The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019
Open accessAbstract
Background: A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)–CoV-2, has infected >75 000 individuals and spread to >20 countries. It is still unclear how fast the virus evolved and how it interacts with other microorganisms in the lung. Methods: We have conducted metatranscriptome sequencing for bronchoalveolar lavage fluid samples from 8 patients with SARS–CoV-2, and also analyzed data from 25 patients with community-acquired pneumonia (CAP), and 20 healthy controls for comparison. Results: The median number of intrahost variants was 1–4 in SARS–CoV-2–infected patients, ranged from 0 to 51 in different samples. The distribution of variants on genes was similar to those observed in the population data. However, very few intrahost variants were observed in the population as polymorphisms, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. Although current evidence did not support the transmission of intrahost variants in a possible person-to-person spread, the risk should not be overlooked. Microbiotas in SARS–CoV-2–infected patients were similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria. Conclusion: SARS–CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intrahost variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“metagenomic sequencing of bronchoalveolar lavage fluid among patients with COVID‐19 demonstrated an increased presence of oral and upper‐respiratory‐tract bacteria.”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [309]
In the citing paper
“Metatranscriptome sequencing for the bronchoalveolar lavage fluid (BALF) of 8 COVID-19 patients revealed the presence of elevated levels of oral and upper respiratory commensal bacteria (Shen et al., 2020).”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Shen et al., 2020
In the citing paper
“with the elevated level of oral commensal bacteria were found from the BALF of COVID-19 patients (Shen et al., 2020)”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Shen et al., 2020
In the citing paper
“The second one is the variety of data of a pandemic virus. This COVID-19 virus ‘SARS-CoV-2’ has been mutating itself over different geographic regions, environments, and time [102], [103]. Therefore, the pandemic dataset collected from one region may not be work to drawn inference on the pandemic of other regions.”
From A survey on deep transfer learning to edge computing for mitigating the COVID-19 pandemic (2020) · cites this paper as [102]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationClinical features of patients infected with 2019 novel coronavirus in Wuhan, China
Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30183-5 · Cited by 48,884
Self-citationfastp: an ultra-fast all-in-one FASTQ preprocessor
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty560 · Cited by 29,721
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., et al. (2020) · Nature · doi:10.1038/s41586-020-2012-7 · Cited by 21,969
Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30211-7 · Cited by 21,415
Self-citationAligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 10,846
Mandell, L. A., Wunderink, R. G., Anzueto, A., Bartlett, J. G., Campbell, G. D., Dean, N. C., Dowell, S. F., File, T. M., Musher, D. M., Niederman, M. S., et al. (2007) · Clinical Infectious Diseases · doi:10.1086/511159 · Cited by 6,182
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,155
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 401–500 of 515
Did the SARS-CoV-2 Come from Wild, Mutagenic or Artificial Type? Complete Genome Analysis
Dawood, A. A., Al-Rrassam, Z. T., & Altobje, M. A. (2022) · Research Journal of Science and Technology · doi:10.52711/2349-2988.2022.00003 · Cited by 3
Tripartite Communication in COVID-19 Infection: SARS-CoV-2 Pathogenesis, Gut Microbiota and ACE2
Badi, S. A., Khatami, S., & Siadat, S. D. (2022) · Future Virology · doi:10.2217/fvl-2021-0231 · Cited by 4
Zhou, Y., Lu, S., Wei, X., Hu, Y., Li, H., Wang, J., Lin, Y., Li, M., Wang, M., Ma, J., et al. (2022) · Biomolecules · doi:10.3390/biom13010006 · Cited by 3
Self-citationNaso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19
Viana, M. C., Curty, G., Furtado, C., Singh, B., Bendall, M. L., Viola, J. P. B., de Melo, A. C., Soares, M. A., & Moreira, M. Â. M. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1074382 · Cited by 3
Deep Learning-based Analysis and Classification of COVID Patients Through CT Images
Alam, M., Akram, M. U., & Fareed, W. (2023) · doi:10.1109/icai58407.2023.10136653 · Cited by 3
Post-mortem findings in Spanish patients with COVID-19; a special focus on superinfections
Ruiz-Cáceres, I., Romero, T. H., Guerra‐Merino, I., Zapirain, J. P., Perez‐Mies, B., Sánchez‐Conde, M., Alonso, M., Rubio, R., Alen, J. F., González, Á. V., et al. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2023.1151843 · Cited by 3
Intra-host variability of SARS-CoV-2: Patterns, causes and impact on COVID-19
Jones, L. R. (2024) · Virology · doi:10.1016/j.virol.2024.110366 · Cited by 3
Evaluation of thorax computed tomographic findings in COVID-19 variant cases
Gökharman, F. D., Ertem, G. T., Aydın, S., BÜYÜKDEMİRCİ, A., Yüksekkaya, E., Tokur, O., & Koşar, P. N. (2022) · Respiratory Investigation · doi:10.1016/j.resinv.2021.11.013 · Cited by 3
Li, Y., Wang, Y., Qiu, Y., Gong, Z. H., Deng, L., Pan, M., Yang, H., Xu, J., Li, Y., & Li, J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.04.077842 · Cited by 3
Ren, L., Wang, Y., Zhong, J., Zhang, D., Xiao, Y., Yang, J., Fan, G., Guo, L., Shen, Z., Liu, W., et al. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3719095 · Cited by 3
Self-citationThe value of repeat patient testing for SARS-CoV-2: real-world experience during the first wave
Zhu, A. M., Creagh, M., Qi, C., Galvin, S., Bolon, M. K., & Zembower, T. (2021) · Access Microbiology · doi:10.1099/acmi.0.000239 · Cited by 2
Goya, S., Sosa, E. J., Jodar, M. S. N., Torres, C., König, G. A., Acuña, D., Ceballos, S. G., Distéfano, A. J., Dopazo, H., dos Santos, M. D. M., et al. (2022) · Virus Research · doi:10.1016/j.virusres.2022.199035 · Cited by 2
Alterations in microbiome of COVID-19 patients and its impact on forensic investigations
Mir, T. U. G., Manhas, S., Wani, A. K., Akhtar, N., Shukla, S., & Prakash, A. (2023) · Science & Justice · doi:10.1016/j.scijus.2023.12.002 · Cited by 2
Overview of diagnostic tools and nano-based therapy of SARS-CoV-2 infection
Bhattacharjee, B., Rynjah, D., Ahmed, A. B., Newar, A., Sengupta, S., Chakrabarty, S., Sahu, R. K., & Khan, J. (2024) · Chemical Papers · doi:10.1007/s11696-023-03271-8 · Cited by 2
Neurological manifestations in hospitalized COVID-19 patients: a cross-sectional study
Kashipazha, D., Shalilahmadi, D., Shamsaei, G., & Porkar, N. F. (2024) · The Egyptian Journal of Neurology Psychiatry and Neurosurgery · doi:10.1186/s41983-024-00818-8 · Cited by 2
A case of asymptomatic SARS-CoV-2 infection followed by secondary community acquired pneumonia
Chen, J., Tian, C., Cheng, X., Wang, R., Zhou, H., & Zeng, X. (2020) · Quantitative Imaging in Medicine and Surgery · doi:10.21037/qims-20-847 · Cited by 2
Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality
Yang, W., & Jin, G. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa208 · Cited by 2
Li, Y., CHEN, Y., Ni, H., Yi, B., Zhang, D., Zhang, J., Wang, W., Liu, Y., Jiao, S., Xu, G., et al. (2021) · Polish Journal of Microbiology · doi:10.33073/pjm-2021-029 · Cited by 2
AbdelMassih, A. F., Hassan, A. A., Abouzeid, A., Hassan, A., Hussein, E., Gadalla, M., Hussein, M., Eid, M. A., ElAhmady, M., Nahhas, N. E., et al. (2021) · Cardiovascular Endocrinology & Metabolism · doi:10.1097/xce.0000000000000242 · Cited by 2
Barengolts, E. I., & Smith, E. D. (2020) · Endocrine Practice · doi:10.4158/ep-2020-0336 · Cited by 2
Li, M., Ren, L., Wang, Y., Zhong, J., Zhang, D., Xiao, Y., Li, J., Yang, J., Fan, G., Guo, L., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-95239/v1 · Cited by 2
Self-citationUnlocking capacities of viral genomics for the COVID-19 pandemic responsePreprint
Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Comarova, Z., Lu, A., Porozov, Y. B., et al. (2021) · PubMed · doi:10.48550/arxiv.2104.14005 · Cited by 2
A Visual Framework of Meta Genomic Analysis on Variations of Whole SARS-CoV-2 SequencesPreprint
Zheng, J., & Liu, J. (2021) · Research Square · doi:10.21203/rs.3.rs-65152/v3 · Cited by 2
Perfil epidemiológico da pandemia de COVID-19 e características do agente etiológico: Revisão
Nogueira, A. B., Silva, C. V. D. S., da Silva, L. M., de Freitas, M. R., & Knackfuss, F. B. (2021) · PubVet · doi:10.31533/pubvet.v15n06a845.1-11 · Cited by 1
Mutations in SARS-CoV-2 genomes and future strategies
Nimavat, N. K., Singh, S., Agrawal, A., Rafi, M. A., Bhatti, B., Parmar, G. R., & Shah, A. P. (2021) · Clinical Epidemiology and Global Health · doi:10.1016/j.cegh.2021.100875 · Cited by 1
Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease
Jochum, M. D., Lee, M., Curry, K. D., Zaksas, V., Vitalis, E., Treangen, T. J., Aagaard, K. M., & Ternus, K. L. (2022) · Scientific Reports · doi:10.1038/s41598-022-25463-0 · Cited by 1
Succint review on biological and clinical aspects of Coronavirus disease 2019 (COVID-19)
Ahmadi, S. E., Farzanehpour, M., Fard, A. M. M., Fard, M. M., & Ghaleh, H. E. G. (2022) · Romanian Journal of Military Medicine · doi:10.55453/rjmm.2022.125.3.2 · Cited by 1
Sandler, I. V., & Амхадова, М. А. (2023) · Stomatology for all / International Dental Review · doi:10.35556/idr-2023-1(102)48-55 · Cited by 1
Lou, S., Yang, M., Li, T., Zhao, W., Cevasco, H., Yang, Y., & Gerstein, M. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011222 · Cited by 1
Grigoli, E. C. A., Sejópoles, M. D., Gomes, L. T., & Fontes, C. J. F. (2023) · Journal of Advances in Medicine and Medical Research · doi:10.9734/jammr/2023/v35i225256 · Cited by 1
SARS-CoV-2 Variants Genotyping and Diagnostic Performance of a 2-Genes Detection Assay
Matheka, C., Kilonzo, J., Mbugua, E., Munshi, Z., Nyasinga, J., Revathi, G., & Njau, A. N. (2024) · The Journal of Applied Laboratory Medicine · doi:10.1093/jalm/jfad127 · Cited by 1
Impact of COVID-19 on gut–lung microbiota a mini review
Emadi, R., Yousefi, P., & Tabibzadeh, A. (2025) · Reviews in Medical Microbiology · doi:10.1097/mrm.0000000000000423 · Cited by 1
On the Scalability of Computing Genomic Diversity Using SparkLeBLAST: A Feasibility Study
Prabhu, R., Moussad, B., Youssef, K., Vatai, E., & Feng, W.-C. (2024) · IEEE High Performance Extreme Computing Conference · doi:10.1109/hpec62836.2024.10938466 · Cited by 1
¿CUÁL ES EL MECANISMO QUE PERMITE AL SARS-CoV-2 ENTRAR A LAS CÉLULAS HUMANAS?
