Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador

Abstract

Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2–7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4–5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76–6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.

Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

“…Many studies conducted during the COVID-19 pandemic reported possible coinfections of SARS-CoV-2 with other respiratory pathogens, including bacteria, fungi, and viruses [ 12 , 34 , 35 ]. In our three-year follow-up study, a rate of 7.2% of coinfections was detected, which is consistent with other reports [ 4 , 36 , 37 ].…”

“…A study conducted in Italy between 2021 and 2022 also reported a high prevalence of RSV coinfection with SARS-CoV-2 in children [ 38 ]. Similarly, a 2020–2021 study in Ecuador found RSV to be the second most common co-pathogen after influenza A [ 35 ]. Much of the research conducted early in the pandemic reported the presence of coinfections [ 14 , 34 , 39 ].…”

“…The COVID-19 pandemic affected the prevalence, seasonality, and incidence of seasonal respiratory viral infections, which also had an impact on the epidemiology of coinfections [ 35 ]. At the beginning of the pandemic, strict anti-epidemic measures were implemented that resulted in a low rate of reported coinfections, even in countries with a high prevalence of SARS-CoV-2 [ 41 ].…”

SARS-CoV-2 co-detection with influenza and human respiratory syncytial virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022

“…In Ecuador, co-infections with other respiratory viruses were detected in 12% of SARSCoV-2-positive patients. The most prevalent co-infection was with influenza virus at 4.4%, followed by respiratory syncytial virus with 3.1% [11].…”

“…Firstly, in high-risk COVID-19 patients (older adults, children, and COPD patients), co-infection can exacerbate the condition and raise the chance of death [3,16] A severe inflammatory process that results in lung damage, an extended hospital stays, a change in the course and length of treatment, and a higher death rate are just some of the clinical implications associated with increased complications [11,17,18]. In addition, co-infections in outpatients may alter the way respiratory pathogens spread in community settings, putting vulnerable groups like children and the elderly at risk and enabling viruses to infect families and community groups [11]. Therefore, early detection of co-infection may help to initiate proper management to avoid unnecessary complications and to reduce the transmission.…”