Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community

Motivation. Influenza is a rapidly mutating RNA virus responsible for annual epidemics causing substantial morbidity, mortality, and economic loss. Characterizing influenza virus mutational diversity and evolutionary processes within and between human hosts can provide tools to help track and understand transmission events. In this study we investigated possible differences between the intrahost genomic content of influenza virus in upper respiratory swabs and exhaled aerosols thought to be enriched for virus from the lower respiratory tract. Results. We examined the sequences of specimens collected from influenza A virus (IAV) infected college community members from December 2012 through May 2013. We analyzed four types of IAV samples μm aerosols (N=38), coarse >5μm aerosols (N=27), nasopharyngeal (N=53), and oropharyngeal swabs (N=47)) collected from 42 study participants with 60 sampling instances. Eighteen (42.9%) participants had data from four sample types (nasopharyngeal swab, oropharyngeal swab, coarse aerosol, fine aerosol) included in the analysis, 10 (23.8%) had data from 3 sample types, 10 (23.8%) had data from 2 sample types, and 4 (9.5%) had data from one type of sample included in the analysis. We found that 481 (53.3%) consensus single nucleotide polymorphisms are shared by all sample types and 600 (66.5%) are shared by at least three different sample types. We observed that within a single patient consensus and non-consensus single nucleotide variants are shared across all sample types. Finally, we inferred a phylogenetic tree using consensus sequences and found that samples derived from a single patient are monophyletic. Conclusions. Single nucleotide polymorphisms did not differentiate between samples with varying origin along the respiratory tree. We found that signatures of variation in non-consensus intrahost single nucleotide variants are host and sample, but not site-specific. We conclude that the genomic information available does not allow us to discern a transmission route. Future investigation into whether any site-specific mutational signatures emerge over a longer period of infection, for example in immunocompromised hosts, can be interesting from the virus evolution perspective.

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Kallikrein-Related Peptidase 5 Contributes to H3N2 Influenza Virus Infection in Human Lungs

Journal of Virology ◽

10.1128/jvi.00421-17 ◽

2017 ◽

Vol 91 (16) ◽

Cited By ~ 7

Author(s):

Mélia Magnen ◽

Fabien Gueugnon ◽

Antoine Guillon ◽

Thomas Baranek ◽

Virginie C. Thibault ◽

...

Keyword(s):

Influenza Virus ◽

Respiratory Tract ◽

Serine Proteases ◽

Lower Respiratory Tract ◽

Influenza A ◽

Seasonal Influenza ◽

Influenza Viruses ◽

H3n2 Virus ◽

Influenza A Viruses

ABSTRACT Hemagglutinin (HA) of influenza virus must be activated by proteolysis before the virus can become infectious. Previous studies indicated that HA cleavage is driven by membrane-bound or extracellular serine proteases in the respiratory tract. However, there is still uncertainty as to which proteases are critical for activating HAs of seasonal influenza A viruses (IAVs) in humans. This study focuses on human KLK1 and KLK5, 2 of the 15 serine proteases known as the kallikrein-related peptidases (KLKs). We find that their mRNA expression in primary human bronchial cells is stimulated by IAV infection. Both enzymes cleaved recombinant HA from several strains of the H1 and/or H3 virus subtype in vitro, but only KLK5 promoted the infectivity of A/Puerto Rico/8/34 (H1N1) and A/Scotland/20/74 (H3N2) virions in MDCK cells. We assessed the ability of treated viruses to initiate influenza in mice. The nasal instillation of only the KLK5-treated virus resulted in weight loss and lethal outcomes. The secretion of this protease in the human lower respiratory tract is enhanced during influenza. Moreover, we show that pretreatment of airway secretions with a KLK5-selective inhibitor significantly reduced the activation of influenza A/Scotland/20/74 virions, providing further evidence of its importance. Differently, increased KLK1 secretion appeared to be associated with the recruitment of inflammatory cells in human airways regardless of the origin of inflammation. Thus, our findings point to the involvement of KLK5 in the proteolytic activation and spread of seasonal influenza viruses in humans. IMPORTANCE Influenza A viruses (IAVs) cause acute infection of the respiratory tract that affects millions of people during seasonal outbreaks every year. Cleavage of the hemagglutinin precursor by host proteases is a critical step in the life cycle of these viruses. Consequently, host proteases that activate HA can be considered promising targets for the development of new antivirals. However, the specific proteases that activate seasonal influenza viruses, especially H3N2 viruses, in the human respiratory tract have remain undefined despite many years of work. Here we demonstrate that the secreted, extracellular protease KLK5 (kallikrein-related peptidase 5) is efficient in promoting the infectivity of H3N2 IAV in vitro and in vivo. Furthermore, we found that its secretion was selectively enhanced in the human lower respiratory tract during a seasonal outbreak dominated by an H3N2 virus. Collectively, our data support the clinical relevance of this protease in human influenza pathogenesis.

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Role of the Host Genetic Susceptibility to 2009 Pandemic Influenza A H1N1

Viruses ◽

10.3390/v13020344 ◽

2021 ◽

Vol 13 (2) ◽

pp. 344

Author(s):

Gloria Pérez-Rubio ◽

Marco Antonio Ponce-Gallegos ◽

Bruno André Domínguez-Mazzocco ◽

Jaime Ponce-Gallegos ◽

Román Alejandro García-Ramírez ◽

...

Keyword(s):

Genetic Susceptibility ◽

Complement Activation ◽

Influenza A ◽

Infectious Agent ◽

Nucleotide Polymorphisms ◽

Medical Subject Headings ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Pubmed Database ◽

Influenza A H1n1

Influenza A virus (IAV) is the most common infectious agent in humans, and infects approximately 10–20% of the world’s population, resulting in 3–5 million hospitalizations per year. A scientific literature search was performed using the PubMed database and the Medical Subject Headings (MeSH) “Influenza A H1N1” and “Genetic susceptibility”. Due to the amount of information and evidence about genetic susceptibility generated from the studies carried out in the last influenza A H1N1 pandemic, studies published between January 2009 to May 2020 were considered; 119 papers were found. Several pathways are involved in the host defense against IAV infection (innate immune response, pro-inflammatory cytokines, chemokines, complement activation, and HLA molecules participating in viral antigen presentation). On the other hand, single nucleotide polymorphisms (SNPs) are a type of variation involving the change of a single base pair that can mean that encoded proteins do not carry out their functions properly, allowing higher viral replication and abnormal host response to infection, such as a cytokine storm. Some of the most studied SNPs associated with IAV infection genetic susceptibility are located in the FCGR2A, C1QBP, CD55, and RPAIN genes, affecting host immune responses through abnormal complement activation. Also, SNPs in IFITM3 (which participates in endosomes and lysosomes fusion) represent some of the most critical polymorphisms associated with IAV infection, suggesting an ineffective virus clearance. Regarding inflammatory response genes, single nucleotide variants in IL1B, TNF, LTA IL17A, IL8, IL6, IRAK2, PIK3CG, and HLA complex are associated with altered phenotype in pro-inflammatory molecules, participating in IAV infection and the severest form of the disease.

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Salivary Blockade Protects the Lower Respiratory Tract of Mice from Lethal Influenza Virus Infection

Journal of Virology ◽

10.1128/jvi.00624-17 ◽

2017 ◽

Vol 91 (14) ◽

Cited By ~ 11

Author(s):

Karen Ivinson ◽

Georgia Deliyannis ◽

Leanne McNabb ◽

Lara Grollo ◽

Brad Gilbertson ◽

...

Keyword(s):

Influenza Virus ◽

Virus Infection ◽

Respiratory Tract ◽

Lower Respiratory Tract ◽

Influenza A ◽

Lethal Dose ◽

Laboratory Mouse ◽

Influenza Virus Infection ◽

Upper Respiratory Tract ◽

Upper Respiratory

ABSTRACT It is possible to model the progression of influenza virus from the upper respiratory tract to the lower respiratory tract in the mouse using viral inoculum delivered in a restricted manner to the nose. In this model, infection with the A/Udorn/307/72 (Udorn) strain of virus results ultimately in high viral titers in both the trachea and lungs. In contrast, the A/Puerto Rico/8/34 (PR8) strain causes an infection that is almost entirely limited to the nasal passages. The factors that govern the progression of virus down the respiratory tract are not well understood. Here, we show that, while PR8 virus grows to high titers in the nose, an inhibitor present in the saliva blocks further progression of infection to the trachea and lungs and renders an otherwise lethal dose of virus completely asymptomatic. In vitro, the salivary inhibitor was capable of potent neutralization of PR8 virus and an additional 20 strains of type A virus and two type B strains that were tested. The exceptions were Udorn virus and the closely related H3N2 strains A/Port Chalmers/1/73 and A/Victoria/3/75. Characterization of the salivary inhibitor showed it to be independent of sialic acid and other carbohydrates for its function. This and other biochemical properties, together with its virus strain specificity and in vivo function, indicate that the mouse salivary inhibitor is a previously undescribed innate inhibitory molecule that may have evolved to provide pulmonary protection of the species from fatal influenza virus infection. IMPORTANCE Influenza A virus occasionally jumps from aquatic birds, its natural host, into mammals to cause outbreaks of varying severity, including pandemics in humans. Despite the laboratory mouse being used as a model to study influenza virus pathogenesis, natural outbreaks of influenza have not been reported in the species. Here, we shed light on one mechanism that might allow mice to be protected from influenza in the wild. We show that virus deposited in the mouse upper respiratory tract will not progress to the lower respiratory tract due to the presence of a potent inhibitor of the virus in saliva. Containing inhibitor-sensitive virus to the upper respiratory tract renders an otherwise lethal infection subclinical. This knowledge sheds light on how natural inhibitors may have evolved to improve survival in this species.