Gordillo, J. M. L., Sosa, M. A., Marín, A. H., Montejo-Méndez, H. B., Valdés-Marín, A., de la Cruz, M. Z., & Reyes, E. B. R. (2020) · Kuxulkab · doi:10.19136/kuxulkab.a26n56.3838 · Cited by 1
COVID-19 – the challenge to treat a disease and not a positive RT-PCR test
Moneva-Sakelarieva, M. G., Kobakova, Y. A., Atanasov, P. Y., Obreshkova, D. P., Ivanova, S. A., & Stankova, E. K. (2021) · Pharmacia · doi:10.3897/pharmacia.68.e61906 · Cited by 1
Yang, R., Wei, J., Hu, W., Xiong, J., Liu, M., & Hu, K. (2021) · Annals of Palliative Medicine · doi:10.21037/apm-20-2222 · Cited by 1
Behavioural factors and the risk of viral infection: essential aspects in the COVID-19 pandemic
Rychter, A. M., Zawada, A. E., Szymczak‐Tomczak, A., Ratajczak, A. E., Dobrowolska, A., & Krela‐Kaźmierczak, I. (2021) · Polskie Archiwum Medycyny Wewnętrznej · doi:10.20452/pamw.15994 · Cited by 1
Predominant Mutations of SARS-CoV-2: Their Geographical Distribution and Potential Consequences
Ünlü, S., Güçlü, A. Ü., & BAŞUSTAOĞLU, A. C. (2021) · Mediterranean Journal of Infection Microbes and Antimicrobials · doi:10.4274/mjima.galenos.2021.2021.15 · Cited by 1
Hwang, E.-H., Chung, H., Kim, G., Oh, H., An, Y. J., Kang, P., Ryu, C., Park, J., Hong, J., & Koo, B. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.694897 · Cited by 2
Piot, N., & Smagghe, G. J. (2022) · Viruses · doi:10.3390/v14030503 · Cited by 1
SARS-CoV-2 Molecular Diagnostics in China
Lu, Y., & Sun, Z. (2022) · Clinics in Laboratory Medicine · doi:10.1016/j.cll.2022.03.003 · Cited by 1
Russo, E., Curini, L., Fabbrizzi, A., & Amedei, A. (2022) · Springer eBooks · doi:10.1007/978-981-16-8957-4_14 · Cited by 1
Overview on COVID-19 outbreak indicators across Brazilian federative unitsPreprint
Guerra‐Shinohara, E. M., Weber, S. S., Paniz, C., Gomes, G. W., Shinohara, E. J., Gandra, T. B. R., Pereira, I. C., Jarcem, K. G., Zanre, R. F. D. A., Barreto, A. G., et al. (2020) · medRxiv · doi:10.1101/2020.06.02.20120220 · Cited by 1
Early detection of SARS-CoV-2 in circulating immune cells in a mouse modelPreprint
Geng, T., Keilich, S. R., Tafas, T. P., & Wang, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.30.450531 · Cited by 1
Rahmasari, R., Raekiansyah, M., Azallea, S. N., Nethania, M., Bilqisthy, N., Rozaliyani, A., Bowolaksono, A., & Sauriasari, R. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3951700 · Cited by 1
Mostafa, M., Barhoum, A., Sehit, E., Gewaid, H. E., Mostafa, E., Omran, M. M., Abdalla, M. S., Altıntaş, Z., & Forster, R. J. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4016299 · Cited by 1
Gromov, D., & Romero-Severson, E. O. (2019) · arXiv (Cornell University) · doi:10.3390/math8091500
Babalola, M. O. (2020) · The University of Louisville Journal of Respiratory Infections · doi:10.18297/jri/vol4/iss1/45
Yu, L., Wang, Y., He, H.-Q., Chu, Y., Feng, H., Wei, Y., Zhou, J., Song, Q., & Gong, H. (2020) · doi:10.21203/rs.3.rs-19186/v1
A Visual Framework of Meta Genomic Analysis on Variations of Whole SARS-CoV-2 SequencesPreprint
Zheng, J., & Liu, J. (2020) · Research Square · doi:10.21203/rs.3.rs-65152/v2
Qi, M., liu, S., Wang, Y., Liu, J., Wu, L., Liu, Z., & Yu, X. (2020) · doi:10.21203/rs.3.rs-55362/v1
