Efficient whole genome sequencing of influenza A viruses Article Swipe
Marina Escalera‐Zamudio
,
Ana G. Cobián-Güemes
,
Blanca Taboada
,
Irma López‐Martínez
,
Joel Armando Vázquez-Pérez
,
Maricela Montalvo-Corral
,
Jesús Hernández
,
José Alberto Díaz-Quiñónez
,
Gisela Barrera Badillo
,
Susana López
,
Carlos F. Arias
,
Pavel Iša
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/749234
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/749234
The constant threat of emergence for novel pathogenic influenza A viruses with pandemic potential, makes full-genome characterization of circulating influenza viral strains a high priority, allowing detection of novel and re-assorting variants. Sequencing the full-length genome of influenza A virus traditionally required multiple amplification rounds, followed by the subsequent sequencing of individual PCR products. The introduction of high-throughput sequencing technologies has made whole genome sequencing easier and faster. We present a simple protocol to obtain whole genome sequences of hypothetically any influenza A virus, even with low quantities of starting genetic material. The complete genomes of influenza A viruses of different subtypes and from distinct sources (clinical samples of pdmH1N1, tissue culture-adapted H3N2 viruses, or avian influenza viruses from cloacal swabs) were amplified with a single multisegment reverse transcription-PCR reaction and sequenced using Illumina sequencing platform. Samples with low quantity of genetic material after initial PCR amplification were re-amplified by an additional PCR using random primers. Whole genome sequencing was successful for 66% of the samples, whilst the most relevant genome segments for epidemiological surveillance (corresponding to the hemagglutinin and neuraminidase) were sequenced with at least 93% coverage (and a minimum 10x) for 98% of the samples. Low coverage for some samples is likely due to an initial low viral RNA concentration in the original sample. The proposed methodology is especially suitable for sequencing a large number of samples, when genetic data is urgently required for strains characterization, and may also be useful for variant analysis.
Related Topics
Concepts
Biology
Genome
Neuraminidase
DNA sequencing
Whole genome sequencing
Virology
Virus
Genetics
Hemagglutinin (influenza)
Deep sequencing
Influenza A virus
Computational biology
Gene
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/749234
- https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdf
- OA Status
- green
- Cited By
- 2
- References
- 32
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2970479043
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W2970479043Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/749234Digital Object Identifier
- Title
-
Efficient whole genome sequencing of influenza A virusesWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2019Year of publication
- Publication date
-
2019-08-29Full publication date if available
- Authors
-
Marina Escalera‐Zamudio, Ana G. Cobián-Güemes, Blanca Taboada, Irma López‐Martínez, Joel Armando Vázquez-Pérez, Maricela Montalvo-Corral, Jesús Hernández, José Alberto Díaz-Quiñónez, Gisela Barrera Badillo, Susana López, Carlos F. Arias, Pavel IšaList of authors in order
- Landing page
-
https://doi.org/10.1101/749234Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdfDirect OA link when available
- Concepts
-
Biology, Genome, Neuraminidase, DNA sequencing, Whole genome sequencing, Virology, Virus, Genetics, Hemagglutinin (influenza), Deep sequencing, Influenza A virus, Computational biology, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2023: 1, 2021: 1Per-year citation counts (last 5 years)
- References (count)
-
32Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W2970479043 |
|---|---|
| doi | https://doi.org/10.1101/749234 |
| ids.doi | https://doi.org/10.1101/749234 |
| ids.mag | 2970479043 |
| ids.openalex | https://openalex.org/W2970479043 |
| fwci | 0.19627481 |
| type | preprint |
| title | Efficient whole genome sequencing of influenza A viruses |
| biblio.issue | |
| biblio.volume | |
| biblio.last_page | |
| biblio.first_page | |
| topics[0].id | https://openalex.org/T10167 |
| topics[0].field.id | https://openalex.org/fields/27 |
| topics[0].field.display_name | Medicine |
| topics[0].score | 1.0 |
| topics[0].domain.id | https://openalex.org/domains/4 |
| topics[0].domain.display_name | Health Sciences |
| topics[0].subfield.id | https://openalex.org/subfields/2713 |
| topics[0].subfield.display_name | Epidemiology |
| topics[0].display_name | Influenza Virus Research Studies |
| topics[1].id | https://openalex.org/T10521 |
| topics[1].field.id | https://openalex.org/fields/13 |
| topics[1].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[1].score | 0.9958999752998352 |
