scholarly journals Impact of Pregnancy on Intra-Host Genetic Diversity of Influenza A Viruses in Hospitalised Women: A Retrospective Cohort Study

2019 ◽  
Vol 8 (11) ◽  
pp. 1974 ◽  
Author(s):  
Gregory Destras ◽  
Maxime Pichon ◽  
Bruno Simon ◽  
Martine Valette ◽  
Vanessa Escuret ◽  
...  
Keyword(s):  
Influenza A ◽  
Immune Modulation ◽  
Pregnant Mouse ◽  
Influenza A Viruses ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Host Diversity ◽  
Significant Difference ◽  
Host Genetic ◽  
Host Evolution

Characterising dynamics of Influenza A Viruses (IAV) within-host evolution is an active field of research which may lead to a better understanding of viral pathogenesis. Using a pregnant mouse model, a study has recently suggested that immune modulation during pregnancy could promote the emergence of IAV quasispecies with increased virulence. Herein, we assess the clinical relevance of these findings in humans. We studied IAV intra-host diversity (ihD) in pregnant (n = 36) and non-pregnant (n = 23) women hospitalized in Lyon for IAV infection (01/2015–05/2018). Whole IAV genomes present in nasopharyngeal samples were sequenced in duplicate to analyze reproducible intra-host single nucleotide variants (ihSNV). Counts, relative frequencies and locations of ihSNV were used as indicators of ihD. The median ihSNV/kb counts per segment were between 0 and 1.3. There was >81% ihSNV at relative frequencies between 1–5% for H1N1 and >51% for H3N2 IAV. No significant difference was noted between pregnant and non-pregnant women when considering all or only non-synonymous ihSNV. Seven convergent non-synonymous ihSNV were found; none were significantly associated with pregnancy. These results suggest that modulation of the immune system during pregnancy in humans does not impact IAV ihD, in contrast to mice.

scholarly journals PRESENCE OF RESPIRATORY VIRUSES IN EQUINES IN BRAZIL

2014 ◽  
Vol 56 (3) ◽  
pp. 191-195
Author(s):  
Dalva Assunção Portari Mancini ◽  
Aparecida Santo Pietro Pereira ◽  
Rita Maria Zucatelli Mendonça ◽  
Adelia Hiroko Nagamori Kawamoto ◽  
Rosely Cabette Barbosa Alves ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Viruses ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
Equine Influenza ◽  
Hemagglutination Inhibition Test ◽  
Parainfluenza Viruses ◽  
Significant Difference ◽  
Antibody Titers ◽  
The Difference

Equines are susceptible to respiratory viruses such as influenza and parainfluenza. Respiratory diseases have adversely impacted economies all over the world. This study was intended to determine the presence of influenza and parainfluenza viruses in unvaccinated horses from some regions of the state of São Paulo, Brazil. Blood serum collected from 72 equines of different towns in this state was tested by hemagglutination inhibition test to detect antibodies for both viruses using the corresponding antigens. About 98.6% (71) and 97.2% (70) of the equines responded with antibody protective titers (≥ 80 HIU/25µL) H7N7 and H3N8 subtypes of influenza A viruses, respectively. All horses (72) also responded with protective titers (≥ 80) HIU/25µL against the parainfluenza virus. The difference between mean antibody titers to H7N7 and H3N8 subtypes of influenza A viruses was not statistically significant (p > 0.05). The mean titers for influenza and parainfluenza viruses, on the other hand, showed a statistically significant difference (p < 0.001). These results indicate a better antibody response from equines to parainfluenza 3 virus than to the equine influenza viruses. No statistically significant differences in the responses against H7N7 and H3N8 subtypes of influenza A and parainfluenza 3 viruses were observed according to the gender (female, male) or the age (≤ 2 to 20 years-old) groups. This study provides evidence of the concomitant presence of two subtypes of the equine influenza A (H7N7 and H3N8) viruses and the parainfluenza 3 virus in equines in Brazil. Thus, it is advisable to vaccinate equines against these respiratory viruses.

scholarly journals Biological Cloth Face Coverings - The Reduction of SARS-CoV-2 and Influenza (H1N1) Infectivity by ViruferrinTM Treatment