Diagnostic tests for SARS-CoV-2: current status and issues
Mazumder, S., & Hoque, M. M. (2021) · IMC Journal of Medical Science · doi:10.3329/imcjms.v14i2.52831
Zhou, Y., Lu, S., Li, M., Wang, M., Ma, J., Mao, Y., Zhu, Z., Min, J., Xiao, J., Qiu, R., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-490714/v1
Self-citationPoelvoorde, L. A. E. V., Gand, M., Fraiture, M.-A., de Keersmaecker, S. D., Verhaegen, B., van Hoorde, K., Cay, A., Balmelle, N., Herman, P., & Roosens, N. (2021) · Research Square · doi:10.21203/rs.3.rs-590427/v1
THE RELEVANCE OF RT-PCR TEST TO THE INFECTION WITH SARS-COV-2 VIRUS.
Agrawal, S. N. (2021) · INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH · doi:10.36106/ijsr/5902964
Atienza, J. E. (2006) · Temas para el debate
Nasopharyngeal Microbiota Profiling of Pregnant Women with SARS-CoV-2 InfectionPreprint
Crovetto, F., Selma‐Royo, M., Crispi, F., Carbonetto, B., Pascal, R., Larroya, M., Casas, I., Tortajada, M., Escudero, N., Muñoz‐Almagro, C., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3989789
Unlocking the Mysteries of the Human Microbiome to Combat COVID-19
Muthuirulan, P., Bandyopadhyay, M., Mamillapalli, S., & Sharma, P. (2022) · Springer eBooks · doi:10.1007/978-981-16-7672-7_11
Diagnostic Approaches for Covid-19: Present Status and Future Prospects
(2022) · Letters in Applied NanoBioScience · doi:10.33263/lianbs121.022
Nasopharyngeal Microbiota Profiling of Pregnant Women With Sars-Cov-2 InfectionPreprint
Crovetto, F., Selma‐Royo, M., Crispi, F., Carbonetto, B., Pascal, R., Larroya, M., Casas, I., Tortajada, M., Escudero, N., Muñoz‐Almagro, C., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1232752/v1
Recent developments of molecular/biosensor diagnostics for SARS-CoV-2 detection
Mishra, R. K., Pai, N., Goud, K. Y., Niraj, R. R. K., Kumar, D., Patel, G., Gour, V. S., Zareei, A., Rahimi, R., Sharma, V., et al. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-824494-4.00014-x
Aziz, K. M. A., Othman, A., Alqahtani, W. A., & Azhar, S. (2021) · Iberoamerican Journal of Medicine · doi:10.53986/ibjm.2021.0023 · Cited by 2
Perfil epidemiológico da pandemia de COVID-19 e características do agente etiológico: Revisão
de Freitas, M. R., Barreto, A., Vasconcelos, C., de Melo, L. N., & Knackfuss, F. B. (2021) · PubVet · doi:10.31533/pubvet.v15n03a845.1-11
Dudouet, P., Colson, P., Aherfi, S., Levasseur, A., Beye, M., Delerce, J., Burel, E., Lavrard, P., Bader, W., Lagier, J., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1850887/v1
Current clinical testing approach of COVID
Bhardwaj, M., & Kakkar, P. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90280-9.00003-1
COVID-19 in periodontal patients
Perszke, M., & Egierska, D. M. (2022) · Journal of Education Health and Sport · doi:10.12775/jehs.2022.12.09.014
Progress of hollow materials in diagnosis of COVID-19
Hussain, A., Shabbir, S., Faizan, M., & Tajwar, M. A. (2022) · Chemical Reports · doi:10.25082/cr.2022.01.002
COVID‐19, Microbiota, and Probiotics
Mozota, M., Fernández, L., & Rodríguez, J. M. (2022) · doi:10.1002/9781119762621.ch5
Vani, G. S., & Swapna, M. (2022) · IP International Journal of Medical Microbiology and Tropical Diseases · doi:10.18231/j.ijmmtd.2022.055