| topics[1].domain.id | https://openalex.org/domains/1 |
| topics[1].domain.display_name | Life Sciences |
| topics[1].subfield.id | https://openalex.org/subfields/1312 |
| topics[1].subfield.display_name | Molecular Biology |
| topics[1].display_name | RNA and protein synthesis mechanisms |
| topics[2].id | https://openalex.org/T11243 |
| topics[2].field.id | https://openalex.org/fields/27 |
| topics[2].field.display_name | Medicine |
| topics[2].score | 0.9847000241279602 |
| topics[2].domain.id | https://openalex.org/domains/4 |
| topics[2].domain.display_name | Health Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/2713 |
| topics[2].subfield.display_name | Epidemiology |
| topics[2].display_name | Respiratory viral infections research |
| is_xpac | False |
| apc_list | |
| apc_paid | |
| concepts[0].id | https://openalex.org/C86803240 |
| concepts[0].level | 0 |
| concepts[0].score | 0.7753645181655884 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[0].display_name | Biology |
| concepts[1].id | https://openalex.org/C141231307 |
| concepts[1].level | 3 |
| concepts[1].score | 0.7680534720420837 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q7020 |
| concepts[1].display_name | Genome |
| concepts[2].id | https://openalex.org/C134164806 |
| concepts[2].level | 3 |
| concepts[2].score | 0.5705420970916748 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q409485 |
| concepts[2].display_name | Neuraminidase |
| concepts[3].id | https://openalex.org/C51679486 |
| concepts[3].level | 3 |
| concepts[3].score | 0.5646075010299683 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q380546 |
| concepts[3].display_name | DNA sequencing |
| concepts[4].id | https://openalex.org/C24432333 |
| concepts[4].level | 4 |
| concepts[4].score | 0.511522650718689 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q2068526 |
| concepts[4].display_name | Whole genome sequencing |
| concepts[5].id | https://openalex.org/C159047783 |
| concepts[5].level | 1 |
| concepts[5].score | 0.4992659091949463 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q7215 |
| concepts[5].display_name | Virology |
| concepts[6].id | https://openalex.org/C2522874641 |
| concepts[6].level | 2 |
| concepts[6].score | 0.49828028678894043 |
| concepts[6].wikidata | https://www.wikidata.org/wiki/Q808 |
| concepts[6].display_name | Virus |
| concepts[7].id | https://openalex.org/C54355233 |
| concepts[7].level | 1 |
| concepts[7].score | 0.4922007620334625 |
| concepts[7].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[7].display_name | Genetics |
| concepts[8].id | https://openalex.org/C2778692840 |
| concepts[8].level | 3 |
| concepts[8].score | 0.47976407408714294 |
| concepts[8].wikidata | https://www.wikidata.org/wiki/Q9136673 |
| concepts[8].display_name | Hemagglutinin (influenza) |
| concepts[9].id | https://openalex.org/C132917006 |
| concepts[9].level | 4 |
| concepts[9].score | 0.43935853242874146 |
| concepts[9].wikidata | https://www.wikidata.org/wiki/Q5250436 |
| concepts[9].display_name | Deep sequencing |
| concepts[10].id | https://openalex.org/C2777546802 |
| concepts[10].level | 3 |
| concepts[10].score | 0.4306841492652893 |
| concepts[10].wikidata | https://www.wikidata.org/wiki/Q834390 |
| concepts[10].display_name | Influenza A virus |
| concepts[11].id | https://openalex.org/C70721500 |
| concepts[11].level | 1 |
| concepts[11].score | 0.39640289545059204 |
| concepts[11].wikidata | https://www.wikidata.org/wiki/Q177005 |
| concepts[11].display_name | Computational biology |
| concepts[12].id | https://openalex.org/C104317684 |
| concepts[12].level | 2 |
| concepts[12].score | 0.25269365310668945 |
| concepts[12].wikidata | https://www.wikidata.org/wiki/Q7187 |
| concepts[12].display_name | Gene |
| keywords[0].id | https://openalex.org/keywords/biology |
| keywords[0].score | 0.7753645181655884 |
| keywords[0].display_name | Biology |
| keywords[1].id | https://openalex.org/keywords/genome |
| keywords[1].score | 0.7680534720420837 |
| keywords[1].display_name | Genome |
| keywords[2].id | https://openalex.org/keywords/neuraminidase |
| keywords[2].score | 0.5705420970916748 |
| keywords[2].display_name | Neuraminidase |
| keywords[3].id | https://openalex.org/keywords/dna-sequencing |
| keywords[3].score | 0.5646075010299683 |
| keywords[3].display_name | DNA sequencing |
| keywords[4].id | https://openalex.org/keywords/whole-genome-sequencing |
| keywords[4].score | 0.511522650718689 |
| keywords[4].display_name | Whole genome sequencing |
| keywords[5].id | https://openalex.org/keywords/virology |
| keywords[5].score | 0.4992659091949463 |
| keywords[5].display_name | Virology |
| keywords[6].id | https://openalex.org/keywords/virus |
| keywords[6].score | 0.49828028678894043 |
| keywords[6].display_name | Virus |
| keywords[7].id | https://openalex.org/keywords/genetics |
