cdi.2020.44.30 COVID-19, Australia: Epidemiology Report 10€¦ · tion of cases of COVID-19 in Australia. Of cases with a reported place of acquisition, 16% (n = 903) were acquired

2 0 2 0 V o l u m e 4 4https://doi.org/10.33321/cdi.2020.44.30

COVID-19, Australia: Epidemiology Report 10:Reporting week ending 23:59 AEST 5 April 2020

COVID-19 National Incident Room Surveillance Team

Communicable Diseases Intelligence ISSN: 2209-6051 Online

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1 of 21 health.gov.au/cdi Commun Dis Intell (2018) 2020;44 (https://doi.org/10.33321/cdi.2020.44.30) Epub 9/4/2020

Weekly epidemiological report

COVID-19, Australia: Epidemiology Report 10:Reporting week ending 23:59 AEST 5 April 2020

COVID-19 National Incident Room Surveillance Team

Notified cases of COVID-19 and associated deaths reported to the National Notifiable Diseases Surveillance System (NNDSS) to 5 April 2020.

Summary

Notifications in Australia remain predomi-nantly among people with recent overseas travel, with some locally-acquired cases being detected. Most locally-acquired cases are able to be linked back to a confirmed case, with a small portion unable to be epidemiologically linked. The dis-tribution of overseas-acquired cases to locally acquired cases varies by jurisdiction.

Early indications are that reduction in interna-tional travel, domestic movement, social dis-tancing measures and public health action are slowing the spread of the disease (Figure 1).

Internationally, cases continue to increase, with high rates of increase observed in the European

Confirmed cases in Australia notified up to 5 April 2020i

Notifications 5,805

Deaths 33

region and the United States of America. The epidemiology differs from country to country depending not only on the disease, but also on differences in case detection, testing and imple-mented public health measures.

Keywords: SARS-CoV-2; novel coronavirus; 2019-nCoV; coronavirus disease 2019; COVID-19; acute respiratory disease; case definition; epidemiology; Australia

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dynamic nature of the NNDSS, data in this extract are subject to retrospective revision and may vary from data reported in published

NNDSS reports and reports of notification data by states and territories.

2 of 21 health.gov.au/cdiCommun Dis Intell (2018) 2020;44 (https://doi.org/10.33321/cdi.2020.44.30) Epub 9/4/2020

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Australian cases: descriptive epidemiology

National trends

• Over the past week, 1,646 cases of COVID-19 were notified to the NNDSS, bringing the total number of confirmed cases notified in Australia to 5,805 (up to 23:59 AEST 5 April 2020). This is a 30% decrease in weekly new cases compared to the previous reporting period (n = 2,355);

• Forty-one cases (0.8%) have been reported in Aboriginal and Torres Strait Islander persons since the start of the outbreak. These cases were reported across several jurisdictions, with the majority reported in areas classi-fied as ‘major cities of Australia’ based on the case’s usual place of residence. Across all Australian cases, completeness of the Indig-enous status field was approximately 79%,

with 21% of cases with a reported value of ‘unknown’; and

• The median time between onset of symptoms and laboratory testing was 3 days (range 0–42 days).

Geographical Distribution

• Cases of COVID-19 continue to be reported at varying rates in all jurisdictions (Table 1);

• New South Wales had the highest rate of COVID-19 notifications (32.9 per 100,000) and the Northern Territory had the lowest (11.0 per 100,000); and

• Most cases were reported to reside in major metropolitan areas, with a small number of cases residing outside these areas (Figure 2 and Figure 3).

Table 1: Notifications and rates of COVID-19 and diagnostic tests performed, Australia, by jurisdiction

Jurisdiction Number of new cases this reporting period (00:00 AEDT 30 March to 23:59 AEST 5 April 2020)

Total cases(to 23:59 AEST 5 April 2020)

Rate(per 100,000 population)

Cumulative number of tests performed (proportion of tests positive %)

NSW 678 2,659 32.9 121,443 (2.2%)

Vic 494 1,167 17.7 56,000 (2.1%)

Qld 193 931 18.3 57,795 (1.6%)

WA 131 444 16.9 18,197 (2.4%)

SA 105 409 23.3 32,863 (1.2%)

Tas 17 76 14.2 2,845 (2.7%)

NT 13 27 11.0 2,753 (1.0%)

ACT 15 92 21.6 5,258 (1.7%)

Australia 1,646 5,805 22.9 297,154 (2.0%)


Age and gender distribution

• Cases of COVID-19 were reported across all age groups. The median age of all COVID-19 cases was 47 years (range: 0 to 100 years);

• The number of cases was highest in the 20–29 years age group, and the highest rate of disease was among those in the 60–69 years age group (Figure 4); and

• Notifications by gender were approximately equal, although there was some variation across age groups.

