Vigilance for severe respiratory infections

Dr Sean Tobin and Robin Gilmour, Communicable Disease Branch

Hear Sean Tobin talking about flu, AI and MERS

An important part of health protection work is the surveillance for infections that cause severe respiratory infections. Influenza is one of these, and is difficult to control, in part because of its propensity to mutate. Small mutations can occur (known as a “drift” in its genetic makeup) causing annual seasonal influenza outbreaks. Larger changes can occur when different influenza viruses swap genetic material or mutate more substantially (known as a “shift” in its genetic makeup) occasionally causing massive global outbreaks known as pandemics.

Seasonal influenza, caused in recent years mainly by influenza A strains (H1N1 – that emerged with the 2009 “swine flu” pandemic[1], or H3N2 – that emerged with the 1968 “Hong Kong flu” pandemic [2] or influenza B (that only “drifts”), presents an annual challenge for all of us in terms of how to best prevent it, avoid its spread and ensuring people recover quickly from it.

Emerging infections, such as avian influenza A(H7N9) (first identified in parts of China in March 2013 [3]) and MERS coronavirus (first identified in parts of the Middle East in September 2012 [4]) present different challenges. Although neither virus has been shown to efficiently spread from person to person, there are concerns that they may develop the ability to do so, and so NSW Health and other jurisdictions have been developing early warning and response systems to detect and respond to their possible arrival into Australia.

Here we provide an overview of the current situation with each of these potentially dangerous viruses.

Seasonal influenza

Although it’s impossible to predict just how bad the coming flu season will be or exactly when it will occur, we can be certain that influenza will again cause wide-spread disease, hospitalisations and deaths this winter. In recent years, the influenza season has peaked anytime from July to September (see figure 1). Just how widespread depends on several factors, including the virulence of the circulating viral strains (we can get an indication of this from the viruses circulating here last season and in the northern hemisphere’s recent winter), the proportion of the population who have lingering immunity following previous infection with similar strains, and the proportion of the population that has received this season’s vaccine.


In January and February this year, influenza A(H1N1)2009 and influenza A(H3N2) were circulating at higher than usual levels, but have since declined to the usual pre-season levels. Influenza B has circulated at even lower levels. These strains also circulated here in 2013 and have been targeted in the 2014 seasonal influenza vaccine [5]. Moderate to severe influenza activity was reported last winter in the northern hemisphere [6]. The influenza A(H1N1)2009 virus predominated in North America while Europe saw both influenza A strains circulating. Influenza B viruses circulated across many countries but at low levels.

Early indications suggest that the impact of these viruses in NSW may be less than in 2013, given that the strains which are likely to predominate also circulated in 2013 (so many people will have acquired immunity) and that the 2014 vaccine will be better matched to these strains than last year [7]. NSW Health surveillance data indicate that the elderly have been more at risk when influenza A(H3N2) strains circulated compared to years when influenza A(H1N1)2009 was the dominant influenza A strain.

Key prevention messages

For all of us, there are 4 simple prevention messages:

  1. Get vaccinated if you want to avoid influenza. Influenza vaccination is particularly recommended – and is free -- for all people aged ≥ 65 years old, Aboriginal people aged ≥ 15 years old, pregnant women, and all people aged ≥ 6 months with medical conditions predisposing to severe influenza. See: /immunisation/Pages/seasonal_flu_vaccination.aspx
  2. Cover your coughs and sneezes with a tissue and bin the tissue
  3. Wash your hands for at least 15 seconds with soap and running water, or use an alcohol based hand cleaner after you cough or sneeze, and regularly throughout the day
  4. Stay at home if you are sick with symptoms of the flu (fever, cough, runny nose, fatigue, aches and pains) - don’t spread it on public transport, at work, or other crowded areas.

Additional recommendations for health care providers are:

  1. Promote vaccination to patients and staff. Contact your local Public Health Unit for advice on ordering influenza vaccine for staff and patients.
  2. Minimise transmission of influenza in health care facilities:
    • use influenza signs at key locations (such as posters at hospital entrances, waiting areas and wards), and posters to promote respiratory and hand hygiene. Examples of signage are available at the NSW Health Influenza website /infectious/influenza/
    • isolate patients with influenza-like illness by placing bed more than two metres apart, or use between-bed curtains and space beds at least 1 metre apart, or use single rooms if available
    • promote respiratory hygiene and cough etiquette among staff, patients and visitors (such as covering coughs and sneezes, encouraging the use of surgical masks by patients with influenza-like illness)
    • promote hand hygiene according to the current NSW Hand Hygiene policy (PD2010_058)
    • promptly investigate and control respiratory illness outbreaks, especially in high-risk settings
    • report suspected influenza outbreaks to your local Public Health Unit (call 1300 066 055)
    • see Influenza - Minimising Transmission of Influenza in Healthcare Facilities (GL2010_006) for further information.
  3. Treat patients at risk of severe outcomes early – ideally within 48 hours of onset – with influenza antiviral medicines (oseltamivir or zanamivir). Groups for whom treatment may be most useful are: people medically assessed as having moderate or severe influenza, those who show signs of rapidly deterioration, and people with an influenza-like illness (ILI) who are at high-risk of severe influenza because of their underlying conditions. Laboratory confirmation is not necessary prior to commencing antiviral treatment when clinically indicated.