| keywords[7].score | 0.4922007620334625 |
| keywords[7].display_name | Genetics |
| keywords[8].id | https://openalex.org/keywords/hemagglutinin |
| keywords[8].score | 0.47976407408714294 |
| keywords[8].display_name | Hemagglutinin (influenza) |
| keywords[9].id | https://openalex.org/keywords/deep-sequencing |
| keywords[9].score | 0.43935853242874146 |
| keywords[9].display_name | Deep sequencing |
| keywords[10].id | https://openalex.org/keywords/influenza-a-virus |
| keywords[10].score | 0.4306841492652893 |
| keywords[10].display_name | Influenza A virus |
| keywords[11].id | https://openalex.org/keywords/computational-biology |
| keywords[11].score | 0.39640289545059204 |
| keywords[11].display_name | Computational biology |
| keywords[12].id | https://openalex.org/keywords/gene |
| keywords[12].score | 0.25269365310668945 |
| keywords[12].display_name | Gene |
| language | en |
| locations[0].id | doi:10.1101/749234 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S4306402567 |
| locations[0].source.issn | |
| locations[0].source.type | repository |
| locations[0].source.is_oa | False |
| locations[0].source.issn_l | |
| locations[0].source.is_core | False |
| locations[0].source.is_in_doaj | False |
| locations[0].source.display_name | bioRxiv (Cold Spring Harbor Laboratory) |
| locations[0].source.host_organization | https://openalex.org/I2750212522 |
| locations[0].source.host_organization_name | Cold Spring Harbor Laboratory |
| locations[0].source.host_organization_lineage | https://openalex.org/I2750212522 |
| locations[0].license | cc-by-nc-nd |
| locations[0].pdf_url | https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdf |
| locations[0].version | acceptedVersion |
| locations[0].raw_type | posted-content |
| locations[0].license_id | https://openalex.org/licenses/cc-by-nc-nd |
| locations[0].is_accepted | True |
| locations[0].is_published | False |
| locations[0].raw_source_name | |
| locations[0].landing_page_url | https://doi.org/10.1101/749234 |
| indexed_in | crossref |
| authorships[0].author.id | https://openalex.org/A5024545469 |
| authorships[0].author.orcid | https://orcid.org/0000-0002-4773-2773 |
| authorships[0].author.display_name | Marina Escalera‐Zamudio |
| authorships[0].countries | GB, MX |
| authorships[0].affiliations[0].institution_ids | https://openalex.org/I884181516 |
| authorships[0].affiliations[0].raw_affiliation_string | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[0].affiliations[1].institution_ids | https://openalex.org/I40120149 |
| authorships[0].affiliations[1].raw_affiliation_string | Dpartmnt of Zoology, Oxford Univrsity, Parks Rd Oxford, OX1 3PS, UK |
| authorships[0].institutions[0].id | https://openalex.org/I40120149 |
| authorships[0].institutions[0].ror | https://ror.org/052gg0110 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I40120149 |
| authorships[0].institutions[0].country_code | GB |
| authorships[0].institutions[0].display_name | University of Oxford |
| authorships[0].institutions[1].id | https://openalex.org/I884181516 |
| authorships[0].institutions[1].ror | https://ror.org/03rzb4f20 |
| authorships[0].institutions[1].type | education |
| authorships[0].institutions[1].lineage | https://openalex.org/I884181516 |
| authorships[0].institutions[1].country_code | MX |
| authorships[0].institutions[1].display_name | Universidad Autónoma del Estado de Morelos |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Marina Escalera-Zamudio |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Dpartmnt of Zoology, Oxford Univrsity, Parks Rd Oxford, OX1 3PS, UK, Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[1].author.id | https://openalex.org/A5075888842 |
| authorships[1].author.orcid | https://orcid.org/0000-0002-0755-5864 |
| authorships[1].author.display_name | Ana G. Cobián-Güemes |
| authorships[1].countries | MX |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I884181516 |
| authorships[1].affiliations[0].raw_affiliation_string | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[1].institutions[0].id | https://openalex.org/I884181516 |
| authorships[1].institutions[0].ror | https://ror.org/03rzb4f20 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I884181516 |
| authorships[1].institutions[0].country_code | MX |
| authorships[1].institutions[0].display_name | Universidad Autónoma del Estado de Morelos |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Ana Georgina Cobián-Güemes |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[2].author.id | https://openalex.org/A5008177172 |
| authorships[2].author.orcid | https://orcid.org/0000-0003-1896-5962 |
| authorships[2].author.display_name | Blanca Taboada |
| authorships[2].countries | MX |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I884181516 |
| authorships[2].affiliations[0].raw_affiliation_string | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[2].institutions[0].id | https://openalex.org/I884181516 |
| authorships[2].institutions[0].ror | https://ror.org/03rzb4f20 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I884181516 |
| authorships[2].institutions[0].country_code | MX |
| authorships[2].institutions[0].display_name | Universidad Autónoma del Estado de Morelos |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Blanca Taboada |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[3].author.id | https://openalex.org/A5048535012 |
| authorships[3].author.orcid | https://orcid.org/0000-0002-0538-474X |
| authorships[3].author.display_name | Irma López‐Martínez |
| authorships[3].countries | MX |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I4210095685 |
| authorships[3].affiliations[0].raw_affiliation_string | Instituto de Diagnóstico y Referencia Epidemiológicos, “Dr. Manuel Marínez Báez” (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, CDMX |
| authorships[3].institutions[0].id | https://openalex.org/I4210095685 |
| authorships[3].institutions[0].ror | https://ror.org/0082wq496 |
| authorships[3].institutions[0].type | government |
| authorships[3].institutions[0].lineage | https://openalex.org/I4210095685 |
| authorships[3].institutions[0].country_code | MX |
| authorships[3].institutions[0].display_name | Secretaria de Salud |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Irma López-Martínez |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Instituto de Diagnóstico y Referencia Epidemiológicos, “Dr. Manuel Marínez Báez” (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, CDMX |
| authorships[4].author.id | https://openalex.org/A5041652374 |
| authorships[4].author.orcid | https://orcid.org/0000-0002-8508-3698 |
| authorships[4].author.display_name | Joel Armando Vázquez-Pérez |
| authorships[4].countries | MX |
| authorships[4].affiliations[0].institution_ids | https://openalex.org/I4210102695 |
| authorships[4].affiliations[0].raw_affiliation_string | Instituto Naional de Enfermedades Respiratorias, Calzada de Tlalpan 4502, Seión XVI, Tlalpan Méxio CDMX |
| authorships[4].institutions[0].id | https://openalex.org/I4210102695 |
| authorships[4].institutions[0].ror | https://ror.org/017fh2655 |
| authorships[4].institutions[0].type | facility |
| authorships[4].institutions[0].lineage | https://openalex.org/I4210095685, https://openalex.org/I4210102695 |
| authorships[4].institutions[0].country_code | MX |
| authorships[4].institutions[0].display_name | Instituto Nacional de Enfermedades Respiratorias |
| authorships[4].author_position | middle |
| authorships[4].raw_author_name | Joel Armando Vázquez-Pérez |
| authorships[4].is_corresponding | False |
| authorships[4].raw_affiliation_strings | Instituto Naional de Enfermedades Respiratorias, Calzada de Tlalpan 4502, Seión XVI, Tlalpan Méxio CDMX |
| authorships[5].author.id | https://openalex.org/A5011758095 |
| authorships[5].author.orcid | https://orcid.org/0000-0002-0070-7490 |
| authorships[5].author.display_name | Maricela Montalvo-Corral |
| authorships[5].countries | MX |
| authorships[5].affiliations[0].institution_ids | https://openalex.org/I4210100172 |
| authorships[5].affiliations[0].raw_affiliation_string | Centro e Investigación en Alimentación y Desarrollo, A.C. Gustavo Astiaza Astiazarán Rosas No. 46. AP1735. CP 83304 Hermosillo, Sonora, Mexico |
| authorships[5].institutions[0].id | https://openalex.org/I4210100172 |
| authorships[5].institutions[0].ror | https://ror.org/015v43a21 |
| authorships[5].institutions[0].type | government |
| authorships[5].institutions[0].lineage | https://openalex.org/I4210100172 |
| authorships[5].institutions[0].country_code | MX |
| authorships[5].institutions[0].display_name | Centro de Investigación en Alimentación y Desarrollo |
| authorships[5].author_position | middle |
| authorships[5].raw_author_name | Maricela Montalvo-Corral |
| authorships[5].is_corresponding | False |
| authorships[5].raw_affiliation_strings | Centro e Investigación en Alimentación y Desarrollo, A.C. Gustavo Astiaza Astiazarán Rosas No. 46. AP1735. CP 83304 Hermosillo, Sonora, Mexico |
| authorships[6].author.id | https://openalex.org/A5011435230 |
| authorships[6].author.orcid | https://orcid.org/0000-0002-5131-3600 |
| authorships[6].author.display_name | Jesús Hernández |
| authorships[6].countries | MX |
| authorships[6].affiliations[0].institution_ids | https://openalex.org/I4210100172 |
| authorships[6].affiliations[0].raw_affiliation_string | Centro e Investigación en Alimentación y Desarrollo, A.C. Gustavo Astiaza Astiazarán Rosas No. 46. AP1735. CP 83304 Hermosillo, Sonora, Mexico |
| authorships[6].institutions[0].id | https://openalex.org/I4210100172 |
| authorships[6].institutions[0].ror | https://ror.org/015v43a21 |
