Data in Brief (Feb 2022)
16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients
- Julia Galeeva,
- Vladislav Babenko,
- Ramiz Bakhtyev,
- Vladimir Baklaushev,
- Larisa Balykova,
- Pavel Bashkirov,
- Julia Bespyatykh,
- Anna Blagonravova,
- Daria Boldyreva,
- Dmitry Fedorov,
- Ilshat Gafurov,
- Raushaniya Gaifullina,
- Elena Galova,
- Alina Gospodaryk,
- Elena Ilina,
- Konstantin Ivanov,
- Daria Kharlampieva,
- Polina Khromova,
- Ksenia Klimina,
- Konstantin Kolontarev,
- Nadezhda Kolyshkina,
- Andrey Koritsky,
- Vyacheslav Kuropatkin,
- Vasily Lazarev,
- Alexander Manolov,
- Valentin Manuvera,
- Daria Matyushkina,
- Maxim Morozov,
- Ekaterina Moskaleva,
- Varvara Musarova,
- Oleg Ogarkov,
- Elizaveta Orlova,
- Alexander Pavlenko,
- Alla Petrova,
- Natalia Pozhenko,
- Dmitry Pushkar,
- Alexander Rumyantsev,
- Sergey Rumyantsev,
- Vladimir Rumyantsev,
- Lyubov Rychkova,
- Alexander Samoilov,
- Irina Shirokova,
- Vyacheslav Sinkov,
- Svetlana Solovieva,
- Elizaveta Starikova,
- Polina Tikhonova,
- Galina Trifonova,
- Alexander Troitsky,
- Alexander Tulichev,
- Yuri Udalov,
- Anna Varizhuk,
- Alexander Vasiliev,
- Vladimir Veselovsky,
- Rinat Vereshchagin,
- Alexey Volnukhin,
- Gaukhar Yusubalieva,
- Vadim Govorun
Affiliations
- Julia Galeeva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation; Corresponding author.
- Vladislav Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Ramiz Bakhtyev
- City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium, Vuchetich str, 21, Moscow 127206, Russian Federation
- Vladimir Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Orekhovy Boulevard, 28, Moscow 115682, Russian Federation
- Larisa Balykova
- City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium, Vuchetich str, 21, Moscow 127206, Russian Federation
- Pavel Bashkirov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Julia Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Anna Blagonravova
- Privolzhsky Research Medical University, 10/1, Minin and Pozharsky Sq., Nizhny Novgorod 603950, Russian Federation
- Daria Boldyreva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Dmitry Fedorov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Ilshat Gafurov
- Kazan Federal University, 18 Kremlyovskaya str, Kazan 420008, Russian Federation
- Raushaniya Gaifullina
- Kazan Federal University, 18 Kremlyovskaya str, Kazan 420008, Russian Federation
- Elena Galova
- Privolzhsky Research Medical University, 10/1, Minin and Pozharsky Sq., Nizhny Novgorod 603950, Russian Federation
- Alina Gospodaryk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Konstantin Ivanov
- Hospital of the Russian Academy of Sciences, Oktyabrsky prospect, 3, Troitsk 108840, Russian Federation
- Daria Kharlampieva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Polina Khromova
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Ksenia Klimina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Konstantin Kolontarev
- City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium, Vuchetich str, 21, Moscow 127206, Russian Federation
- Nadezhda Kolyshkina
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Orekhovy Boulevard, 28, Moscow 115682, Russian Federation
- Andrey Koritsky
- Hospital of the Russian Academy of Sciences, Oktyabrsky prospect, 3, Troitsk 108840, Russian Federation
- Vyacheslav Kuropatkin
- Burnasyan Federal Medical Biophysical Center, Moscow, ul. Marshala Novikova, house 23, Moscow 123098, Russian Federation
- Vasily Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Alexander Manolov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Valentin Manuvera
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Daria Matyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Maxim Morozov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Ekaterina Moskaleva
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Varvara Musarova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Oleg Ogarkov
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Elizaveta Orlova
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Alexander Pavlenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Alla Petrova
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Natalia Pozhenko
- Hospital of the Russian Academy of Sciences, Oktyabrsky prospect, 3, Troitsk 108840, Russian Federation
- Dmitry Pushkar
- City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium, Vuchetich str, 21, Moscow 127206, Russian Federation
- Alexander Rumyantsev
- Hospital of the Russian Academy of Sciences, Oktyabrsky prospect, 3, Troitsk 108840, Russian Federation
- Sergey Rumyantsev
- Hospital of the Russian Academy of Sciences, Oktyabrsky prospect, 3, Troitsk 108840, Russian Federation
- Vladimir Rumyantsev
- Hospital of the Russian Academy of Sciences, Oktyabrsky prospect, 3, Troitsk 108840, Russian Federation
- Lyubov Rychkova
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Alexander Samoilov
- Burnasyan Federal Medical Biophysical Center, Moscow, ul. Marshala Novikova, house 23, Moscow 123098, Russian Federation
- Irina Shirokova
- Privolzhsky Research Medical University, 10/1, Minin and Pozharsky Sq., Nizhny Novgorod 603950, Russian Federation
- Vyacheslav Sinkov
- Scientific Centre for Family Health and Human Reproduction Problems, 16 Timiryazev str., Irkutsk 664003, Russian Federation
- Svetlana Solovieva
- Burnasyan Federal Medical Biophysical Center, Moscow, ul. Marshala Novikova, house 23, Moscow 123098, Russian Federation
- Elizaveta Starikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Polina Tikhonova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Galina Trifonova
- Privolzhsky Research Medical University, 10/1, Minin and Pozharsky Sq., Nizhny Novgorod 603950, Russian Federation
- Alexander Troitsky
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Orekhovy Boulevard, 28, Moscow 115682, Russian Federation
- Alexander Tulichev
- Privolzhsky Research Medical University, 10/1, Minin and Pozharsky Sq., Nizhny Novgorod 603950, Russian Federation
- Yuri Udalov
- Burnasyan Federal Medical Biophysical Center, Moscow, ul. Marshala Novikova, house 23, Moscow 123098, Russian Federation
- Anna Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Alexander Vasiliev
- City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium, Vuchetich str, 21, Moscow 127206, Russian Federation
- Vladimir Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Rinat Vereshchagin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Alexey Volnukhin
- City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium, Vuchetich str, 21, Moscow 127206, Russian Federation
- Gaukhar Yusubalieva
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Orekhovy Boulevard, 28, Moscow 115682, Russian Federation
- Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow 119435, Russian Federation
- Journal volume & issue
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Vol. 40
p. 107770
Abstract
The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the patient's susceptibility to infection and disease severity due to its ability to modulate the immune system response of the host organism.This data article describes the microbiome dataset from the upper respiratory tract of SARS-CoV-2 positive patients from Russia. This dataset reports the microbial community profile of 335 human nasopharyngeal swabs collected between 2020-05 and 2021-03 during the first and the second epidemic waves. Samples were collected from both inpatients and outpatients in 4 cities of the Russian Federation (Moscow, Kazan, Irkutsk, Nizhny Novgorod) and sequenced using the 16S rRNA gene amplicon sequencing of V3-V4 region. Data contains information about the patient such as age, sex, hospitalization status, percent of damaged lung tissue, oxygen saturation (SpO2), respiratory rate, need for supplemental oxygen, chest computer tomography severity score, SARS-CoV-2 lineage, and also information about smoking and comorbidities.The amplicon sequencing data were deposited at NCBI SRA as BioProject PRJNA751478.