Emerging infections

Avian influenza A(H7N9) in China

As of 28 February 2014, the World Health Organization (WHO) has reported a total of 375 human infections, including 115 deaths, caused by the avian influenza A(H7N9) virus.[8] Of these, 230 cases were reported this year. All cases have been acquired in China, with most presumed to have contracted the infection directly from infected animals or their environment, particularly as a result of visiting live animal markets. WHO reports that there has been no evidence of efficient person-to-person transmission identified to date but there have been several reports of clusters of cases within families. Genetic studies of this virus suggest that there is a real risk that it may trigger a new influenza pandemic. The situation in China is being monitored closely and case management advice has been circulated. For further information see the NSW Health H7N9 Avian Influenza alert.

Middle East respiratory syndrome coronavirus (MERS-CoV)

MERS-CoV continues to cause human infections and presents a serious threat for respiratory disease outbreaks in health-care settings. As of 7 May 2014, WHO has reported 496 laboratory-confirmed cases, including at least 93 deaths since April 2012. [9] To date, all cases have either occurred in the Middle East, have had direct links to a primary case infected in the Middle East, or have returned from this area. Over 200 new MERS-CoV cases have been reported in the past month, including cases exported to the United States, Malaysia and Greece. There is clear evidence of human-to-human transmission to close contacts and in hospital settings, but there is still no evidence of sustained transmission among humans. Although MERS-CoV has been detected in camels in the Middle East, it is still unclear whether infected camels play a role in transmission to humans. See the NSW Health MERS-CoV fact sheet for more information.

Initial management of suspected cases

For clinicians, initial infection control and investigation recommendations are similar when presented with a patient suspected of having either MERS-CoV or avian influenza.

Where a patient presents with acute pneumonia or pneumonitis and has a history of travel to:

  • China within 7 days of illness onset, or contact with known confirmed or probable cases (and therefore AI is suspected)
  • Arabian Peninsula in the 14 days before illness onset, or contact with known confirmed or probable cases in the 14 days before illness onset (and therefore MERS-CoV is suspected) ,


  1. Place the patient in a single room with negative pressure air-handling, or a single room from which the air does not circulate to other areas.
  2. Implement standard and transmission-based precautions (contact and airborne), including the use of personal protective equipment. Airborne transmission precautions include routine use of a P2 respirator, disposable gown, gloves, and eye protection when entering a patient care area. Contact precautions include close attention to hand hygiene. If it is necessary to transfer a confirmed or probable case outside the negative pressure room, then ask the patient to wear a “surgical” face mask while they are being transferred and to follow respiratory hygiene and cough etiquette.
  3. Investigate and manage the patient as for community acquired pneumonia. Appropriate specimens should also be collected for influenza or MERS-CoV PCR testing (depending on the exposure history).
  4. Report suspect cases immediately by phone to your Public Health Unit on 1300 066 055. (Both avian influenza and MERS coronavirus are notifiable under the NSW Public Health Act 2010.)


  1. Girard MP et al. The 2009 A (H1N1) influenza virus pandemic: a review. Vaccine, 2010, 28:4895–4902.doi:10.1016/j.vaccine.2010.05.031 PMID:20553769
  2. Glezen WP. Emerging infections – pandemic influenza. Epidemiol Rev Vol. 18, No. 1, 1996. Accessed at
  3. The fight against bird flu. Nature 496 (7446): 397. April 24, 2013. doi:10.1038/496397a. PMID 23627002
  4. ECDC Novel Coronavirus Rapid Risk Assessment. 26 September 2013.
  5. Australian Influenza Vaccine Committee. AIVC recommendations for the composition of influenza vaccine for Australia in 2014. Accessed at
  6. World Health Organization (WHO). Influenza surveillance updates. Accessed at
  7. NSW Health. Influenza surveillance reports 2014.
  8. World Health Organization. Monthly risk assessment of human infection with influenza A(H7N9) virus. Accessed at
  9. World Health Organization. Middle East respiratory syndrome coronavirus (MERS-CoV) – update - 26 April 2014. Accessed at

Current as at: Monday 26 May 2014
Contact page owner: Health Protection NSW