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The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life

Microorganisms ◽

10.3390/microorganisms9071446 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1446

Author(s):

Ivo Hoefnagels ◽

Josephine van de Maat ◽

Jeroen J.A. van Kampen ◽

Annemarie van Rossum ◽

Charlie Obihara ◽

...

Keyword(s):

Respiratory Tract ◽

Disease Severity ◽

Lower Respiratory Tract ◽

Influenza A ◽

Pediatric Population ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Detection Rates ◽

Tract Infections ◽

Respiratory Microbiome

Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiome, viral, and clinical data to find associations with the severity of LRTI. Nasopharyngeal aspirates of children aged one month to five years included in the STRAP study (Study to Reduce Antibiotic prescription in childhood Pneumonia), who presented at the emergency department (ED) with fever and cough or dyspnea, were sequenced with nanopore 16S-rRNA gene sequencing and subsequently analyzed with hierarchical clustering to identify respiratory microbiome profiles. Samples were also tested using a panel of 15 respiratory viruses and Mycoplasma pneumoniae, which were analyzed in two groups, according to their reported virulence. The primary outcome was hospitalization, as measure of disease severity. Nasopharyngeal samples were isolated from a total of 167 children. After quality filtering, microbiome results were available for 54 children and virology panels for 158 children. Six distinct genus-dominant microbiome profiles were identified, with Haemophilus-, Moraxella-, and Streptococcus-dominant profiles being the most prevalent. However, these profiles were not found to be significantly associated with hospitalization. At least one virus was detected in 139 (88%) children, of whom 32.4% had co-infections with multiple viruses. Viral co-infections were common for adenovirus, bocavirus, and enterovirus, and uncommon for human metapneumovirus (hMPV) and influenza A virus. The detection of enteroviruses was negatively associated with hospitalization. Virulence groups were not significantly associated with hospitalization. Our data underlines high detection rates and co-infection of viruses in children with respiratory symptoms and confirms the predominant presence of Haemophilus-, Streptococcus-, and Moraxella-dominant profiles in a symptomatic pediatric population at the ED. However, we could not assess significant associations between microbiome profiles and disease severity measures.

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Tropism of avian influenza A (H5N1) in the upper and lower respiratory tract

Nature Medicine ◽

10.1038/nm1529 ◽

2007 ◽

Vol 13 (2) ◽

pp. 147-149 ◽

Cited By ~ 232

Author(s):

J M Nicholls ◽

M C W Chan ◽

W Y Chan ◽

H K Wong ◽

C Y Cheung ◽

...

Keyword(s):

Avian Influenza ◽

Respiratory Tract ◽

Lower Respiratory Tract ◽

Influenza A

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Radiologic Findings of Childhood Lower Respiratory Tract Infection by Influenza Virus

Journal of the Korean Radiological Society ◽

10.3348/jkrs.2002.47.2.227 ◽

2002 ◽

Vol 47 (2) ◽

pp. 227 ◽

Cited By ~ 1

Author(s):

Hotaek Song ◽

Choong Ki Park ◽

Hee Jung Shin ◽

Yo Won Choi ◽

Seok Chol Jeon ◽

...

Keyword(s):

Influenza Virus ◽

Tract Infection ◽

Respiratory Tract ◽

Respiratory Tract Infection ◽

Lower Respiratory Tract Infection ◽

Lower Respiratory Tract ◽

Radiologic Findings

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Molecular epidemiologic characteristics of hemagglutinin from five waves of avian influenza A (H7N9) virus infection, from 2013 to 2017, in Zhejiang Province, China

Archives of Virology ◽

10.1007/s00705-021-05233-5 ◽

2021 ◽

Author(s):

Yi Sun ◽

Haiyan Mao ◽

Xiuyu Lou ◽

Xinying Wang ◽

Yin Chen ◽

...

