Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season

Simon, Bruno; Pichon, Maxime; Valette, Martine; Burfin, Gwendolyne; Richard, Mathilde; Lina, Bruno; Josset, Laurence

doi:10.3390/v11020108

Cited by 37 publications

(40 citation statements)

References 41 publications

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“…In recent 30 years, three subtypes of IAVs, including H1N1pdm09 virus causing 2009 flu pandemic [22], and two highly pathogenic avian viruses, H5N1 and H7N9 viruses, had caused severe respiratory diseases and resulted in thousands of deaths or high mortality in humans [23,24]. The majority subtype of seasonal IAVs is H3N2 [25]. The polygenetic tree in Fig.…”

Section: Virusesmentioning

confidence: 99%

Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season

Jiang

Yao

Zhao

et al. 2020

Microbes and Infection

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to sweep the world, causing infection of millions and death of hundreds of thousands. The respiratory disease that it caused, COVID-19 (stands for coronavirus disease in 2019), has similar clinical symptoms with other two CoV diseases, severe acute respiratory syndrome and Middle East respiratory syndrome (SARS and MERS), of which causative viruses are SARS-CoV and MERS-CoV, respectively. These three CoVs resulting diseases also share many clinical symptoms with other respiratory diseases caused by influenza A viruses (IAVs). Since both CoVs and IAVs are general pathogens responsible for seasonal cold, in the next few months, during the changing of seasons, clinicians and public heath may have to distinguish COVID-19 pneumonia from other kinds of viral pneumonia. This is a discussion and comparison of the virus structures, transmission characteristics, clinical symptoms, diagnosis, pathological changes, treatment and prevention of the two kinds of viruses, CoVs and IAVs. It hopes to provide information for practitioners in the medical field during the epidemic season.

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Section: Virusesmentioning

confidence: 99%

Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season

Jiang

Yao

Zhao

et al. 2020

Microbes and Infection

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show abstract

“…The rapid result of a direct PCR assay on a targeted mutation, such as A(H1N1), H275Y; A(H3N2), R292K, E119V; A(H7N9), R294K, can be useful for guiding clinical management [24]. Nextgeneration sequencing allows simultaneous detection of quasi-species harboring resistance mutations even at low frequencies (1%), providing insights into intra-host viral genetic diversity and evolution including the emergence of variants with increased virulence (e.g., D222G, typically found in the lower respiratory tract of critically ill patients) [25][26][27].…”

Section: Take-home Messagementioning

confidence: 99%

Severe flu management: a point of view

et al. 2020

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Annual flu seasons are typically characterized by changes in types and subtypes of influenza, with variations in terms of severity. Despite remarkable improvements in the prevention and management of patients with suspected or laboratory-confirmed diagnosis of influenza, annual seasonal influenza continues to be associated with a high morbidity and mortality. Admission to the intensive care unit is required for patients with severe forms of seasonal influenza infection, with primary pneumonia being present in most of the cases. This review summarizes the most recent knowledge on the diagnosis and treatment strategies in critically ill patients with influenza, focused on diagnostic testing methods, antiviral therapy, use of corticosteroids, antibacterial and antifungal therapy, and supportive measures. The review focuses on diagnostic testing methods, antiviral therapy, use of corticosteroids, antibacterial and antifungal therapy, supportive measures and relevant existing evidence, in order to provide the non-expert clinician a useful overview. An enhanced understanding of current diagnostic and treatment aspects of influenza infection can contribute to improve outcomes and reduce mortality among ICU patients with influenza.

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“…Therefore, studies on the within-and between-host virus diversity are crucial for the understanding of the virus adaptation, crossing host species barrier, and evolution phenomena [18,19]. This question has been investigated extensively in recent years in the case of influenza infections in humans and other mammals [20][21][22][23][24][25]. However, the within-host diversity of avian influenza viruses in birds is poorly explored, given the wide range of hosts and their manifold roles in the evolution and epidemiology of AIV.…”

Section: Introductionmentioning

confidence: 99%

A Turkey-origin H9N2 Avian Influenza Virus Shows Low Pathogenicity but Different Within-host Diversity in Experimentally Infected Turkeys, Quail and Ducks

Świętoń

Tarasiuk

Olszewska-Tomczyk

et al. 2020

Viruses

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Avian influenza virus (AIV) is a highly diverse and widespread poultry pathogen. Its evolution and adaptation may be affected by multiple host and ecological factors, which are still poorly understood. In the present study, a turkey-origin H9N2 AIV was used as a model to investigate the within-host diversity of the virus in turkeys, quail and ducks in conjunction with the clinical course, shedding and seroconversion. Ten birds were inoculated oculonasally with a dose of 106 EID50 of the virus and monitored for 14 days. Virus shedding, transmission and seroconversion were evaluated, and swabs collected at selected time-points were characterized in deep sequencing to assess virus diversity. In general, the virus showed low pathogenicity for the examined bird species, but differences in shedding patterns, seroconversion and clinical outcome were noted. The highest heterogeneity of the virus population as measured by the number of single nucleotide polymorphisms and Shannon entropy was found in oropharyngeal swabs from quail, followed by turkeys and ducks. This suggests a strong bottleneck was imposed on the virus during replication in ducks, which can be explained by its poor adaptation and stronger selection pressure in waterfowl. The high within-host virus diversity in quail with high level of respiratory shedding and asymptomatic course of infection may contribute to our understanding of the role of quail as an intermediate host for adaptation of AIV to other species of poultry. In contrast, low virus complexity was observed in cloacal swabs, mainly from turkeys, showing that the within-host diversity may vary between different replication sites. Consequences of these observations on the virus evolution and adaptation require further investigation.

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Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season

Cited by 37 publications

References 41 publications

Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season

Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season

Severe flu management: a point of view

A Turkey-origin H9N2 Avian Influenza Virus Shows Low Pathogenicity but Different Within-host Diversity in Experimentally Infected Turkeys, Quail and Ducks

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