Source of infection

• To date, most of the reported COVID-19 cases in Australia acquired their infection overseas;

• Of cases with a reported place of acquisition, 66% had a recent international travel history and 32% were considered to have been lo-cally acquired (Figure 5):

◦ The majority of overseas-acquired cases reported a travel history to the Euro-pean Region, the Americas Region or on board cruise ships (Figure 6);

◦ Of the locally-acquired cases, most were considered to be contacts of a confirmed case, with a very small proportion of cases not able to be epidemiologically linked to a confirmed case; and

◦ Cases where a place of acquisition has not been reported (2%) are currently under public health investigation.

Cluster and outbreak investigations

Investigations are taking place in states and ter-ritories in relation to a number of clusters and outbreaks of COVID-19. To date the largest out-breaks have been associated with cruise ships.

Cruise ships account for a substantial propor-tion of cases of COVID-19 in Australia. Of cases with a reported place of acquisition, 16% (n = 903) were acquired at sea on a cruise ship. This is a 35% increase in COVID-19 cases acquired on a cruise ship since the last reporting period. There have been 14 deaths among cases acquired on cruise ships in Australia.

Cluster:

• The term ‘cluster’ in relation to COV-ID-19 refers to two or more cases that are epidemiologically related in time, place or person where a common source (such as an event or within a commu-nity) of infection is suspected but not yet established.

Outbreak:

• The term ‘outbreak’ in relation to COVID-19 refers to two or more cases among a specific group of people and/or over a specific period of time where illness is associated with a common source (such as an event or within a community).


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Figure 7: Variation in combinations of COVID-19 symptoms in confirmed cases, Australiaa

a This figure shows the variation in combinations of symptoms observed in reported cases (n = 4,237) for the five most frequently

observed symptoms (cough, fever, sore throat, headache, runny nose). The horizontal bars on the left show the frequency of symptom

occurrence in any combination with other symptoms. The circles and lines indicate particular combinations of symptoms observed in

individual patients. The vertical green bars indicate the frequency of occurrence of the corresponding combination of symptoms


Symptom profile

• Of the symptoms reported, cough (71%) was the most common (Figure 7);

• Forty-nine percent reported fever, 44% reported sore throat, and 39% reported headache. Only 4% or fewer of all cases re-ported either pneumonia or acute respiratory disease (ARD); and

• In addition, loss of taste was reported from 324 cases and loss of smell from 322 cases. These conditions were reported in at least 5.5% of cases, noting that this is currently not a standard field in NNDSS, and is likely to under-represent those presenting with these symptoms.

Severity

• Of the total cases of COVID-19 (n = 5,805) notified, 11% (n = 628) were admitted to hospital:

◦ The median age of hospitalised cases was 59.5 years (range 0–94 years), with the highest proportion of hospitalised cases in the 60–69 years age group:

◦ The most commonly reported comor-bid condition among hospitalised cases was cardiac disease (7.5%), followed by diabetes (7.2%);

• Of the hospitalised COVID-19 cases, 13% (n = 82) were admitted to an intensive care unit (ICU), with 29 cases requiring ventilation;

• Thirty-three COVID-19 associated deaths were confirmed in Australia up to 5 April 2020:

◦ The median age of cases who died was 80 years (range 60–94 years);

◦ 21 of the cases were male and 12 were female; and

◦ The most commonly reported comorbid conditions among COVID-19 deaths were chronic respiratory conditions (15%) and diabetes (15%).

Additional surveillance activities

Enhanced surveillance within schools and child care settings

The National Centre for Immunisation Research and Surveillance (NCIRS) and the NSW Ministry of Health have commenced an investigation into the transmission of SARS COV-2 in school and child-care centre settings. Preliminary find-ings suggest low onward transmission among children with 1.9% of close contacts who were children testing positive for the virus.

This investigation includes follow up of labora-tory notifications and in some settings enhanced clinical investigation including additional ques-tionnaire, active nasopharyngeal sampling and serology testing of close contacts via school/home visiting teams.


Preliminary activities and findings to date:

• Twenty-one educational settings with COVID cases have been identified to date: eleven secondary schools, two primary schools, and eight childcare centres;

• Index cases have been adult staff in ten sites and children in eleven sites;

• Total close contacts identified were: 903 chil-dren and 179 staff from 17 sites (contact lists are pending for 4 sites);

• Enhanced investigations is underway in five sites, with three additional sites in planning stage; and

• Of the 16 sites where nasopharyngeal sam-pling nucleic acid testing data is available for close contacts:

◦ 7/361 children tested and 7/84 adults tested have been positive for SARS-CoV-2 within the 14 days after last known exposure.

Results of serologic testing (in symptomatic and asymptomatic contacts) is pending for some sites and will be reported when available.

Results presented are preliminary and are sub-ject to change as the study progress, and as such should be interpreted with caution.

Public health response

Since COVID-19 first emerged internationally, Australia has implemented public health meas-ures in response to the disease’s epidemiology, both overseas and in Australia. During the current reporting period, the Australian Health Protection Principal Committee (AHPPC) has issued advice to inform the national public health response to the pandemic including manage-ment of Early Childhood and Learning Centres (ECLC) in relation to community transmission of COVID-19, special provisions to vulnerable people in the workplace, and regional additional

social distancing measures. As part of the com-prehensive public health response taking place across Australia, social distancing plays a vital role in reducing transmission and flattening the curve. Additional public health responses are listed below in Table 2.


Tabl

e 2:

Tim

elin

e of

key

CO

VID

-19

rela

ted

even

ts, i

nclu

ding

Aus

tral

ian

publ

ic h

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resp

onse

act

iviti

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31

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r 201

9 to

5 A

pril

2020

.

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eEv

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resp

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2020

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ses

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ures

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cons

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ces

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International situation3

• As at 23:59 AEST 5 April 2020, the number of confirmed COVID-19 cases reported to the World Health Organization (WHO) was 1,133,758 globally;

• The number of new cases reported glob-ally has continued to increase. As of the last reporting week, with COVID-19 reported across a total of 199 countries, territories and areas;

• The reported epidemiology varies by country with different trajectories of outbreaks after their first 100 cases. Figure 8 highlights that for a number of countries outside of main-land China which have reported more than 100 cases, their rates of increase continue to be high, particularly USA, Spain and Italy. For several other countries or regions includ-ing Hong Kong, Singapore and Japan, there continues to be a slow rate of increase in their number of new cases, with the Republic of Korea reporting very few new cases each day. Reported case numbers will be influ-enced by rates of testing, case definition, and case detection as well as overall health system capacity;

• Globally, 62,784 deaths have been reported. The risk of death is reported to increase with age; and

• The case fatality rate is reported as ap-proximately 6%. This is highly likely to be an overestimate due to variable levels of under-ascertainment of cases, especially those with mild infections. For several other countries or regions including Japan and Republic of Korea, there continues to be a slow increase in their number of deaths, with both coun-tries reporting few new deaths each day (Figure 9).

Background

The current estimates on epidemiological param-eters including severity, transmissibility and incubation period are uncertain. Estimates are likely to change as more information becomes available.

Transmission

• Human-to-human transmission of SARS-CoV-2 is via droplets and fomites from an infected person to a close contact;4

• A virological analysis of nine hospitalised cases found active virus replication in up-per respiratory tract tissues, with pharyn-geal virus shedding during the first week of symptoms. However, current evidence does not support airborne or faecal-oral spread as major factors in transmission;

• A study in China showed an association between household contacts and travel with a confirmed COVID-19 case and an increased risk of infection;5 and

• A recent study suggests that children do not play a key role in household transmission and are unlikely to be the primary source of household infections.6

Incubation period

• Estimates of median incubation period, based on seven published studies, are 5 to 6 days (ranging from 0 to 14 days). Patients with long incubation periods do occasionally occur, however they are likely to be ‘outliers’ who should be studied further but are un-likely to represent a change in epidemiology of the virus.7,8


Molecular epidemiology

• Since December 2019, the virus has diversi-fied into multiple lineages as it has spread globally with some degree of geographical clustering;

• The whole genome sequences currently available from Australian cases are mostly in returned travellers from China, the Islamic Republic of Iran, Europe and the USA, and thereby reflect this global diversity; and

• Recent work describes an emerging clade linked to the epidemic in the Islamic Repub-lic of Iran.9

Clinical features

• COVID-19 presents as mild illness in the majority of cases with cough and fever being the most commonly reported symptoms. Severe or fatal outcomes are more likely to occur in the elderly or those with comorbid conditions;4,10

• Some COVID-19 patients show neurological signs such as headache, nausea and vomiting. There is evidence that SARS-CoV-2 viruses are not always confined to the respiratory tract and may invade the central nervous system inducing neurological symptoms. As such, it is possible that invasion of the central nervous system is partially responsible for the acute respiratory failure of COVID-19 patients;11