2021 ◽  
Author(s):  
Emily Medina Magues ◽  
Anna Stedman ◽  
Paul Hope ◽  
Jorge E. Osorio
Keyword(s):  
Influenza A ◽  
Infectious Virus ◽  
Positive Control ◽  
Influenza A Viruses ◽  
Virus Particles ◽  
Significant Difference ◽  
Untreated Material ◽  
Fabric Material ◽  
Influenza H1n1 ◽  
Time Point

Fabric material was coated with Viruferrin&trade; and tested for its inactivating properties against the pandemic severe acute respiratory syndrome 2 (SARS-CoV-2) and influenza A viruses. A statistically significant (p&lt;0.0001) decrease in the number of infectious virus particles exposed to Viruferrin-treated fabric when compared with the cotton control for both SARS-CoV-2 and influenza A viruses was observed. For both SARS-CoV-2 and influenza A, Viruferrin-treated fabrics experienced a &gt; 99% virus reduction without saliva after five minutes of contact when compared to the positive control at time point 0. Furthermore, the reusability of the Viruferrin treated fabric was demonstrated by stability for up to 10 washes. The level of anti-viral (SARS-CoV-2) activity remained constant from 5 to 10 washes and demonstrated a significant difference (p&lt;0.0001) from the unwashed untreated material. Applications for this treated fabric are far-reaching, and as a biological face covering offers not only a unique 2-way protection but also is unlikely to cause onward touch transmission.

scholarly journals Correction: Impact of Pregnancy on Intra-Host Genetic Diversity of Influenza A Viruses in Hospitalised Women: A Retrospective Cohort Study. J. Clin. Med. 2020, 9, 1974

2019 ◽  
Vol 9 (1) ◽  
pp. 58
Author(s):  
Gregory Destras ◽  
Maxime Pichon ◽  
Bruno Simon ◽  
Martine Valette ◽  
Vanessa Escuret ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cohort Study ◽  
Retrospective Cohort Study ◽  
Retrospective Cohort ◽  
Influenza A ◽  
Influenza A Viruses ◽  
Host Genetic

The authors wish to make the following corrections to this paper [...]

scholarly journals Stochastic processes dominate the within and between host evolution of influenza virus

2017 ◽  
Author(s):  
John T. McCrone ◽  
Robert J. Woods ◽  
Emily T. Martin ◽  
Ryan E. Malosh ◽  
Arnold S. Monto ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Stochastic Processes ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Influenza A Viruses ◽  
Effective Population ◽  
The Individual ◽  
Host Evolution

AbstractThe global evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define the dynamics of influenza A virus populations in human hosts through next generation sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected over 5 seasons from individuals in a prospective community-based cohort, they are broadly representative of natural human infections with seasonal viruses. We used viral sequence data from 35 serially sampled individuals to estimate a within host effective population size of 30-70 and an in vivo mutation rate of 4x10−5 per nucleotide per cellular infectious cycle. These estimates are consistent across several models and robust to the models' underlying assumptions. We also identified 43 epidemiologically linked and genetically validated transmission pairs. Maximum likelihood optimization of multiple transmission models estimates an effective transmission bottleneck of 1-2 distinct genomes. Our data suggest that positive selection of novel viral variants is inefficient at the level of the individual host and that genetic drift and other stochastic processes dominate the within and between host evolution of influenza A viruses.

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

2021 ◽  
Author(s):  
Nicolae Sapoval ◽  
P. Jacob Bueno de Mesquita ◽  
Yunxi Liu ◽  
Roger Wang ◽  
Tian Rui Liu ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Influenza A ◽  
Nucleotide Polymorphisms ◽  
Single Patient ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Site Specific ◽  
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.

scholarly journals Genome-Wide Analysis of Off-Target CRISPR/Cas9 Activity in Single-Cell-Derived Human Hematopoietic Stem and Progenitor Cell Clones

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1501
Author(s):  
Richard H. Smith ◽  
Yun-Ching Chen ◽  
Fayaz Seifuddin ◽  
Daniel Hupalo ◽  
Camille Alba ◽  
...  
Keyword(s):  
Single Cell ◽  
Statistical Significance ◽  
Target Cells ◽  
Causal Connection ◽  
Structural Variants ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Hematopoietic Stem ◽  
Genome Wide ◽  
Significant Difference

