key: cord-0840474-aca1pt8d
authors: Galeeva, Julia; Babenko, Vladislav; Bakhtyev, Ramiz; Baklaushev, Vladimir; Balykova, Larisa; Bashkirov, Pavel; Bespyatykh, Julia; Blagonravova, Anna; Boldyreva, Daria; Fedorov, Dmitry; Gafurov, Ilshat; Gaifullina, Raushaniya; Galova, Elena; Gospodaryk, Alina; Ilina, Elena; Ivanov, Konstantin; Kharlampieva, Daria; Khromova, Polina; Klimina, Ksenia; Kolontarev, Konstantin; Kolyshkina, Nadezhda; Koritsky, Andrey; Kuropatkin, Vyacheslav; Lazarev, Vasily; Manolov, Alexander; Manuvera, Valentin; Matyushkina, Daria; Morozov, Maxim; Moskaleva, Ekaterina; Musarova, Varvara; Ogarkov, Oleg; Orlova, Elizaveta; Pavlenko, Alexander; Petrova, Alla; Pozhenko, Natalia; Pushkar, Dmitry; Rumyantsev, Alexander; Rumyantsev, Sergey; Rumyantsev, Vladimir; Rychkova, Lyubov; Samoilov, Alexander; Shirokova, Irina; Sinkov, Vyacheslav; Solovieva, Svetlana; Starikova, Elizaveta; Tikhonova, Polina; Trifonova, Galina; Troitsky, Alexander; Tulichev, Alexander; Udalov, Yuri; Varizhuk, Anna; Vasiliev, Alexander; Veselovsky, Vladimir; Vereshchagin, Rinat; Volnukhin, Alexey; Yusubalieva, Gaukhar; Govorun, Vadim
title: 16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients
date: 2021-12-29
journal: Data Brief
DOI: 10.1016/j.dib.2021.107770
sha: 3e56c52b3f17a4a8b5ff7aafedf7777a50b25950
doc_id: 840474
cord_uid: aca1pt8d

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.

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. • This data will be especially interesting to investigators interested in the association between 6 upper respiratory tract microbiome composition and COVID-19 severity. 7 • This data will be useful to investigators interested in the association between the host's age, 

The study involved both inpatients and outpatients with COVID-19 who had a confirmed PCR 28 test for the presence of SARS-CoV-2 and signed informed consent to participate in the study. 29 The study did not include patients with cancer. 

Resources, Methodology; Elizaveta 87 Orlova : Resources, Conceptualization; Alexander Pavlenko : Conceptualization, Methodology, 88 Supervision; Alla Petrova : Resources, Methodology; Natalia Pozhenko : Resources, Conceptu-89 alization; Dmitry Pushkar : Resources, Conceptualization; Alexander Rumyantsev : Resources, 90 Data curation; Sergey Rumyantsev : Resources, Data curation; Vladimir Rumyantsev : Resources, 91 Data curation

Irina Shirokova : Resources, Conceptualization; Vyacheslav Sinkov : Resources, 93 Data curation; Svetlana Solovieva : Resources, Data curation; Elizaveta Starikova : Writing -re-94 view & editing; Polina Tikhonova : Formal analysis

Resources, Methodology; Alexander Tulichev : Resources, Conceptu-96 alization; Yuri Udalov : Resources, Methodology; Anna Varizhuk : Resources, Conceptualization

Alexander Vasiliev : Resources, Data curation; Vladimir Veselovsky : Investigation, Methodology

Formal analysis; Alexey Volnukhin : Resources, Conceptualization; Gaukhar 99 Yusubalieva : Resources, Data curation

Trimmomatic: a flexible trimmer for Illumina sequence data

DADA2: high-resolution sample infer-108 ence from Illumina amplicon data

VSEARCH: a versatile open source tool for metagenomics

Deblur rapidly resolves 112 single-nucleotide community sequence patterns

16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients