Coinfections with SARS-CoV-2 and other respiratory pathogens

Hazra, Aniruddha; Collison, Maggie; Pisano, Jennifer; Kumar, Madan; Oehler, Cassandra; Ridgway, Jessica P

doi:10.1017/ice.2020.322

Cited by 58 publications

(69 citation statements)

References 4 publications

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“…Our results suggest that coinfection with other respiratory pathogens could be detected in saliva samples. In the present study, coinfection was uncommon among patients with COVID-19; although the rate was consistent with that reported in previous studies reporting SARS-CoV-2 coinfection rates in NPS samples [28], it was lower than the rate of viral coinfection reported among patients with SARS-CoV-2 using respiratory virome characterization [29]. Determining the coinfection rate and its consequent clinical impacts on COVID-19 is critical, particularly where therapeutic interventions are available for some coinfecting agents such as influenza virus.…”

Section: Discussionsupporting

confidence: 93%

Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings?

Masse

Bonnet

Vilcu

et al. 2021

Viruses

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Background: The present study was set up to evaluate the efficacy of virological surveillance using posterior oropharyngeal saliva samples to monitor the COVID-19 pandemic in general practice. Methods: Posterior oropharyngeal saliva samples were collected without restriction on timing or alimentation by general practitioners from patients with acute respiratory infection (ARI) seen in consultation. Saliva samples were tested by real-time reverse transcription polymerase chain reaction for SARS-CoV-2 and 21 other respiratory pathogens. Results for SARS-CoV-2 in saliva samples were compared to results obtained using a nasopharyngeal swab (NPS) collected in a certified medical laboratory before or after the ARI consultation. Results: Overall, 143 ARI patients were enrolled between 6 June 2020, and 19 January 2021. SARS-CoV-2 RNA was detected in 37.0% (n = 53) of saliva samples and in 39.0% (n = 56) of NPS. Both saliva and NPS were positive in 51 patients. Positive and negative results were concordant between saliva samples and NPS in 51 (96.2%) and in 85 (94.4%) patients, respectively, with a Cohen’s Kappa coefficient of 0.89 (95% CI 0.82–0.97, p < 0.001). Other respiratory viruses were detected in 28.0% (n = 40) of the 143 saliva samples. Conclusions: Findings suggest that saliva samples could represent an attractive alternative to NPS for surveillance of SARS-CoV-2 in patients consulting for an ARI in primary care.

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Section: Discussionsupporting

confidence: 93%

Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings?

Masse

Bonnet

Vilcu

et al. 2021

Viruses

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“…In parallel, the provincial public health laboratory maintained broad, syndromic nucleic acid testing for additional viral and bacterial pathogens, rapidly amassing data on 18 respiratory pathogens from 52,285 respiratory specimens, including SARS-CoV-2. As a result, to our knowledge this study represents the largest singleyear eCoV study [2][3][4][5] and by far the largest eCoV study during the COVID-19 pandemic [7][8][9][10][11][12][13]. This broad testing approach helps to address a pivotal diagnostic gap amidst the emergence of a novel pathogen: co-infection and possible cross-reactivity with other pathogens that can cause similar clinical presentations.…”

Section: Discussionmentioning

confidence: 96%

“…Since SARS-CoV-2 emerged, there has been little research on the concurrent circulation of these other respiratory viruses, which had been the subject of broad surveillance in the years prior [2][3][4][5]: only a handful of case reports have described co-infections between SARS-CoV-2 and other respiratory viruses able to cause similar symptoms [6][7][8][9][10][11][12][13]. With unprecedented demand on clinical diagnostics, re-prioritized surveillance is one of many ways that laboratories have had to prioritize and adapt throughout this pandemic [14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Broad respiratory testing to identify SARS-CoV-2 viral co-circulation and inform diagnostic stewardship in the COVID-19 pandemic

Marshall

Kariyawasam

Zelyas

et al. 2021

Virol J

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Background SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms. Methods This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada (March-May, 2020). By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses. Results SARS-CoV-2 was identified in 2.2% of all specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these SARS-CoV-2-positive specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses. Conclusions Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.

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“…Richardson et al [ 16 ] reported that the rate of co-infection with other pathogens was 2.1% among 5700 COVID-19 patients in New York City. Hazra et al [ 17 ] also reported that at least 1 respiratory pathogen combined with SARS-CoV-2 occurred in 3.3% of detected specimens. These studies suggested that there are relatively great differences in the number and types of co-infecting respiratory pathogens in COVID-19 patients across countries and regions.…”

Section: Discussionmentioning

confidence: 99%

Co-Infection with Common Respiratory Pathogens and SARS-CoV-2 in Patients with COVID-19 Pneumonia and Laboratory Biochemistry Findings: A Retrospective Cross-Sectional Study of 78 Patients from a Single Center in China

et al. 2021

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Coinfections with SARS-CoV-2 and other respiratory pathogens

Cited by 58 publications

References 4 publications

Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings?

Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings?

Broad respiratory testing to identify SARS-CoV-2 viral co-circulation and inform diagnostic stewardship in the COVID-19 pandemic

Co-Infection with Common Respiratory Pathogens and SARS-CoV-2 in Patients with COVID-19 Pneumonia and Laboratory Biochemistry Findings: A Retrospective Cross-Sectional Study of 78 Patients from a Single Center in China

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