Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance

Tang, Julian W.; Lam, Tommy Tsan-Yuk; Zaraket, Hassan; Lipkin, W. Ian; Drews, Steven J.; Hatchette, Todd F.; Heraud, Jean‐Michel; Koopmans, Marion; Abraham, Asha Mary; Baraket, Amal; Bialasiewicz, Seweryn; Caniza, Miguela; Chan, Paul K.S.; Cohen, Cheryl; Corriveau, André; Cowling, Benjamin J.; Echavarría, Marcela; Fouchier, Ron A. M.; Fraaij, Pieter LA; Hachette, Todd F; Jalal, Hamid; Jennings, Lance C.; Kabanda, Alice; Kadjo, Hervé A.; Khanani, Rafiq; Koay, Evelyn S C; Krajden, Mel; Lee, Hong Kai; Lutwama, Julius J.; Marchant, David; Nishimura, Hidekazu; Nymadawa, Pagbajabyn; Pinsky, Benjamin A.; Rughooputh, Sanjiv; Rukelibuga, Joseph; Saiyed, Taslimarif; Shet, Anita; Sloots, Theo P.; Tamfum, JJ Muyembe; Tempia, Stefano; Tozer, Sarah; Treurnicht, Florette K.; Waris, Matti; Watanabe, Aripuanã Sakurada Aranha; Wemakoy, Emile Okitolonda

doi:10.1016/s1473-3099(17)30238-4

Cited by 107 publications

(109 citation statements)

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“…Currently, although the full INSPIRE network does include multiple members in Africa and those with collaborators in South America, 8 this current study does lack large data sets from these continents. This is mainly due to a lack of funding for routine screening for non-influenza respiratory viruses.…”

Section: Discussionmentioning

confidence: 99%

“…A global network of collaborators with shared clinical, public health, and epidemiological research interests in respiratory viruses was recently established -the I nternational N etwork for the S equencing of Res pir atory Virus e s (INSPIRE). 8 This long-term INSPIRE project aims to share viral incidence and other related data, obtained through routine diagnostic testing, in a crosssectional, contemporaneous manner to reveal and compare reallife (i.e. outside of prospective, planned studies) global trends in viral epidemiology and feed into potential healthcare burden estimates.…”

Section: Introductionmentioning

confidence: 99%

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Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015

Lam

Tang

Lai

et al. 2019

Journal of Infection

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s u m m a r yObjectives: To improve our understanding of the global epidemiology of common respiratory viruses by analysing their contemporaneous incidence at multiple sites. Methods: 2010-2015 incidence data for influenza A (IAV), influenza B (IBV), respiratory syncytial (RSV) and parainfluenza (PIV) virus infections were collected from 18 sites (14 countries), consisting of local ( n = 6), regional ( n = 9) and national ( n = 3) laboratories using molecular diagnostic methods. Each site submitted monthly virus incidence data, together with details of their patient populations tested and diagnostic assays used.Results: For the Northern Hemisphere temperate countries, the IAV, IBV and RSV incidence peaks were 2-6 months out of phase with those in the Southern Hemisphere, with IAV having a sharp out-of-phase difference at 6 months, whereas IBV and RSV showed more variable out-of-phase differences of 2-6 months. The tropical sites Singapore and Kuala Lumpur showed fluctuating incidence of these viruses throughout the year, whereas subtropical sites such as Hong Kong, Brisbane and Sydney showed distinctive biannual peaks for IAV but not for RSV and PIV. Conclusions: There was a notable pattern of synchrony of IAV, IBV and RSV incidence peaks globally, and within countries with multiple sampling sites (Canada, UK, Australia), despite significant distances between these sites.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015

Lam

Tang

Lai

et al. 2019

Journal of Infection

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“…If they were not already, RNA viruses have become the star child of evolutionary biologists, whether for day-by-day or eon-by-eon examples of evolution (Koonin, 2007;Koonin et al, 2008Koonin et al, , 2015Shi et al, 2016;Xue et al, 2017). With our world expanded and our place in it shrunk, there is still much to do regarding viral sequencing for our own quotidian human RNA viruses (Tang et al, 2017). There is but one way to ensure that we find no more viruses.…”

Section: Make It Stopmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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“…Influenza and acute respiratory infections (ARI) are major contributors to disease burden in the pediatric age group with highest mortality rates in resource‐limited settings …”

Section: Introductionmentioning

confidence: 99%

Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review

Conrad

Alchikh

et al. 2018

Reviews in Medical Virology

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Studies have shown that the predictive value of "clinical diagnoses" of influenza and other respiratory viral infections is low, especially in children. In routine care, pediatricians often resort to clinical diagnoses, even in the absence of robust evidence-based criteria. We used a dual approach to identify clinical characteristics that may help to differentiate infections with common pathogens including influenza, respiratory syncytial virus, adenovirus, metapneumovirus, rhinovirus, bocavirus-1, coronaviruses, or parainfluenza virus: (a) systematic review and meta-analysis of 47 clinical studies published in Medline (June 1996 to March 2017, PROSPERO registration number: CRD42017059557) comprising 49 858 individuals and (b) data-driven analysis of an inception cohort of 6073 children with ILI (aged 0-18 years, 56% male, December 2009 to March 2015) examined at the point of care in addition to blinded PCR testing. We determined pooled odds ratios for the literature analysis and compared these to odds ratios based on the clinical cohort dataset. This combined analysis suggested significant associations between influenza and fever or headache, as well as between respiratory syncytial virus infection and cough, dyspnea, and wheezing. Similarly, literature and cohort data agreed on significant associations between HMPV infection and cough, as well as adenovirus infection and fever. Importantly, none of the abovementioned features were unique to any particular pathogen but were also observed in association with other respiratory viruses. In summary, our "real-world" dataset confirmed published literature trends, but no individual feature allows any particular type of viral infection to be ruled in or ruled out. For the time being, laboratory confirmation remains essential. More research is needed to develop scientifically validated decision models to inform best practice guidelines and targeted diagnostic algorithms.

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Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance

Cited by 107 publications

References 70 publications

Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015

Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015

A decade of RNA virus metagenomics is (not) enough

Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review

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