly identify patients with suspected infection and implement effective infection control measures. Based on clinical features, it can be difficult to distinguish patients with COVID-19 from those with other respiratory viral infections, including influenza. Although the original case series described fever in almost all patients, further experience has noted cases with only respiratory symptoms, and even a small proportion with gastrointestinal symptoms. This has resulted in constant changes to case definitions, initially limited to those with febrile respiratory infections from Wuhan, but now including the full spectrum of illness in patients from a broader geographical area. Clinicians should refer to current information to guide testing and management (Box 1).

Box 1: Useful sources of official information

Australian information

International situation reports and resources

Nucleic acid assays for SARS-CoV-2 are available at several Australian reference laboratories and commercial tests are expected in the near future for diagnostic laboratories. Current World Health Organization advice is to test patients who meet the case definition for COVID-19, regardless of whether another respiratory virus is detected, as co-infections may occur. However, the need to maintain a low threshold of suspicion must be balanced with the capacity of laboratories to perform high throughput and timely tests.

Lessons of the past are instructive for Australia, particularly the experience in Canada with its similar federated government and comparable health care system. In 2003, an outbreak of SARS coronavirus in Toronto infected 438 people and caused 44 deaths, including many health care workers. Following this public health disaster, two important reviews were conducted: the National Advisory Committee on SARS and Public Health, and Ontario’s SARS Commission. The former reinforced the need for a strong and adequately funded nationally coordinated public health and laboratory system and led to the establishment of the Public Health Agency of Canada.

The SARS Commission made detailed recommendations, including endorsing the “importance of the precautionary principle that reasonable efforts to reduce risk need not await scientific proof [which] was demonstrated over and over during SARS”. It made recommendations regarding clear governance, preparing for the need for unexpected interventions (including the closure of three hospitals to control the outbreak), effective distribution of outbreak alerts and directives, the need for effective crisis communication, and the value of robust and timely surveillance. With the involvement of health care workers as cases, the Commission highlighted the need to the need to listen to frontline workers and unions and ensure a robust safety culture and effective infection control.

We have many more information (and misinformation) sharing tools than were available in 2003. It has been breathtaking to watch the scientific process unfold in almost real time. Rapid genomic sequencing and online databases are being used to generate and analyse primary data. Preprint servers and rapid review in traditional journals are quickly publishing research findings. Research centres and platforms are responding to rapidly collect data and evaluate interventions. Social media and traditional media platforms are disseminating public health messages and findings.

However, the fundamental structure of our public health care system remains unchanged, with the same channels of formal, sometimes protracted, communication and direction through a national network-based system of public health. It is too early to tell how this outbreak will unfold on a global scale, with many major unresolved clinical and public health issues

Box 2. Major unresolved clinical and public health issues
* Optimal samples for diagnostic testing (upper versus lower respiratory tract samples)
* Utility of existing and investigational antiviral agents
* Duration of infectiousness based on current nucleic acid testing, including requirement for repeat testing
* Host risk factors associated with poor clinical outcomes
Public health and control
* Effectiveness of national and international travel restrictions on outbreak containment
* Quantitation of the spectrum of disease severity
* Optimal, yet pragmatic, infection control measures
* Utility of case and contact tracing in outbreak containment in low and high incidence settings

In Australia, we need to continue to be prepared at all levels of the health care system, with a key tenet of this response being rapid and reliable communication. This should include advice to clinicians and patients on who should be tested, how and when testing should be performed, and how best to manage patients with suspected and confirmed infection. Australia has not been significantly challenged by the two previous zoonotic coronavirus outbreaks. However, current indications are that this new pathogen is more transmissible than previous coronaviruses. With cases now reported in Australia, public health authorities, governments at all levels, researchers and clinicians, laboratories and the community need to continue to work together in a timely manner to ensure an effective response.

Professor Allen Cheng is Director of the Infection Prevention and Healthcare Epidemiology Unit, Alfred Health; School of Public Health and Preventive Medicine, Monash University.

Professor Deborah Williamson is from the Department of Microbiology, Melbourne Health Pathology; Microbiological Diagnostic Unit, University of Melbourne.



The statements or opinions expressed in this article reflect the views of the authors and do not represent the official policy of the AMA, the MJA or InSight+ unless so stated.


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11 thoughts on “An outbreak of COVID-19 caused by a new coronavirus – what we know so far

  1. Anonymous says:

    Is it possible COVID-19 could have been circulating in Australia since early Dec 2019? I am an RN working in a major public hospital in SA. Around Dec 3, we had a cluster of around six staff become ill with a mystery virus after nursing a patient who was very unwell with respiratory symptoms. In subsequent weeks multiple others came down with flu like symptoms and very bad cough. Many staff presented to their GP for swabs, and those who did were negative for flu viruses. I believe throughout the hospital many others got the same virus and some were off work for several weeks. Whatever it was was not an identified virus, yet was very contagious. Incidentally the patient I believe tested positive for influenza A. We assumed the patient was the source, but have a multicultural workforce with several Chinese nurses whose parents had flown into Adelaide around that time. Guess a serology test to test for antibodies will be our only way if knowing. Interested in your thoughts. Thanks.

  2. Professor Andrew Taylor-Robinson, Central Queensland University says:

    The unforeseen emergence of nCoV-2019 in China serves as a strict reminder of the continuing threat to global public health of zoonotic diseases. In order to expedite a concerted and collaborative multinational effort for disease control, in the short- to medium-term further significant investments and well-targeted management strategies are required. In evoking a one health philosophy this should be interdisciplinary in nature and encompass experiences from all geographical regions.

    While it appears likely that the Wuhan coronavirus was initially transmitted to humans from animals, the species from which it crossed over, and other possible reservoirs, needs to be identified. This is one of several current unknowns – others include the transmission route, incubation period, epidemic curve, pathogenesis, characteristics of susceptible groups, their survival rates and treatment responses.

    This outbreak brings to mind those of two related coronaviruses, causing severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS), earlier this century. The SARS-CoV arose in China in 2003, spread rapidly in the region but then disappeared as quickly as it came. In contrast, first identified in Saudi Arabia in 2012, the MERS-CoV still re-emerges intermittently through nosocomial outbreaks, community clusters and sporadic cases. It will be interesting to see which, if either, of these two distinct epidemiological pathways nCoV-2019 takes and how much global health security measures can play in disease control and prevention.

  3. Dr. Christoph Ahrens says:

    all very useful. Thanks

  4. Randal says:

    It should be kept in mind that if the higher-end estimates of numbers infected (90,000) is true, then the mortality rate is comparable to what we find from influnenza during each and every flu season (~1 in 1000).

    So yes, due diligence and monitoring are important, but perspective still needs to be kept. Remember the lessons of the swine flu ‘pandemic’.

  5. Anonymous says:

    We have received information on recommendations for school children and students returning from China, has there been any consideration of HCWs returning from China and how to manage them based on risk of exposure in China and the workplace specialty they are returning to. Should we be asking them to observe an incubation period as well?

  6. Allen Cheng says:

    Secondary bacterial infections were described in 4 of the 41 patients in the nCoV series in the Lancet. It’s not clear if these were pneumonia, or other ICU-related infections eg central line infections, UTIs.

  7. Peter Lake says:

    Do we have any idea yet whether secondary bacterial infection is involved especially in those patients who have died or are seriously ill?

  8. Anonymous says:

    please remind me what specific treatment there is for Coronavirus ?
    there is none !
    therefore otherwise healthy young people with nothing more than a fever or a runny nose
    should be dissuaded from flooding our Emergency departments and medical clinics for no real benefit
    to them but at risk to staff and other patients.

  9. Dr. Rey Tiquia says:

    Here is report from a frontline practitioner of traditional Chinese medicine in Jinan city, Shandong provice in China
    who looked after several patients when the Wuhan corona virus epidemic broke out. I have translated the report from Chinese into English.

    FromThe Perspective of Traditional Chinese Medicine We Look at the Wuhan Pneumonia of Unknown Cause and Origins
    SinaCom Internet Blog 新浪博客. January 8, 2020 :Yi San Sheng 一三生
    Translated from Chinese by Rey Tiquia