Keyword(s):

Amino Acid ◽

Influenza A ◽

Zhejiang Province ◽

Personal Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Amino Acid Mutations ◽

Influenza Outbreaks ◽

Epidemiological Characteristics ◽

The Waves

AbstractThere have been five waves of influenza A (H7N9) epidemics in Zhejiang Province between 2013 and 2017. Although the epidemiological characteristics of the five waves have been reported, the molecular genetics aspects, including the phylogeny, evolution, and mutation of hemagglutinin (HA), have not been systematically investigated. A total of 154 H7N9 samples from Zhejiang Province were collected between 2013 and 2017 and sequenced using an Ion Torrent Personal Genome Machine. The starting dates of the waves were 16 March 2013, 1 July 2013, 1 July 2014, 1 July 2015, and 1 July 2016. Single-nucleotide polymorphisms (SNPs) and amino acid mutations were counted after the HA sequences were aligned. The evolution of H7N9 matched the temporal order of the five waves, among which wave 3 played an important role. The 55 SNPs and 14 amino acid mutations with high frequency identified among the five waves revealed the dynamic occurrence of mutation in the process of viral dissemination. Wave 3 contributed greatly to the subsequent epidemic of waves 4 and 5 of H7N9. Compared with wave 1, wave 5 was characterized by more mutations, including A143V and R148K, two mutations that have been reported to weaken the immune response. In addition, some amino acid mutations were observed in wave 5 that led to more lineages. It is necessary to strengthen the surveillance of subsequent H7N9 influenza outbreaks.

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Impact of Pre and Post Variant Filtration Strategies on Imputation

10.21203/rs.3.rs-128366/v1 ◽

2020 ◽

Author(s):

Celine Charon ◽

Rodrigue Allodji ◽

Vincent Meyer ◽

Jean-François Deleuze

Keyword(s):

Quality Control ◽

Rare Variants ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Direct Effects ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Genome Wide ◽

Conservative Post

Abstract Quality control methods for genome-wide association studies and fine mapping are commonly used for imputation, however, they result in loss of many single nucleotide polymorphisms (SNPs). To investigate the consequences of filtration on imputation, we studied the direct effects on the number of markers, their allele frequencies, imputation quality scores and post-filtration events. We pre-phrased 1,031 genotyped individuals from diverse ethnicities and compared the imputed variants to 1,089 NCBI recorded individuals for additional validation.Without variant pre-filtration based on quality control (QC), we observed no impairment in the imputation of SNPs that failed QC whereas with pre-filtration there was an overall loss of information. Significant differences between frequencies with and without pre-filtration were found only in the range of very rare (5E-04-1E-03) and rare variants (1E-03-5E-03) (p < 1E-04). Increasing the post-filtration imputation quality score from 0.3 to 0.8 reduced the number of single nucleotide variants (SNVs) <0.001 2.5 fold with or without QC pre-filtration and halved the number of very rare variants (5E-04). As a result, to maintain confidence and enough SNVs, we propose here a 2-step post-filtration approach to increase the number of very rare and rare variants compared to conservative post-filtration methods.

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The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections

Viruses ◽

10.3390/v10090504 ◽

2018 ◽

Vol 10 (9) ◽

pp. 504

Author(s):

Olivier Ferraris ◽

Jean-Sébastien Casalegno ◽

Emilie Frobert ◽

Maude Bouscambert Duchamp ◽

Martine Valette ◽

...

Keyword(s):

Influenza Virus ◽

Respiratory Tract ◽

Lower Respiratory Tract ◽

Target Cells ◽

Virus Infections ◽

Reassortment Event ◽

Highly Pathogenic ◽

2009 H1n1 ◽

Reassortant Viruses

In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract. To investigate the capacity of the emergence of reassortant viruses, we characterized viruses obtained from the co-infection of cells with H5N1 (A/Turkey/13/2006) and H1N1pdm09 (A/Lyon/969/2009 H1N1). In our analysis, all the screened reassortants possessed the PB2, HA, and NP segments from H5N1 and acquired one or two of the H1N1pdm09 segments. Moreover, the in vivo infections showed that the acquisition of the NS segment from H1N1pdm09 increased the virulence of H5N1 in mice. We conclude, therefore, that reassortment can occur between these two viruses, even if this process has never been detected in nature.

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