Surveillance of seasonal respiratory viruses among Chilean patients during the COVID‐19 pandemic

The StudySARS-CoV-2 has generated over 122 million cases worldwide. Non-pharmaceuticals interventions such as confinements and lockdowns started in Chile on March 18th 2020. In Europe, confinements and lockdowns have been accompanied by a decrease in the circulation of other respiratory viruses such as Influenza A virus(IAV), Influenza B virus(IBV) or respiratory syncytial virus(RSV) (1). Although changes in circulation patterns of respiratory viruses have been reported, limited information regarding the southern hemisphere is available where the SARS-CoV-2 pandemic merged with the winter season. We conducted viral surveillance of respiratory viruses and we evaluated their presence and establishing whether they were co-circulating with SARS-CoV-2.

Few south hemisphere countries reported the same pattern as Europe where non-pharmaceutical measures began before the winter season, 2,3 but to the best of our knowledge, no report has been generated containing information from Chile. Here, we collected 11 093 nasopharyngeal-swab samples (NSS) from 13 healthcare centers belonging part to the northern area of Santiago; the 13 health centers represent all centers to get SARS-CoV-2 tested in the selected area in Santiago of Chile, between 1 April and 31 July 2020 ( Figure 1). All samples were collected from patients with at least one COVID-19 symptom. Six thousand seventy-two samples were determined as positive for SARS-CoV-2. Exactly 58.54% was SARS-CoV-2 positive showed age range between 18 and 50 years reach a 2.27 incidence rate between 31 and 40 years old (Table S1).
Next, based on geographic location, we divided the positive samples into three groups (A, B, and C). Location (A) contains the highest number of SARS-CoV-2 cases, contributing more than 50% of the positive samples analyzed in this study ( Figure 1). This high positivity could be explained by the population density of Location A, which contains at least 4-fold more inhabitants than Locations B and C ( Figure 1). Nevertheless, the health centers located at Location B ( Figure 1) presented an incidence rate (IR) higher than Location A for SARS-CoV2 (Table 1) lyzed. Location C is the farthest location from downtown; however, its IR was 3.82 (Table 1).
Taken together, our data show a high frequency of positive samples throughout the healthcare centers evaluated, suggesting the population density as a risk factor for SARS-CoV-2 transmission because Locations A and B concentrate more population than Location C. These results demonstrate that the 2020 winter season in the northern region of Santiago presented a high incidence of SARS-CoV-2 (Tables 1 and 2).
Then, we made a random collection of 800 samples (400 positive to SARS-CoV-2 and 400 negative) to determine in these samples whether SARS-CoV-2 was co-circulating with other respiratory viruses. We chose predominant respiratory viruses in Santiago (winter season), such as IAV, IBV, RSV, and human rhinovirus (HRV) ( Table 1).
Adenovirus, parainfluenza, and metapneumovirus were not evaluated because they are considered all-year viruses. 4 The results showed three samples with coinfection between IAV and SARS-CoV-2 (Table 1). This is congruent to recent studies in Ecuador and Brazil showing a complete decrease of IAV, 5,6 despite the co-circulation or coinfection between IAV and SARS-CoV-2 observed (Table 1) (Table 1). This is lower than the information from the northern hemisphere, where a range between 2% and 10% has been reported. 9,10 Taken together, these results suggest a lower co-circulation of IAV with SARS-CoV-2 and co-circulation below the level of detection of this study for SARS-CoV-2 together with IBV or RSV.
Finally, we focused on HRV, responsible for more than 50% of the cold-like illnesses, with a high preponderance to coinfection with other respiratory viral pathogens. 11 Furthermore, HRV was the predominant virus after SARS-CoV-2 was detected either co-circulating with SARS-CoV-2 or circulating alone. 9 The presence of HRV was assessed, showing that 0.25% of the samples were coinfected F I G U R E 1 Geographical distribution of the samples analyzed in this study SARS-CoV-2/HRV. On the other hand, the HRV co-circulation was 0.8% (Table 1). These results establish HRV co-circulation and the coinfection with SARS-CoV-2. Taken together, these results demonstrate the displacement of seasonal respiratory viruses due to the presence of SARS-CoV-2. Despite this displacement, IAV and HRV are still able to keep co-circulating together with SARS-CoV-2 but to a considerably lesser extent in comparison with previous winter seasons.

| DISCUSSION
To gain insights into the potential co-circulation of the most relevant seasonally circulating respiratory viruses together with SARS-CoV-2, a fact on the current COVID-19 pandemic was that the vast majority of the SARS-CoV-2 testing during the April-July period was indicated only with the presence of symptoms, we arbitrarily selected 200 samples per month (April to July) for a total of 800 NSS from 13 healthcare centers located in the northern zone of Santiago, Chile.
In SARS-CoV-2 samples, we did not observe any difference between sex; however, there is a 2.27 rate of potential new SARS-CoV-2 cases per 1000 habitants between 18 and 40 years old (Table 1).
We detected a high major IR in Location B (Table 1) with a potential of 20 new cases per 1000 habitants, and we observed at least 2-fold coinfections between SARS-CoV-2/IAV or SARS-CoV-2/HRV and no coinfections with IBV and RSV, which is in agreement with previously reported data including the southern hemisphere. 5,12 Furthermore, IAV and HRV were detected from negative SARS-CoV-2 samples, whereas no presence of IBV or RSV was obtained even from the negative SARS-CoV-2 samples (Table 1)  Note: Six thousand seventy-two patients are considered positive for SARS-CoV-2; however, three patients did not provide any information about age and gender.
phenomenon was observed after the 2009 influenza A (H1N1) pan-