    Wen yi 瘟疫 ‘Warm factor epidemics’ occur once after an interval of a number of years. As for the magnitude of the epidemic, it can be as widespread as the SARS (Severe Acute Respiratory Syndrome or that Atypical Pneumonia fei dian非典) epidemic or small scale as just affecting our hand,foot and mouth
    像手足口or that of the ‘swine flu’ 猪流感 epidemic. Hence, there is nothing remarkable about it. It a normal phenomena 常态occurring in nature.The occurrence of warm factor epidemics wen yi n is related to abnormal weather/climactic conditions. After damage without a trace. This year (2019: Year of the Earth Pig 己亥年) the weather in winter was very unusual. The temperature was unusually high. And here, (Jinan, provincial capital of Shandong Province) the temperature was above zero degrees. Snow did not fall and it only rained a little bit. All of a sudden, it only became cold after the Winter Solstice 冬至过后. The coldest was only a dozen degrees below zero. Affected by this weather condition, the common colds 感冒and fevers children suffered were very different from previous years. They are not like the ‘meteorological cold qi damage’ shang han伤寒 from previous years. They are more similar to wen bing ‘warm factor diseases’ accompanied by symptoms resulting from ‘severe influence’ from ‘humidity’ and ‘heat’ 湿热重. Under this conditions, it is more appropriate to use herbal formula like Xiang zi san 香薷散or yin qiao san 银翘散…which are prescribed to people suffering from ‘common cold’ which come about during the summer season (please refer to previous article “Common colds and fevers children suffer this winter) are very different from previous years). More than a month ago, I treated an adult patient suffering from pneumonia with symptoms resulting from being affected by ‘severe humidity and heat’ shi re Zhong 湿热重. I used a materia medica formula with the ingredients of the ancient formula san ren tang 三仁汤 as the core (please refer to previous article ‘ Materia medica formulae for the treatment of pneumonia’). Seasonal diseases shi ling bing 时令病 manifest clinically as symptoms of ‘common cold’ gan mao and ‘cough’ 咳嗽. Compared to previous years, there were much more people suffering from ‘cough’ kesou during the winter season of this year exhibiting symptoms of fever (‘heat’ re) with ‘dampish-phlegm’(‘humidity’ shi) ( please refer to previous article ‘Characteristic Features of ‘winter cough’ in 2019’).

    Based on the abovementioned observations and reflection, I consider the ‘unexplained cases of pneumonia’ currently occurring in Wuhan as ‘humidity/heat type of warm factor epidemic’ shi re wenbing 湿热温病 . And the materia medica formula to be deployed in dealing with this epidemic are the following:
    1. 新加香薷散
    2. 甘露消毒丹
    3. 三仁汤
    4. 达原饮
    5. 千金苇茎汤
    6. 调胃承气汤
    7. 小承气 汤


    This year, 2019, is the Earth-Pig Year 己亥年. Calculations using the system of the Circulating Five Elements and Six Meteorological Qi wuyin liu qi 五运六气, currently, the ‘governing season’ zhuling主令 is the 6th sub-seasonal Qi ‘The六之气 ( xiao xue 小雪 November 22, 2019-Da Han 大寒 Greater Cold January20, 2020). The characterisitic feature of the 6th Subseasonal Qi are:
    1. The ‘Host’ Qi 主气 is “The Great Yang Coldness Water’ 太阳寒水.
    2. The ‘Guest Qi 客氣 is ‘the small yang bright elemental ministerial fire’ 少阳相火.
    3. In the ‘final sub-seasonal qi 终之气, ‘dread of the elemental fire takes command’ 畏火司令.
    4. ‘Dormant insects’ are starting to ‘stir .’ 蛰虫出见.
    5. Running water (in lakes and rivers) are not turning to ice 流水不冰.
    6. The earth qi (coming from the core of the planet) is surging upwards 地气大发.
    7. ‘The grass is raw’ 草乃生.
    8. ‘People still feel comfortable’ 人乃舒.
    9. ‘and the disease the above conditions bring aboutis the pestilential Warm factor epidemic 其病瘟厉.
    These shows that the athmospheric temperature this winter (in China) is rising. And this facilitates the emergence of warm factor epidemics.

  10. Anonymous says:

    What an excellent overview of the issue, risks and importance of clear messages and planning required at all levels of healthcare provision
    Very pertinent is the need to listen to frontline health care workers as per the Canadian reflections and ensure their protection

  11. Dr. Rey Tiquia says:

    What we do not know so far about the current 2019 novel corona virus, severe acute respiratory syndrome (SARS), swine flu etc is the fact that the outbreak of these epidemics are all seasonally mediated. The current epidemic happening in Wuhan China as well as the SARS epidemic that occurred in Southern China 17 years ago occured in winter and spring season, while the swine flu epidemic we experienced in Australia last June 2009 also occurred in winter <>.

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