| authorships[6].institutions[0].type | government |
| authorships[6].institutions[0].lineage | https://openalex.org/I4210100172 |
| authorships[6].institutions[0].country_code | MX |
| authorships[6].institutions[0].display_name | Centro de Investigación en Alimentación y Desarrollo |
| authorships[6].author_position | middle |
| authorships[6].raw_author_name | Jesus Hernandez |
| authorships[6].is_corresponding | False |
| authorships[6].raw_affiliation_strings | Centro e Investigación en Alimentación y Desarrollo, A.C. Gustavo Astiaza Astiazarán Rosas No. 46. AP1735. CP 83304 Hermosillo, Sonora, Mexico |
| authorships[7].author.id | https://openalex.org/A5057031203 |
| authorships[7].author.orcid | https://orcid.org/0000-0002-3503-7079 |
| authorships[7].author.display_name | José Alberto Díaz-Quiñónez |
| authorships[7].countries | MX |
| authorships[7].affiliations[0].institution_ids | https://openalex.org/I8961855 |
| authorships[7].affiliations[0].raw_affiliation_string | División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, CDMX |
| authorships[7].affiliations[1].institution_ids | https://openalex.org/I4210095685 |
| authorships[7].affiliations[1].raw_affiliation_string | Instituto de Diagnóstico y Referencia Epidemiológicos, “Dr. Manuel Marínez Báez” (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, CDMX |
| authorships[7].institutions[0].id | https://openalex.org/I4210095685 |
| authorships[7].institutions[0].ror | https://ror.org/0082wq496 |
| authorships[7].institutions[0].type | government |
| authorships[7].institutions[0].lineage | https://openalex.org/I4210095685 |
| authorships[7].institutions[0].country_code | MX |
| authorships[7].institutions[0].display_name | Secretaria de Salud |
| authorships[7].institutions[1].id | https://openalex.org/I8961855 |
| authorships[7].institutions[1].ror | https://ror.org/01tmp8f25 |
| authorships[7].institutions[1].type | education |
| authorships[7].institutions[1].lineage | https://openalex.org/I8961855 |
| authorships[7].institutions[1].country_code | MX |
| authorships[7].institutions[1].display_name | Universidad Nacional Autónoma de México |
| authorships[7].author_position | middle |
| authorships[7].raw_author_name | José Alberto Díaz-Quiñonez |
| authorships[7].is_corresponding | False |
| authorships[7].raw_affiliation_strings | División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, CDMX, Instituto de Diagnóstico y Referencia Epidemiológicos, “Dr. Manuel Marínez Báez” (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, CDMX |
| authorships[8].author.id | https://openalex.org/A5007874650 |
| authorships[8].author.orcid | |
| authorships[8].author.display_name | Gisela Barrera Badillo |
| authorships[8].countries | MX |
| authorships[8].affiliations[0].institution_ids | https://openalex.org/I4210095685 |
| authorships[8].affiliations[0].raw_affiliation_string | Instituto de Diagnóstico y Referencia Epidemiológicos, “Dr. Manuel Marínez Báez” (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, CDMX |
| authorships[8].institutions[0].id | https://openalex.org/I4210095685 |
| authorships[8].institutions[0].ror | https://ror.org/0082wq496 |
| authorships[8].institutions[0].type | government |
| authorships[8].institutions[0].lineage | https://openalex.org/I4210095685 |
| authorships[8].institutions[0].country_code | MX |
| authorships[8].institutions[0].display_name | Secretaria de Salud |
| authorships[8].author_position | middle |
| authorships[8].raw_author_name | Gisela Barrera Badillo |
| authorships[8].is_corresponding | False |
| authorships[8].raw_affiliation_strings | Instituto de Diagnóstico y Referencia Epidemiológicos, “Dr. Manuel Marínez Báez” (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, CDMX |
| authorships[9].author.id | https://openalex.org/A5089461814 |
| authorships[9].author.orcid | https://orcid.org/0000-0001-6336-9209 |
| authorships[9].author.display_name | Susana López |
| authorships[9].countries | MX |
| authorships[9].affiliations[0].institution_ids | https://openalex.org/I884181516 |
| authorships[9].affiliations[0].raw_affiliation_string | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[9].institutions[0].id | https://openalex.org/I884181516 |
| authorships[9].institutions[0].ror | https://ror.org/03rzb4f20 |
| authorships[9].institutions[0].type | education |
| authorships[9].institutions[0].lineage | https://openalex.org/I884181516 |
| authorships[9].institutions[0].country_code | MX |
| authorships[9].institutions[0].display_name | Universidad Autónoma del Estado de Morelos |
| authorships[9].author_position | middle |
| authorships[9].raw_author_name | Susana López |
| authorships[9].is_corresponding | False |
| authorships[9].raw_affiliation_strings | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[10].author.id | https://openalex.org/A5101407113 |