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)-mediated genome editing holds remarkable promise for the treatment of human genetic diseases. However, the possibility of off-target Cas9 activity remains a concern. To address this issue using clinically relevant target cells, we electroporated Cas9 ribonucleoprotein (RNP) complexes (independently targeted to two different genomic loci, the CXCR4 locus on chromosome 2 and the AAVS1 locus on chromosome 19) into human mobilized peripheral blood-derived hematopoietic stem and progenitor cells (HSPCs) and assessed the acquisition of somatic mutations in an unbiased, genome-wide manner via whole genome sequencing (WGS) of single-cell-derived HSPC clones. Bioinformatic analysis identified >20,000 total somatic variants (indels, single nucleotide variants, and structural variants) distributed among Cas9-treated and non-Cas9-treated control HSPC clones. Statistical analysis revealed no significant difference in the number of novel non-targeted indels among the samples. Moreover, data analysis showed no evidence of Cas9-mediated indel formation at 623 predicted off-target sites. The median number of novel single nucleotide variants was slightly elevated in Cas9 RNP-recipient sample groups compared to baseline, but did not reach statistical significance. Structural variants were rare and demonstrated no clear causal connection to Cas9-mediated gene editing procedures. We find that the collective somatic mutational burden observed within Cas9 RNP-edited human HSPC clones is indistinguishable from naturally occurring levels of background genetic heterogeneity.

scholarly journals Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants

2021 ◽  
Author(s):  
Justin Landis ◽  
Razia Moorad ◽  
Linda J. Pluta ◽  
Carolina Caro-Vegas ◽  
Ryan P. McNamara ◽  
...  
Keyword(s):  
Public Health ◽  
Sequence Evolution ◽  
Clinical Progression ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Viral Genomes ◽  
Synonymous Mutations ◽  
Health Measures ◽  
Broad Public Health ◽  
Host Evolution

Variants of concern (VOC) in SARS-CoV-2 refer to viral genomes that differ significantly from the ancestor virus and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Yet, little is known regarding how frequently different viral variants emerge and under what circumstances. We report a longitudinal study to determine the degree of SARS-CoV-2 sequence evolution in 94 COVID-19 cases and to estimate the frequency at which highly diverse variants emerge. 2 cases accumulated 9 single-nucleotide variants (SNVs) over a two-week period and 1 case accumulated 23 SNVs over a three-week period, including three non-synonymous mutations in the Spike protein (D138H, E554D, D614G). We estimate that in 2% of COVID cases, viral variants with multiple mutations, including in the Spike glycoprotein, can become the dominant strains in as little as one month of persistent in patient virus replication. This suggests the continued local emergence of VOC independent of travel patterns. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of re-infection, and (iii) patients with diminished immune function may offer broad public health benefits.

scholarly journals Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alvin X Han ◽  
Zandra C Felix Garza ◽  
Matthijs RA Welkers ◽  
René M Vigeveno ◽  
Nhu Duong Tran ◽  
...  
Keyword(s):  
Young Children ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Purifying Selection ◽  
Influenza Viruses ◽  
Human Influenza ◽  
Influenza A Viruses ◽  
Virus Diversity ◽  
Host Evolution

The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analysed the within-host evolution of 82 longitudinally-sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titres decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.

scholarly journals Diversity and Reassortment Rate of Influenza A Viruses in Wild Ducks and Gulls

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1010
Author(s):  
Yulia Postnikova ◽  
Anastasia Treshchalina ◽  
Elizaveta Boravleva ◽  
Alexandra Gambaryan ◽  
Aydar Ishmukhametov ◽  
...  
Keyword(s):  
Influenza A ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Viral Gene ◽  
Viral Diversity ◽  
Influenza A Viruses ◽  
Significant Difference ◽  
Complete Genomes ◽  
Gene Reassortment ◽  
Wild Mallard

Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of H1N1, H1N2, H3N1, H3N2, H3N6, H3N8, H4N6, H5N3, H6N2, H11N6, and H11N9 subtypes isolated from wild mallard ducks and gulls resting in a city pond in Moscow, Russia were sequenced. The analysis of phylogenetic trees showed that stable viral genotypes do not persist from year to year in ducks owing to frequent gene reassortment. For comparison, similar analyses were carried out using sequences of IAVs isolated in the same period from ducks and gulls in The Netherlands. Our results revealed a significant difference in diversity and rates of reassortment of IAVs in ducks and gulls.

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