Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes
<p dir="ltr">The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on diseas...
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| مؤلفون آخرون: | , , , , , |
| منشور في: |
2020
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إضافة وسم
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| _version_ | 1864513510857244672 |
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| author | Hebah A. Al Khatib (10494573) |
| author2 | Muna A. Al Maslamani (14777263) Peter V. Coyle (6837260) I. Richard Thompson (4278694) Elmoubasher A. Farag (9913227) Asmaa A. Al Thani (10494576) Hadi M. Yassine (4675846) |
| author2_role | author author author author author author |
| author_facet | Hebah A. Al Khatib (10494573) Muna A. Al Maslamani (14777263) Peter V. Coyle (6837260) I. Richard Thompson (4278694) Elmoubasher A. Farag (9913227) Asmaa A. Al Thani (10494576) Hadi M. Yassine (4675846) |
| author_role | author |
| dc.creator.none.fl_str_mv | Hebah A. Al Khatib (10494573) Muna A. Al Maslamani (14777263) Peter V. Coyle (6837260) I. Richard Thompson (4278694) Elmoubasher A. Farag (9913227) Asmaa A. Al Thani (10494576) Hadi M. Yassine (4675846) |
| dc.date.none.fl_str_mv | 2020-01-17T09:00:00Z |
| dc.identifier.none.fl_str_mv | 10.3390/microorganisms8010133 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Inter-Versus_Intra-Host_Sequence_Diversity_of_pH1N1_and_Associated_Clinical_Outcomes/26232464 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Medical microbiology deep sequencing technology virus diversity intra-host diversity inter-host diversity low-frequency variant haplotype reconstruction |
| dc.title.none.fl_str_mv | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investigating the emergence of LFVs at the consensus level demonstrated that within-host virus evolution recapitulates evolutionary dynamics seen at the global scale. Analysis of virus diversity at the HA haplotype level revealed the clustering of low-frequency haplotypes from early 2015 with dominant strains of 2016, indicating rapid haplotype evolution. Haplotype sharing was also noticed in all years, strongly suggesting haplotype transmission among patients infected during a specific influenza season. Finally, more than half of patients with severe symptoms harbored a larger number of haplotypes, mostly in patients under the age of five. Therefore, patient age, haplotype diversity, and the presence of certain LFVs should be considered when interpreting illness severity. In addition to its importance in understanding virus evolution, sub-consensus virus diversity together with whole genome sequencing is essential to explain variabilities in clinical outcomes that cannot be explained by either analysis alone.</p><h2>Other Information</h2><p dir="ltr">Published in: Microorganisms<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3390/microorganisms8010133" target="_blank">https://dx.doi.org/10.3390/microorganisms8010133</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_042c9489bf4d96b537baaed9b8648d28 |
| identifier_str_mv | 10.3390/microorganisms8010133 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26232464 |
| publishDate | 2020 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical OutcomesHebah A. Al Khatib (10494573)Muna A. Al Maslamani (14777263)Peter V. Coyle (6837260)I. Richard Thompson (4278694)Elmoubasher A. Farag (9913227)Asmaa A. Al Thani (10494576)Hadi M. Yassine (4675846)Biological sciencesGeneticsBiomedical and clinical sciencesClinical sciencesMedical microbiologydeep sequencing technologyvirus diversityintra-host diversityinter-host diversitylow-frequency varianthaplotype reconstruction<p dir="ltr">The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investigating the emergence of LFVs at the consensus level demonstrated that within-host virus evolution recapitulates evolutionary dynamics seen at the global scale. Analysis of virus diversity at the HA haplotype level revealed the clustering of low-frequency haplotypes from early 2015 with dominant strains of 2016, indicating rapid haplotype evolution. Haplotype sharing was also noticed in all years, strongly suggesting haplotype transmission among patients infected during a specific influenza season. Finally, more than half of patients with severe symptoms harbored a larger number of haplotypes, mostly in patients under the age of five. Therefore, patient age, haplotype diversity, and the presence of certain LFVs should be considered when interpreting illness severity. In addition to its importance in understanding virus evolution, sub-consensus virus diversity together with whole genome sequencing is essential to explain variabilities in clinical outcomes that cannot be explained by either analysis alone.</p><h2>Other Information</h2><p dir="ltr">Published in: Microorganisms<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3390/microorganisms8010133" target="_blank">https://dx.doi.org/10.3390/microorganisms8010133</a></p>2020-01-17T09:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.3390/microorganisms8010133https://figshare.com/articles/journal_contribution/Inter-Versus_Intra-Host_Sequence_Diversity_of_pH1N1_and_Associated_Clinical_Outcomes/26232464CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/262324642020-01-17T09:00:00Z |
| spellingShingle | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes Hebah A. Al Khatib (10494573) Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Medical microbiology deep sequencing technology virus diversity intra-host diversity inter-host diversity low-frequency variant haplotype reconstruction |
| status_str | publishedVersion |
| title | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| title_full | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| title_fullStr | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| title_full_unstemmed | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| title_short | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| title_sort | Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes |
| topic | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Medical microbiology deep sequencing technology virus diversity intra-host diversity inter-host diversity low-frequency variant haplotype reconstruction |