| authorships[10].author.orcid | https://orcid.org/0000-0003-3130-4501 |
| authorships[10].author.display_name | Carlos F. Arias |
| authorships[10].countries | MX |
| authorships[10].affiliations[0].institution_ids | https://openalex.org/I884181516 |
| authorships[10].affiliations[0].raw_affiliation_string | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[10].institutions[0].id | https://openalex.org/I884181516 |
| authorships[10].institutions[0].ror | https://ror.org/03rzb4f20 |
| authorships[10].institutions[0].type | education |
| authorships[10].institutions[0].lineage | https://openalex.org/I884181516 |
| authorships[10].institutions[0].country_code | MX |
| authorships[10].institutions[0].display_name | Universidad Autónoma del Estado de Morelos |
| authorships[10].author_position | middle |
| authorships[10].raw_author_name | Carlos F. Arias |
| authorships[10].is_corresponding | False |
| authorships[10].raw_affiliation_strings | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[11].author.id | https://openalex.org/A5076075959 |
| authorships[11].author.orcid | https://orcid.org/0000-0002-3175-0993 |
| authorships[11].author.display_name | Pavel Iša |
| authorships[11].countries | MX |
| authorships[11].affiliations[0].institution_ids | https://openalex.org/I884181516 |
| authorships[11].affiliations[0].raw_affiliation_string | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| authorships[11].institutions[0].id | https://openalex.org/I884181516 |
| authorships[11].institutions[0].ror | https://ror.org/03rzb4f20 |
| authorships[11].institutions[0].type | education |
| authorships[11].institutions[0].lineage | https://openalex.org/I884181516 |
| authorships[11].institutions[0].country_code | MX |
| authorships[11].institutions[0].display_name | Universidad Autónoma del Estado de Morelos |
| authorships[11].author_position | last |
| authorships[11].raw_author_name | Pavel Iša |
| authorships[11].is_corresponding | True |
| authorships[11].raw_affiliation_strings | Instituto de Biotecnologí, Universidd Ncionl Autónom de México, Av. Universidd 2001, Col. Chmilp, Cuernvc, Morelos, México |
| has_content.pdf | True |
| has_content.grobid_xml | True |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdf |
| open_access.oa_status | green |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | Efficient whole genome sequencing of influenza A viruses |
| has_fulltext | True |
| is_retracted | False |
| updated_date | 2025-11-06T03:46:38.306776 |
| primary_topic.id | https://openalex.org/T10167 |
| primary_topic.field.id | https://openalex.org/fields/27 |
| primary_topic.field.display_name | Medicine |
| primary_topic.score | 1.0 |
| primary_topic.domain.id | https://openalex.org/domains/4 |
| primary_topic.domain.display_name | Health Sciences |
| primary_topic.subfield.id | https://openalex.org/subfields/2713 |
| primary_topic.subfield.display_name | Epidemiology |
| primary_topic.display_name | Influenza Virus Research Studies |
| related_works | https://openalex.org/W2036315754, https://openalex.org/W2413764076, https://openalex.org/W2065991003, https://openalex.org/W1528684958, https://openalex.org/W2043473204, https://openalex.org/W4247655581, https://openalex.org/W1990428998, https://openalex.org/W4391064179, https://openalex.org/W2984426833, https://openalex.org/W1556716938 |
| cited_by_count | 2 |
| counts_by_year[0].year | 2023 |
| counts_by_year[0].cited_by_count | 1 |
| counts_by_year[1].year | 2021 |
| counts_by_year[1].cited_by_count | 1 |
| locations_count | 1 |
| best_oa_location.id | doi:10.1101/749234 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S4306402567 |
| best_oa_location.source.issn | |
| best_oa_location.source.type | repository |
| best_oa_location.source.is_oa | False |
| best_oa_location.source.issn_l | |
| best_oa_location.source.is_core | False |
| best_oa_location.source.is_in_doaj | False |
| best_oa_location.source.display_name | bioRxiv (Cold Spring Harbor Laboratory) |
| best_oa_location.source.host_organization | https://openalex.org/I2750212522 |
| best_oa_location.source.host_organization_name | Cold Spring Harbor Laboratory |
| best_oa_location.source.host_organization_lineage | https://openalex.org/I2750212522 |
| best_oa_location.license | cc-by-nc-nd |
| best_oa_location.pdf_url | https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdf |
| best_oa_location.version | acceptedVersion |
| best_oa_location.raw_type | posted-content |
| best_oa_location.license_id | https://openalex.org/licenses/cc-by-nc-nd |
| best_oa_location.is_accepted | True |
| best_oa_location.is_published | False |
| best_oa_location.raw_source_name | |
| best_oa_location.landing_page_url | https://doi.org/10.1101/749234 |
| primary_location.id | doi:10.1101/749234 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S4306402567 |
| primary_location.source.issn | |
| primary_location.source.type | repository |
| primary_location.source.is_oa | False |
| primary_location.source.issn_l | |
| primary_location.source.is_core | False |
| primary_location.source.is_in_doaj | False |
| primary_location.source.display_name | bioRxiv (Cold Spring Harbor Laboratory) |
| primary_location.source.host_organization | https://openalex.org/I2750212522 |
| primary_location.source.host_organization_name | Cold Spring Harbor Laboratory |
| primary_location.source.host_organization_lineage | https://openalex.org/I2750212522 |
| primary_location.license | cc-by-nc-nd |
| primary_location.pdf_url | https://www.biorxiv.org/content/biorxiv/early/2019/08/29/749234.full.pdf |
| primary_location.version | acceptedVersion |
| primary_location.raw_type | posted-content |
| primary_location.license_id | https://openalex.org/licenses/cc-by-nc-nd |
| primary_location.is_accepted | True |
| primary_location.is_published | False |
| primary_location.raw_source_name | |
| primary_location.landing_page_url | https://doi.org/10.1101/749234 |
| publication_date | 2019-08-29 |
| publication_year | 2019 |
| referenced_works | https://openalex.org/W2067142065, https://openalex.org/W2811479613, https://openalex.org/W2168020376, https://openalex.org/W2069831575, https://openalex.org/W2159734253, https://openalex.org/W2070093956, https://openalex.org/W2103093438, https://openalex.org/W2113262676, https://openalex.org/W2052708825, https://openalex.org/W2091526576, https://openalex.org/W2106669223, https://openalex.org/W2166582607, https://openalex.org/W2161271569, https://openalex.org/W2312463092, https://openalex.org/W2078626331, https://openalex.org/W2052733268, https://openalex.org/W2083925087, https://openalex.org/W2023351304, https://openalex.org/W2114356633, https://openalex.org/W2039583570, https://openalex.org/W2901064289, https://openalex.org/W2295808945, https://openalex.org/W2911468020, https://openalex.org/W2912982595, https://openalex.org/W2158073495, https://openalex.org/W2796093810, https://openalex.org/W2076510334, https://openalex.org/W2034628718, https://openalex.org/W2112113834, https://openalex.org/W2095803441, https://openalex.org/W2108234281, https://openalex.org/W2160881014 |
| referenced_works_count | 32 |
| abstract_inverted_index.A | 10, 39, 83, 98 |
| abstract_inverted_index.a | 23, 71, 125, 190, 225 |
| abstract_inverted_index.We | 69 |
| abstract_inverted_index.an | 151, 207 |
| abstract_inverted_index.at | 185 |
| abstract_inverted_index.be | 242 |
| abstract_inverted_index.by | 47, 150 |
| abstract_inverted_index.in | 213 |
| abstract_inverted_index.is | 203, 220, 233 |
| abstract_inverted_index.of | 4, 18, 28, 37, 51, 57, 79, 89, 96, 100, 109, 141, 164, 195, 228 |
| abstract_inverted_index.or | 115 |
| abstract_inverted_index.to | 74, 177, 206 |
| abstract_inverted_index.66% | 163 |
| abstract_inverted_index.93% | 187 |
| abstract_inverted_index.98% | 194 |
| abstract_inverted_index.Low | 198 |
| abstract_inverted_index.PCR | 53, 146, 153 |
| abstract_inverted_index.RNA | 211 |
| abstract_inverted_index.The | 1, 55, 93, 217 |
| abstract_inverted_index.and | 30, 67, 103, 131, 180, 239 |
| abstract_inverted_index.any | 81 |
| abstract_inverted_index.due | 205 |
| abstract_inverted_index.for | 6, 162, 173, 193, 200, 223, 236, 244 |
| abstract_inverted_index.has | 61 |
| abstract_inverted_index.low | 87, 139, 209 |
| abstract_inverted_index.may | 240 |
| abstract_inverted_index.the | 34, 48, 165, 168, 178, 196, 214 |
| abstract_inverted_index.was | 160 |
| abstract_inverted_index.(and | 189 |
| abstract_inverted_index.10x) | 192 |
| abstract_inverted_index.H3N2 | 113 |
| abstract_inverted_index.also | 241 |
| abstract_inverted_index.data | 232 |
| abstract_inverted_index.even | 85 |
| abstract_inverted_index.from | 104, 119 |
| abstract_inverted_index.high | 24 |
| abstract_inverted_index.made | 62 |
| abstract_inverted_index.most | 169 |
| abstract_inverted_index.some | 201 |
| abstract_inverted_index.were | 122, 148, 182 |
| abstract_inverted_index.when | 230 |
| abstract_inverted_index.with | 12, 86, 124, 138, 184 |
| abstract_inverted_index.Whole | 157 |
| abstract_inverted_index.after | 144 |
| abstract_inverted_index.avian | 116 |
| abstract_inverted_index.large | 226 |
| abstract_inverted_index.least | 186 |
| abstract_inverted_index.makes | 15 |
| abstract_inverted_index.novel | 7, 29 |
| abstract_inverted_index.using | 133, 154 |
| abstract_inverted_index.viral | 21, 210 |
| abstract_inverted_index.virus | 40 |
| abstract_inverted_index.whole | 63, 76 |
| abstract_inverted_index.easier | 66 |
| abstract_inverted_index.genome | 36, 64, 77, 158, 171 |
| abstract_inverted_index.likely | 204 |
| abstract_inverted_index.number | 227 |
| abstract_inverted_index.obtain | 75 |
| abstract_inverted_index.random | 155 |