COVID-19 pandemic and oral health care: Cause-and-effect
(2022) · Den norske tannlegeforenings Tidende · doi:10.56373/2022-2-6
Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinityPreprint
Ma, W., Fu, H., Jian, F., Cao, Y., & Li, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.06.527236
Self-citationMolayem, S., & Pontes, C. D. N. (2022) · Journal of the California Dental Association · doi:10.1080/19424396.2022.12220693
Laxminarayana, D. (2023) · Rheumatology & autoimmunity · doi:10.1002/rai2.12065
Sсherbak, S. G., Vologzhanin, D. A., Kamilova, Т. A., Голота, А. С., & Макаренко, С. В. (2023) · Physical and rehabilitation medicine medical rehabilitation · doi:10.36425/rehab121733 · Cited by 2
Progress of Hollow Materials in Diagnosis of Covid-19
Hussain, A., Shabbir, S., & Faizan, M. (2022) · Austin Journal of Pharmacology and Therapeutics · doi:10.26420/austinjpharmacolther.2022.1163
Covid-19 and Vaccine Hesitancy among Public Communities: A Global Health Perspective
(2023) · International Journal of Agriculture and Biosciences · doi:10.47278/book.oht/2023.13 · Cited by 1
Şahin, E. Ö., & Köroğlu, M. (2023) · doi:10.59537/saupress.2337
Alterações histopatológicas pulmonares e patogenia da covid-19: uma revisão literária
Potrich, R., Braga, D. O., Zamoner, B. M., Barbosa, H. L. M., Frota, M. V. M., Zoccal, K. F., & Tefé‐Silva, C. (2023) · Revista Interdisciplinar de Saúde e Educação · doi:10.56344/2675-4827.v4n1a2023.6
Bennani, H., GHOUZRAF, I., MEZOUARI, H. E., & Moutaj, R. (2023) · GSC Advanced Research and Reviews · doi:10.30574/gscarr.2023.17.2.0433
Bennani, H., Guennouni, M., Ouarradi, A. E., Hanchi, A. L., & Soraa, N. (2023) · Iranian Journal of Microbiology · doi:10.18502/ijm.v15i6.14138
Bioinformatics in the study of microbial infections
Snyder, L. A. S. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-818619-0.00039-3
Grădinaru, I. (2023) · The Medical-Surgical Journal · doi:10.22551/msj.2023.04.15
Additional file 1 of Beware of pharyngeal Fusobacterium nucleatum in COVID-19
Bao, L., Zhang, C., Lyu, J., Yan, C., Cao, R., Pan, M., & Li, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16786909
Wang, Y., Wang, D., Zhang, L., Sun, W., Zhang, Z., Chen, W., Zhu, A., Huang, Y., Xiao, F., Yao, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14091609
Self-citationSymptomatology, pathophysiology and treatment perspectives of "long COVID" syndrome
Dobrek, Ł. (2024) · Farmacja Polska · doi:10.32383/farmpol/185761
Le microbiote pulmonaire, perspective d’innovation en microbiologie médicale
Héry-Arnaud, G. (2024) · Revue Francophone des Laboratoires · doi:10.1016/s1773-035x(24)76117-6
Saedi, A. J. L. F. (2024) · Journal of Social Science · doi:10.46799/jss.v5i4.877
Microbiome and the COVID-19 pandemic
Patel, P. R., & Bhattacharjee, M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-90144-4.00008-2
Kamio, N., Tamura, M., Okazaki, S., Sugimoto, K., Cueno, M. E., Tanaka, H., & Imai, K. (2024) · Journal of Oral Science · doi:10.2334/josnusd.24-0211
Jimenez-Campos, A. G., Maestas, L. I., Velappan, N., Beck, B. J., Ye, C., Wernsing, K. A., Mata-Solis, Y., Bruno, W., Bussmann, S. C., Bradfute, S. B., et al. (2024) · PLoS ONE · doi:10.1371/journal.pone.0309305
Scalable and Maintainable Distributed Sequence Alignment Using Spark
Youssef, K., Elnady, Y., Tilevich, E., & Feng, W.-C. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3565188
Comprehensive and translational pathobiology of COVID-19 based on cellular and molecular techniques
Samadani, A. A., Vahidi, S., Babaei, K., Norollahi, S. E., Delpasand, K., & Gharakhyli, E. A. (2025) · Practical Laboratory Medicine · doi:10.1016/j.plabm.2025.e00497
Metataxonomic and functional analysis of the human gut microbiome associated with COVID-19 patients
Machado, N. S., Bernal, S. P. F., Lacerda-Júnior, G. V., Centurion, V. B., Ottoni, J. R., & Passarini, M. R. Z. (2025) · The Microbe · doi:10.1016/j.microb.2025.100548
Azam, I., Alam, S. S. M., Mir, S. A., Ali, S., & Hoque, M. (2025) · In Silico Research in Biomedicine · doi:10.1016/j.insi.2025.100106
PASCALE, G. D., Maio, F. D., Carelli, S., Angelis, G. D., Cacaci, M., Montini, L., Bello, G., Cutuli, S. L., Pintaudi, G., Tanzarella, E. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14746425
Cifuentes, E. A., Sierra, M. A., Yepes, A. F., Baldión, A. M., Rojas, J. A., Moreno, C. A. Á., Anzola, J. M., Zambrano, M. M., & Huertas, M. G. (2022) · Figshare · doi:10.6084/m9.figshare.20155578
Metadata
- Authors
- Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., Guo, L., Zhang, G., Li, H., Xu, Y., Chen, M., Gao, Z., Wang, J., Ren, L., & Li, M.
- Affiliations
- Chinese Academy of Sciences (CN)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Peking University (CN)
- Peking University People's Hospital (CN)
- Southern University of Science and Technology (CN)
- Fujian Provincial Hospital (CN)
- First Affiliated Hospital of Xi'an Jiaotong University (CN)
- Corresponding author
- Li, Mingkun
- ORCID
- Venue
- Clinical Infectious Diseases
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-03-09
- Volume
- 71
- Issue
- 15
- Pages
- 713-720
- ISSN
- 1058-4838 (ISSN-L)
- 1537-6591
- PMC
- PMC7108196
- OpenAlex
- W3009109635
- Cited by
- 513
- References
- 43
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 29 · 2023: 48 · 2022: 86 · 2021: 180 · 2020: 157
- FWCI
- 15.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Clinical Infectious Diseases (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (2016-I2M-1-014)
- National Major Science & Technology Project for Control and Prevention of Major Infectious Diseases in China (2017ZX10103004, 2018ZX10305409, 2018ZX10301401, 2018ZX1073240)
- National Natural Science Foundation of China (31670169, 31871263)
- Open Project of Key Laboratory of Genomic and Precision Medicine, Chinese Academy of Sciences
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- SARS-CoV-2, COVID-19 pandemic, viral evolution, metatranscriptomics, bronchoalveolar lavage fluid, lung microbiome, community-acquired pneumonia, virus transmission, purifying selection, commensal bacteria
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Humans, Pneumonia, Viral, Genetic Variation, Coronavirus, Coronavirus Infections, Genomics, Severe Acute Respiratory Syndrome, Pandemics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
