key: cord-252761-ro5tj0tx
authors: Marriott, Deborah; Beresford, Rohan; Mirdad, Feras; Stark, Damien; Glanville, Allan; Chapman, Scott; Harkness, Jock; Dore, Gregory J; Andresen, David; Matthews, Gail V
title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW.
date: 2020-08-25
journal: Clin Infect Dis
DOI: 10.1093/cid/ciaa1256
sha: 
doc_id: 252761
cord_uid: ro5tj0tx

Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. Following travel bans and physical distancing, SARS-CoV-2 and other respiratory viruses diagnoses fell dramatically. Increasing rhinovirus diagnoses as social control measures were relaxed may indirectly indicate an elevated risk of COVID-19 resurgence

A c c e p t e d M a n u s c r i p t diagnoses increased rapidly to a peak of 460 daily cases on 28 th March, before declining to fewer than less than ten per day by mid-April. Stage 3 requirements were relaxed by the end of April and by mid-May restaurants and businesses had largely re-opened. By 14 th May a total of 6,989 COVID-19 cases had been diagnosed, with almost half in New South Wales (NSW). 6 A screening service for SARS-CoV-2, using a multiplex PCR assay was established on 9 th March at St. Vincent"s Hospital, a University-affiliated hospital in inner-Sydney, NSW. Two community satellite testing services were opened in April. We report the prevalence of SARS-CoV-2 and other respiratory pathogens including co-infection, and evaluate the A c c e p t e d M a n u s c r i p t 4 temporal pattern of respiratory infections alongside the introduction, and subsequent relaxation, of physical distancing measures.

Nasopharyngeal (NP) swabs were collected by trained nurses using appropriate infection control measures at the dedicated COVID-19 clinic at St Vincent"s Hospital and satellite clinics at Bondi Beach and East Sydney. Testing was performed in the hospital Emergency Department (ED) when clinically indicated. A small proportion of specimens were referred from other sites such as rural laboratories, correctional facilities and general practitioners.

Testing was carried out in accordance with NSW Health policy during the study period.

Initially, testing was offered to individuals with respiratory symptoms who had returned from overseas, had severe respiratory illness, had been in contact with a known COVID-19 case, or had healthcare employment. These criteria were subsequently expanded to include anyone with fever or respiratory symptoms in local "hot spots" (30 th March 2020), defined 

Over the eleven-week period from 12 th March to 27 th May 2020, 21,808 people were tested. The proportion of people in whom any respiratory pathogen was detected declined markedly during the study period, from 32.5% in week one to 3.1% in week eight before rising again to 12.9% in week 11 (Figure) (p<0.001 for each subsequent week, compared to baseline, in a two-sample test of proportions). In most cases a greater than 10-fold reduction was observed: rhinovirus, 19.9% to 1.7% (before increasing again to 11.8% by late-May); parainfluenza, A c c e p t e d M a n u s c r i p t 6 3.0% to 0.1%; and non-SARS-COV-2 coronaviruses, 2.3% to less than 0.1%. Of note, nonviral respiratory pathogens such as Bordetella pertussis, Mycoplasma pneumoniae and Pneumocystis jiroveci did not demonstrate marked reduction. (Supplementary Table) .

At a major hospital serving the initial geographical epicentre of Australian SARS-CoV-2 diagnoses, 175 cases were identified over an 11-week period. Despite the broadening of testing criteria, an increase in total testing numbers, and a move into cooler months, SARS- CoV-2 cases to similarly rise supports the absence of circulating SARS CoV-2 in the NSW community during that period, but the increased rhinovirus transmission does raise concern that SARS CoV-2 may also spread readily if reintroduced. Singaporean report 10 showed a 76% reduction over historical rates. To our knowledge, ours is the first report from the Southern hemisphere demonstrating a reduction during a move into the cooler months, and also the first to document simultaneous trends in other infectious respiratory pathogens.

Among individuals with SARS-CoV-2, 5% had co-infection with other respiratory pathogens, with rhinovirus most common. Limited data have been reported on co-infection between SARS-CoV-2 and other respiratory viruses. In a Seattle surveillance study, 11 4 of 25 people (16%) with SARS-CoV-2 had rhinovirus coinfections. Interestingly, in that study (as in ours) no coinfections between SARS-CoV-2 and non-pandemic coronaviruses were found. This raises the hypothesis that co-exposure to different human coronaviruses may lead to only one establishing infection, or that shared viral epitopes lead to some degree of cross-immunity within the coronavirus group. A Californian report, 12 however, has shown occasional coinfections between SARS-CoV-2 and non-pandemic coronaviruses.

There are some key limitations of our study. Firstly, during the eleven-week period the SARS-CoV-2 testing criteria changed, with broadened testing initially in local geographical "hotspots" then our entire catchment area. However, guidance was consistent that only people with fever or other respiratory tract symptoms should be tested. Secondly, detailed data on A c c e p t e d M a n u s c r i p t 8 the timing of testing in relation to symptom onset were not available. In general, however, most people were tested within a few days of symptom onset, when SARS-CoV-2 should have remained detectable. Thirdly, we are unable to determine which SARS-CoV-2 prevention measures had the greatest impact on respiratory virus prevalence, as they were introduced in rapid succession. It is also unclear how much impact a shift in SARS-CoV-2 cases from largely returned overseas travellers (predominantly from North America and Europe) to locally acquired cases had on temporal trends in respiratory viral pathogen prevalence. Higher prevalence of all respiratory viral pathogens would have been expected among returned travellers from the Northern Hemisphere late in the Northern winter, and these may have reduced naturally over time even without local COVID-19 prevention measures. Our study period is too short however to assess any seasonal trends.

In conclusion, the introduction of multiple public health measures to minimise SARS-CoV-2 transmission in Australia from mid to late-March 2020 had a major impact on the prevalence of all respiratory viral infections highlighting the effectiveness of this approach. Changes in the prevalence of circulating respiratory viruses may provide a useful reflection of the success of ongoing measures including physical distancing restrictions. M a n u s c r i p t 11 9. Kuo S-C et al (2020 

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