Respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) continue to be rare one year into the coronavirus disease 2019 (COVID-19) pandemic in Alberta, Canada (June 2020–May 2021)

Kanji, Jamil N.; Zelyas, Nathan; Granger, David; Wong, Anita; Murphy, Stephanie A.; Buss, Emily; MacDonald, Clayton; Berenger, Byron M.; Diggle, Mathew; Marshall, Natalie C.; Conly, John

doi:10.1017/ice.2021.495

Cited by 7 publications

(9 citation statements)

References 13 publications

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“…Our subgroup analyses revealed that the rate of co‐infection was significantly higher in paediatric than in adult patients (9.39% vs. 3.51%, p ‐value = 0.03). These results are consistent with a recent study examining co‐infection rates for paediatric (10.0%) and adult (2.4%) patients 37 . The immature immune system in the youngest patients compared to adults and the greater interaction of children can explain the higher probability of co‐infection detection.…”

Section: Discussionsupporting

confidence: 92%

“…These results are consistent with a recent study examining co‐infection rates for paediatric (10.0%) and adult (2.4%) patients. 37 The immature immune system in the youngest patients compared to adults and the greater interaction of children can explain the higher probability of co‐infection detection. Although meta‐analysis revealed a small increase in the co‐infection rate for female patients (11.1% in male vs. 15.5% in female, p ‐value = 0.12), the difference did not reach statistical significance.…”

Section: Discussionmentioning

confidence: 99%

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Respiratory viral co‐infections in patients with COVID‐19 and associated outcomes: A systematic review and meta‐analysis

Krumbein

Kümmel

Fragkou

et al. 2022

Reviews in Medical Virology

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The aim of this systematic review and meta‐analysis was to critically assess the published literature related to community‐acquired viral co‐infections and COVID‐19 and to evaluate the prevalence, most identified co‐pathogens, and relevant risk factors. Furthermore, we aimed to examine the clinical features and outcomes of co‐infected compared to mono‐infected COVID‐19 patients. We systematically searched PubMed, Web of Science, Embase, Scopus, and The Cochrane Library for studies published from 1 November 2019 to 13 August 2021. We included patients of all ages and any COVID‐19 severity who were screened for respiratory viral co‐infection within 48 h of COVID‐19 diagnosis. The main outcome was the proportion of patients with a respiratory viral co‐infection. The systematic review was registered to PROSPERO (CRD42021272235). Out of 6053 initially retrieved studies, 59 studies with a total of 16,643 SARS‐CoV‐2 positive patients were included. The global pooled prevalence was 5.01% (95% CI 3.34%–7.27%; I 2 = 95%) based on a random‐effects model, with Influenza Viruses (1.54%) and Enteroviruses (1.32%) being the most prevalent pathogens. Subgroup analyses showed that co‐infection was significantly higher in paediatric (9.39%) than adult (3.51%) patients ( p ‐value = 0.02). Furthermore, co‐infected patients were more likely to be dyspnoeic and the odds of fatality (OR = 1.66) were increased. Although a relatively low proportion of COVID‐19 patients have a respiratory viral co‐infection, our findings show that multiplex viral panel testing may be advisable in patients with compatible symptoms. Indeed, respiratory virus co‐infections may be associated with adverse clinical outcomes and therefore have therapeutic and prognostic implications.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Respiratory viral co‐infections in patients with COVID‐19 and associated outcomes: A systematic review and meta‐analysis

Krumbein

Kümmel

Fragkou

et al. 2022

Reviews in Medical Virology

View full text Add to dashboard Cite

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“…The next two COVID-19 pandemic seasons (2020-2021 and 2021-2022) were dominated by the emergence of the more transmissible Delta and Omicron SARS-CoV-2 variants with immune escape capacity [4], while influenza had a negligible epidemiological and clinical impact if at all [16,17]. The circulation and morbidity burden of other respiratory viruses [e.g., RSV, human metapneumovirus (hMPV), adenoviruses, rhinoviruses] were also highly impacted by the COVID-19 pandemic, with wide temporal and geographic fluctuations [18][19][20][21][22][23][24][25][26].…”

Section: Introductionmentioning

confidence: 99%

COVID-19 and Respiratory Virus Co-Infections: A Systematic Review of the Literature

Maltezou

Papanikolopoulou

Vassiliu

et al. 2023

Viruses

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Τhe COVID-19 pandemic highly impacted the circulation, seasonality, and morbidity burden of several respiratory viruses. We reviewed published cases of SARS-CoV-2 and respiratory virus co-infections as of 12 April 2022. SARS-CoV-2 and influenza co-infections were reported almost exclusively during the first pandemic wave. It is possible that the overall incidence of SARS-CoV-2 co-infections is higher because of the paucity of co-testing for respiratory viruses during the first pandemic waves when mild cases might have been missed. Animal models indicate severe lung pathology and high fatality; nevertheless, the available literature is largely inconclusive regarding the clinical course and prognosis of co-infected patients. Animal models also indicate the importance of considering the sequence timing of each respiratory virus infection; however, there is no such information in reported human cases. Given the differences between 2020 and 2023 in terms of epidemiology and availability of vaccines and specific treatment against COVID-19, it is rational not to extrapolate these early findings to present times. It is expected that the characteristics of SARS-CoV-2 and respiratory virus co-infections will evolve in the upcoming seasons. Multiplex real-time PCR-based assays have been developed in the past two years and should be used to increase diagnostic and infection control capacity, and also for surveillance purposes. Given that COVID-19 and influenza share the same high-risk groups, it is essential that the latter get vaccinated against both viruses. Further studies are needed to elucidate how SARS-CoV-2 and respiratory virus co-infections will be shaped in the upcoming years, in terms of impact and prognosis.

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“…In this study, simultaneous detection of multiple respiratory co-pathogens was performed using both multiplex real-time PCR and multiplex NGS analysis. Several studies have also used multiplex sequencing analysis to detect the presence of co-pathogens [ 13 , 31 , 60 , 61 , 62 ]. By applying target (t) NGS analysis, we identified SARS-CoV-2 variants found in mixed infections similar to those reported in other studies using this approach [ 63 , 64 , 65 ].…”

Section: Discussionmentioning

confidence: 99%

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

Trifonova,

Korsun,

Madzharova

et al. 2024

Viruses

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This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.

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Respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) continue to be rare one year into the coronavirus disease 2019 (COVID-19) pandemic in Alberta, Canada (June 2020–May 2021)

Cited by 7 publications

References 13 publications

Respiratory viral co‐infections in patients with COVID‐19 and associated outcomes: A systematic review and meta‐analysis

Respiratory viral co‐infections in patients with COVID‐19 and associated outcomes: A systematic review and meta‐analysis

COVID-19 and Respiratory Virus Co-Infections: A Systematic Review of the Literature

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

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