• There is some evidence to suggest that reduc-tion or loss of the sense of smell (hyposmia/anosmia) or taste (hypoguesia/aguesia) is associated with COVID-19.12,13 This is sup-ported by research finding a biological mechanism for the SARS-CoV-2 virus to cause olfactory dysfunction;14,15

• Examination of cases and their close con-tacts in China found a positive association between age and time from symptom onset to recovery. The study also found an associa-

tion between clinical severity and time from symptom onset to time to recovery. Com-pared to people with mild disease, those with moderate and severe disease were associ-ated with a 19% and 58% increase in time to recovery, respectively;5 and

• Several studies have identified cardiovascu-lar implications resulting from COVID-19 infection. Vascular inflammation has been observed in a number of cases and may be a potential mechanism for myocardial injury which can result in cardiac dysfunction and arrhythmias.

Treatment

• Current clinical management of COVID-19 cases focuses on early recognition, isolation, appropriate infection control measures and provision of supportive care.16 Whilst there is no specific antiviral treatment currently recommended for patients with suspected or confirmed SARS-CoV-2 infection, mul-tiple clinical trials are underway to evaluate a number of therapeutic agents, including remdesivir, lopinavir/ritonavir, and chloro-quine.17

Data considerations

Data were extracted from the NNDSS on 7 April 2020, by diagnosis date. Due to the dynamic nature of the NNDSS, data in this extract are subject to retrospective revision and may vary from data reported in published NNDSS reports and reports of notification data by states and territories.


Acknowledgements

This report represents surveillance data reported through CDNA as part of the nationally-coordi-nated response to COVID-19. We thank public health staff from incident emergency operations centres in state and territory health departments, and the Australian Government Department of Health, along with state and territory public health laboratories. We thank John Grewar for providing the R-code to produce Figure 7.

Author details

Corresponding author

COVID-19 National Incident Room Surveillance Team, Communicable Disease Epidemiology and Surveillance Section, Health Protection Policy Branch, Australian Government Department of Health, GPO Box 9484, MDP 14, Canberra, ACT 2601.

Email: [email protected]

References

1. Australian Government Department of Health. Australian Health Protection Princi-pal Committee (AHPPC) coronavirus (COV-ID-19) statement on 3 April 2020. [Internet.] Canberra: Australian Government Depart-ment of Health; 2020. [Accessed 8 April 2020.] Available from: https://www.health.gov.au/news/australian-health-protection-principal-committee-ahppc-coronavirus-covid-19-statement-on-3-april-2020.

2. Australian Government Department of Health. Australian Health Protection Princi-pal Committee (AHPPC) Advice to National Cabinet on 30 March 2020. [Internet.] Can-berra: Australian Government Department of Health; 2020. [Accessed 8 April 2020.] Available from: https://www.health.gov.au/news/australian-health-protection-principal-committee-ahppc-advice-to-national-cabi-net-on-30-march-2020.

3. World Health Organization (WHO). Coro-navirus disease 2019 (COVID-19) situation report – 76. [Internet.] Geneva: WHO; 2020. [Accessed 8 April 2020.] Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200405-sitrep-76-covid-19.pdf.

4. WHO. Report of the WHO-China joint mission on coronavirus disease 2019 (COV-ID-19). [Internet.] Geneva: WHO; 2020. [Ac-cessed 1 Mar 2020.] Available from: https://www.who.int/docs/default-source/corona-viruse/who-china-joint-mission-on-covid-19-final-report.pdf.

5. Bi Q, Wu Y, Mei S, Ye C, Zou X, Zhang Z et al. Epidemiology and transmission of COVID-19 in Shenzhen China: analysis of 391 cases and 1286 of their close contacts. medRxiv. 2020. doi: https://doi.org/10.1101/2020.03.03.20028423.

6. Zhu Y, Bloxham CJ, Hulme KD, Sinclair JE, Tong ZW, Steele LE et al. Children are un-


likely to have been the primary source of household SARS-CoV-2 infections. medRxiv. 2020. doi: https://doi.org/10.1101/2020.03.26.20044826.

7. WHO. Coronavirus disease 2019 (COV-ID-19) situation report – 29. [Internet.] Geneva: WHO; 2020. [Accessed 22 Feb 2020.] Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200218-sitrep-29-covid-19.pdf.

8. Pung R, Chiew CJ, Young BE, Chin S, Chen M, Clapham HE. Investigation of three clusters of COVID-19 in Singapore: implica-tions for surveillance and response measures. Lancet. 2020;395(10229):1039–46.

9. Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. bioRxiv. 2020. doi: https://doi.org/10.1101/2020.03.15.992818.

10. Sun P, Qiu S, Liu Z, Ren J, Xi JJ. Clinical characteristics of 50466 patients with 2019-nCoV infection. medRxiv. 2020. doi: https://doi.org/10.1101/2020.02.18.20024539.

11. Li B, Bai W, Hashikawa T. The neuroinvasive potential of SARS-CoV-2 may be at least par-tially responsible for the respiratory failure of COVID-19 patients. J Med Virol. 2020. doi: https://doi.org/10.1002/jmv.25728.

12. Mao L, Wang M, Chen S, He Q, Chang J, Hong C et al. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. medRxiv. 2020. doi: https://doi.org/10.1101/2020.02.22.20026500.

13. Drew DA, Nguyen LH, Steves CJ, Wolf J, Spector TC, Chan AT. Rapid implementation of mobile technology for real-time epide-miology of COVID-19. medRxiv. 2020. doi: https://doi.org/10.1101/2020.04.02.20051334.

14. Venkatakrishnan AJ, Puranik A, Anand

A, Zemmour D, Yao X, Wu X et al. Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus re-ceptors. bioRxiv. 2020. doi: https://doi.org/10.1101/2020.03.24.005702.

15. Brann DH, Tsukahara T, Weinreb C, Lo-gan DW, Datta SR. Non-neural expres-sion of SARS-CoV-2 entry genes in the olfactory epithelium suggests mecha-nisms underlying anosmia in COVID-19 patients. bioRxiv. 2020. doi: https://doi.org/10.1101/2020.03.25.009084.

16. WHO. Clinical management of severe acute respiratory infection when novel coronavirus (nCoV) infection is suspected. [Internet.] Geneva: WHO; 2020. [Accessed 23 Feb 2020.] Available from: https://www.who.int/publications-detail/clinical-management-of-severe-acute-respiratory-infection-when-novel-coronavirus-(ncov)-infection-is-sus-pected.

17. Harrison C. Coronavirus puts drug re-purposing on the fast track. Nat Biotechnol. 2020. doi: https://doi.org/10.1038/d41587-020-00003-1.


Appendix A: Frequently asked questions

Q: Can I request access to the COVID-19 data behind your CDI weekly reports?

A: National notification data on COVID-19 confirmed cases is collated in the National Notifiable Disease Surveillance System (NNDSS) based on notifications made to state and territory health authorities under the provisions of their relevant public health legislation.

Normally, requests for the release of data from the NNDSS requires agreement from states and territories via the Communicable Diseases Network Australia, and, depending on the sensitivity of the data sought and proposed, ethics approval may also be required.

Due to the COVID-19 response, unfortunately, specific requests for NNDSS data have been put on hold. We are currently looking into options to be able to respond to data requests in the near future.

We will continue to publish regular summaries and analyses of the NNDSS dataset and recom-mend the following resources be referred to in the meantime:

• NNDSS summary tables: http://www9.health.gov.au/cda/source/cda-index.cfm

• Daily case summary of cases: https://www.health.gov.au/news/health-alerts/novel-coronavirus-2019-ncov-health-alert/corona-virus-covid-19-current-situation-and-case-numbers

• Communicable Diseases Intelligence COV-ID-19 weekly epidemiology report: https://www1.health.gov.au/internet/main/publish-ing.nsf/Content/novel_coronavirus_2019_ncov_weekly_epidemiology_reports_aus-tralia_2020.htm

• State and territory public health websites.

Q: Can I request access to data at post-code level of confirmed cases?

A: Data at this level cannot be released without ethics approval and permission would need to be sought from all states and territories via the Communicable Diseases Network Australia. As noted above, specific requests for NNDSS data are currently on hold.

A GIS/mapping analysis of cases will be included in each Communicable Diseases Intelligence COVID-19 weekly epidemiology report. In order to protect privacy of confirmed cases, data in this map will be presented at SA3 level.

Q. Where can I find more detailed data on COVID-19 cases?

A: We are currently looking into ways to pro-vide more in-depth epidemiological analyses of COVID-19 cases, with regard to transmission and severity, including hospitalisation. These analyses will continue to be built upon in future iterations of the weekly Communicable Diseases Intelligence report.

Documents

cdi.2020.44.30 COVID-19, Australia: Epidemiology Report 10€¦ · tion of cases of COVID-19 in Australia. Of cases with a reported place of acquisition, 16% (n = 903) were acquired