| abstract_inverted_index.simple | 72 |
| abstract_inverted_index.single | 126 |
| abstract_inverted_index.swabs) | 121 |
| abstract_inverted_index.threat | 3 |
| abstract_inverted_index.tissue | 111 |
| abstract_inverted_index.useful | 243 |
| abstract_inverted_index.virus, | 84 |
| abstract_inverted_index.whilst | 167 |
| abstract_inverted_index.Samples | 137 |
| abstract_inverted_index.cloacal | 120 |
| abstract_inverted_index.faster. | 68 |
| abstract_inverted_index.genetic | 91, 142, 231 |
| abstract_inverted_index.genomes | 95 |
| abstract_inverted_index.initial | 145, 208 |
| abstract_inverted_index.minimum | 191 |
| abstract_inverted_index.present | 70 |
| abstract_inverted_index.reverse | 128 |
| abstract_inverted_index.rounds, | 45 |
| abstract_inverted_index.sample. | 216 |
| abstract_inverted_index.samples | 108, 202 |
| abstract_inverted_index.sources | 106 |
| abstract_inverted_index.strains | 22, 237 |
| abstract_inverted_index.variant | 245 |
| abstract_inverted_index.viruses | 11, 99, 118 |
| abstract_inverted_index.ABSTRACT | 0 |
| abstract_inverted_index.Illumina | 134 |
| abstract_inverted_index.allowing | 26 |
| abstract_inverted_index.complete | 94 |
| abstract_inverted_index.constant | 2 |
| abstract_inverted_index.coverage | 188, 199 |
| abstract_inverted_index.distinct | 105 |
| abstract_inverted_index.followed | 46 |
| abstract_inverted_index.material | 143 |
| abstract_inverted_index.multiple | 43 |
| abstract_inverted_index.original | 215 |
| abstract_inverted_index.pandemic | 13 |
| abstract_inverted_index.pdmH1N1, | 110 |
| abstract_inverted_index.primers. | 156 |
| abstract_inverted_index.proposed | 218 |
| abstract_inverted_index.protocol | 73 |
| abstract_inverted_index.quantity | 140 |
| abstract_inverted_index.reaction | 130 |
| abstract_inverted_index.relevant | 170 |
| abstract_inverted_index.required | 42, 235 |
| abstract_inverted_index.samples, | 166, 229 |
| abstract_inverted_index.samples. | 197 |
| abstract_inverted_index.segments | 172 |
| abstract_inverted_index.starting | 90 |
| abstract_inverted_index.subtypes | 102 |
| abstract_inverted_index.suitable | 222 |
| abstract_inverted_index.urgently | 234 |
| abstract_inverted_index.viruses, | 114 |
| abstract_inverted_index.(clinical | 107 |
| abstract_inverted_index.amplified | 123 |
| abstract_inverted_index.analysis. | 246 |
| abstract_inverted_index.detection | 27 |
| abstract_inverted_index.different | 101 |
| abstract_inverted_index.emergence | 5 |
| abstract_inverted_index.influenza | 9, 20, 38, 82, 97, 117 |
| abstract_inverted_index.material. | 92 |
| abstract_inverted_index.platform. | 136 |
| abstract_inverted_index.priority, | 25 |
| abstract_inverted_index.products. | 54 |
| abstract_inverted_index.sequenced | 132, 183 |
| abstract_inverted_index.sequences | 78 |
| abstract_inverted_index.variants. | 32 |
| abstract_inverted_index.Sequencing | 33 |
| abstract_inverted_index.additional | 152 |
| abstract_inverted_index.especially | 221 |
| abstract_inverted_index.individual | 52 |
| abstract_inverted_index.pathogenic | 8 |
| abstract_inverted_index.potential, | 14 |
| abstract_inverted_index.quantities | 88 |
| abstract_inverted_index.sequencing | 50, 59, 65, 135, 159, 224 |
| abstract_inverted_index.subsequent | 49 |
| abstract_inverted_index.successful | 161 |
| abstract_inverted_index.circulating | 19 |
| abstract_inverted_index.full-genome | 16 |
| abstract_inverted_index.full-length | 35 |
| abstract_inverted_index.methodology | 219 |
| abstract_inverted_index.introduction | 56 |
| abstract_inverted_index.multisegment | 127 |
| abstract_inverted_index.re-amplified | 149 |
| abstract_inverted_index.re-assorting | 31 |
| abstract_inverted_index.surveillance | 175 |
| abstract_inverted_index.technologies | 60 |
| abstract_inverted_index.amplification | 44, 147 |
| abstract_inverted_index.concentration | 212 |
| abstract_inverted_index.hemagglutinin | 179 |
| abstract_inverted_index.traditionally | 41 |
| abstract_inverted_index.(corresponding | 176 |
| abstract_inverted_index.hypothetically | 80 |
| abstract_inverted_index.neuraminidase) | 181 |
| abstract_inverted_index.culture-adapted | 112 |
| abstract_inverted_index.epidemiological | 174 |
| abstract_inverted_index.high-throughput | 58 |
| abstract_inverted_index.characterization | 17 |
| abstract_inverted_index.characterization, | 238 |
| abstract_inverted_index.transcription-PCR | 129 |
| cited_by_percentile_year.max | 94 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5076075959 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 12 |
| corresponding_institution_ids | https://openalex.org/I884181516 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.8399999737739563 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.5490532 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |