Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019

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

Clinical 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

fastp: 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

Epidemiological and clinical characteristics of 99 cases of 2019 novel Coronavirus pneumonia in Wuhan, China: a descriptive study.

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

Aligning 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

Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults

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

An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome

Desai, S., Rashmi, S., Rane, A., Dharavath, B., Sawant, A., & Dutt, A. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa437 · Cited by 26

Current Updates on Naturally Occurring Compounds Recognizing SARS-CoV-2 Druggable Targets

Romeo, I., Mesiti, F., Lupia, A., & Alcaro, S. (2021) · Molecules · doi:10.3390/molecules26030632 · Cited by 30

Two-dimensional material-based virus detection

Wang, W., Zhai, W., Chen, Y., He, Q., & Zhang, H. (2022) · Science China Chemistry · doi:10.1007/s11426-021-1150-7 · Cited by 30

The gut microbiome: a missing link in understanding the gastrointestinal manifestations of COVID-19?Preprint

Brooks, E. F., & Bhatt, A. S. (2021) · Molecular Case Studies · doi:10.1101/mcs.a006031 · Cited by 29

Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology

Márquez, S., Prado-Vivar, B., Guadalupe, J. J., Gutiérrez, B., Jibaja, M., Galindo, M. A. T., Mora, F., Gaviria, J., García, M., Espinosa, F., et al. (2020) · Microbiology Resource Announcements · doi:10.1128/mra.00996-20 · Cited by 27

Analytical Performance of COVID-19 Detection Methods (RT-PCR): Scientific and Societal Concerns

Verna, R., Alallón, W., Murakami, M., Hayward, C. P. M., Harrath, A. H., Alwasel, S. H., Sumita, N. M., Alataş, Ö., Fedeli, V., Sharma, P., et al. (2021) · Life · doi:10.3390/life11070660 · Cited by 28

Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development—A Perspective Review

Chatterjee, R., Ghosh, M., Sahoo, S., Padhi, S., Misra, N., Raina, V., Suar, M., & Son, Y. (2021) · Vaccines · doi:10.3390/vaccines9080812 · Cited by 27

Periodontal Diseases: Major Exacerbators of Pulmonary Diseases?

Kouanda, B., Sattar, Z., & Geraghty, P. M. (2021) · Pulmonary Medicine · doi:10.1155/2021/4712406 · Cited by 31

Bacterial Ventilator-Associated Pneumonia in COVID-19 Patients: Data from the Second and Third Waves of the Pandemic

Russo, A., Olivadese, V., Trecarichi, E. M., & Torti, C. (2022) · Journal of Clinical Medicine · doi:10.3390/jcm11092279 · Cited by 26

Clinical Effects of Streptococcus salivarius K12 in Hospitalized COVID-19 Patients: Results of a Preliminary Study

Pierro, F. D., Iqtadar, S., Mumtaz, S. U., Bertuccioli, A., Recchia, M., Zerbinati, N., & Khan, A. P. (2022) · Microorganisms · doi:10.3390/microorganisms10101926 · Cited by 28

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

Gand, M., Vanneste, K., Thomas, I., Gucht, S. V., Capron, A., Herman, P., Roosens, N. H. C., & Keersmaecker, S. C. J. D. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21155585 · Cited by 25

Risk factors for severe cases of COVID-19: a retrospective cohort study

He, F., Luo, Q., Lei, M., Fan, L., Shao, X., Huang, G., Zeng, J., Zhao, Z., Qin, S., Yang, Z. X., et al. (2020) · Aging · doi:10.18632/aging.103803 · Cited by 25

Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain

Ip, J. D., Kok, K., Chan, W.-M., Chu, A. W., Wu, W., Yip, C. C., To, W., Tsang, O. T., Leung, W.-S., Chik, T. S., et al. (2020) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2020.10.030 · Cited by 25

Immunotherapeutics for Covid-19 and post vaccination surveillance

Kumar, N. S. S., Chintagunta, A. D., Kumar, S., Roy, S., & Kumar, M. (2020) · 3 Biotech · doi:10.1007/s13205-020-02522-9 · Cited by 25

SARS-CoV-2: The Monster Causes COVID-19

Song, C. C., Li, Z., Li, C., Huang, M., Liu, J., Fang, Q., Cao, Z., Zhang, L., Gao, P., Nie, W., et al. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.835750 · Cited by 25

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID‐19 and its Association with Microbiota in the Gut

Shen, Y., Yu, F., Zhang, D., Zou, Q., Xie, M., Chen, X., Yuan, L., Lou, B., Xie, G., Wang, R., et al. (2022) · Advanced Science · doi:10.1002/advs.202200956 · Cited by 25

The oral manifestations and related mechanisms of COVID-19 caused by SARS-CoV-2 infection

Lin, W.-M., Gao, F., Wang, X., Qin, N., Chen, X., Tam, K. Y., Zhang, C., Zhang, M., & Sha, O. (2023) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2022.1006977 · Cited by 29

Gut microbiota in COVID-19: new insights from inside

Zhou, B., Pang, X., Wu, J., Liu, T., Wang, B., & Cao, H. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2201157 · Cited by 27

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

Farjo, M., Koelle, K., Martin, M. A., Gibson, L. L., Walden, K. K. O., Rendon, G., Fields, C. J., Alnaji, F. G., Gallagher, N., Luo, C. H., et al. (2024) · Journal of Virology · doi:10.1128/jvi.01618-23 · Cited by 27

High‐coverage SARS‐CoV‐2 genome sequences acquired by target capture sequencing

Wen, S., Sun, C., Zheng, H., Wang, L., Zhang, H., Zou, L., Liu, Z., Du, P., Xu, X., Liang, L., et al. (2020) · Journal of Medical Virology · doi:10.1002/jmv.26116 · Cited by 24

SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany

Pfefferle, S., Günther, T., Kobbe, R., Czech‐Sioli, M., Nörz, D., Santer, R., Oh, J. S., Kluge, S., Oestereich, L., Peldschus, K., et al. (2020) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2020.09.034 · Cited by 26

Neurologic sequelae of COVID-19 are determined by immunologic imprinting from previous coronaviruses

Spatola, M., Nziza, N., Jung, W., Deng, Y., Yuan, D., Dinoto, A., Bozzetti, S., Chiodega, V., Ferrari, S., Lauffenburger, D. A., et al. (2023) · Brain · doi:10.1093/brain/awad155 · Cited by 25

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmissionPreprint

Sapoval, N., Mahmoud, M., Jochum, M. D., Liu, Y., Elworth, R. A. L., Wang, Q., Albin, D., Ogilvie, H., Lee, M. D., Villapol, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.02.184481 · Cited by 24

Reliability of real-time RT-PCR tests to detect SARS-Cov-2: A literature review

Bezier, C., Anthoine, G., & Charki, A. (2020) · International Journal of Metrology and Quality Engineering · doi:10.1051/ijmqe/2020014 · Cited by 23

Gene variants of coagulation related proteins that interact with SARS-CoV-2

Holcomb, D. D., Alexaki, A., Hernandez, N. E., Hunt, R., Laurie, K., Kames, J. M., Hamasaki‐Katagiri, N., Komar, A. A., DiCuccio, M. N., & Kimchi‐Sarfaty, C. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008805 · Cited by 25

Related Factors to Streptococcus pneumoniae Invasive Infection and Clinical Manifestations: The Potential Role of Nasopharyngeal Microbiome

Dietl, B., Henares, D., Boix-Palop, L., Muñoz‐Almagro, C., Garau, J., & Calbo, E. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.650271 · Cited by 25

Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection

Serpeloni, J. M., Neto, Q. A. D. L., Lúcio, L. C., Ramão, A., de Oliveira, J. C., Gradia, D. F., Malheiros, D., Ferrasa, A., Marchi, R., Figueiredo, D. L. A., et al. (2021) · Immunobiology · doi:10.1016/j.imbio.2021.152130 · Cited by 25

Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

Shan, K.-J., Wei, C., Wang, Y., Huan, Q., & Qian, W. (2021) · The Innovation · doi:10.1016/j.xinn.2021.100159 · Cited by 24

Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologiesPreprint

Rose, R., Nolan, D. J., Moot, S., Feehan, A. K., Cross, S., Garcia‐Diaz, J., & Lamers, S. L. (2020) · medRxiv · doi:10.1101/2020.04.24.20078691 · Cited by 23

Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneckPreprint

Braun, K. M., Moreno, G. K., Halfmann, P., Hodcroft, E. B., Baker, D. A., Boehm, E. C., Weiler, A. M., Haj, A. K., Hatta, M., Chiba, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.16.384917 · Cited by 22

SARS-CoV-2 Evolution: Implications for Diagnosis, Treatment, Vaccine Effectiveness and Development

Angius, F., Puxeddu, S., Zaimi, S., Canton, S., Nematollahzadeh, S., Pibiri, A., Delogu, I., Alvisi, G., Moi, M. L., & Manzin, A. (2024) · Vaccines · doi:10.3390/vaccines13010017 · Cited by 22

Neurological manifestations and comorbidity associated with COVID-19: an overview

Kumar, M., & Thakur, A. K. (2020) · Neurological Sciences · doi:10.1007/s10072-020-04823-6 · Cited by 22

Contribution of CT Features in the Diagnosis of COVID-19

Zuo, H.-D. (2020) · Canadian Respiratory Journal · doi:10.1155/2020/1237418 · Cited by 22

Novel risk scoring system for predicting acute respiratory distress syndrome among hospitalized patients with coronavirus disease 2019 in Wuhan, China

Liang, M., He, M., Tang, J., He, X., Liu, Z., Feng, S., Chen, P., Li, H., Xue, Y., Bai, T., et al. (2020) · BMC Infectious Diseases · doi:10.1186/s12879-020-05561-y · Cited by 22

Population Genomics Insights into the First Wave of COVID-19

Vasilarou, M., Alachiotis, N., Garefalaki, J., Beloukas, A. I., & Pavlidis, P. (2021) · Life · doi:10.3390/life11020129 · Cited by 30

Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure

Egeren, D. V., Novokhodko, A., Stoddard, M., Tran, U., Zetter, B. R., Rogers, M. S., Joseph‐McCarthy, D., & Chakravarty, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-02148-8 · Cited by 20

Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment

Cifuentes, E. A., Sierra, M. A., Yepes, A., Baldión, A. M., Rojas, J. A., Álvarez, C., Anzola, J. M., Zambrano, M. M., & Huertas, M. G. (2022) · Respiratory Research · doi:10.1186/s12931-022-02086-7 · Cited by 22

Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery

Kangabam, R. D., Sahoo, S., Ghosh, A., Roy, R., Silla, Y., Misra, N., & Suar, M. (2020) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2020.104158 · Cited by 23

Kawasaki disease in the COVID-19 era: a distinct clinical phenotype?

Kam, K., Ong, J. S. M., & Lee, J. H. (2020) · The Lancet Child & Adolescent Health · doi:10.1016/s2352-4642(20)30207-8 · Cited by 21

COVID‐19: emergence and mutational diversification of SARS‐CoV‐2

Brüssow, H. (2021) · Microbial Biotechnology · doi:10.1111/1751-7915.13800 · Cited by 23

Diagnosing COVID‐19 in human sera with detected immunoglobulins IgM and IgG by means of Raman spectroscopy

Goulart, A. C. C., Zângaro, R. A., Carvalho, H. C., & Silveira, L. (2021) · Journal of Raman Spectroscopy · doi:10.1002/jrs.6235 · Cited by 20

Pathophysiology and potential future therapeutic targets using preclinical models of COVID-19

Kumar, R., Lee, M. H., Mickael, C. S., Kassa, B., Pasha, Q., Tuder, R. M., & Graham, B. B. (2020) · ERJ Open Research · doi:10.1183/23120541.00405-2020 · Cited by 20

Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2

Hassan, S. S., Attrish, D., Ghosh, S., Choudhury, P. P., & Roy, B. (2021) · Virus Research · doi:10.1016/j.virusres.2021.198441 · Cited by 19

Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics

Marquioni, V. M., & de Aguiar, M. A. M. (2021) · PLoS ONE · doi:10.1371/journal.pone.0255438 · Cited by 20

Oral Lesions Associated with COVID-19 and the Participation of the Buccal Cavity as a Key Player for Establishment of Immunity against SARS-CoV-2

Gutiérrez-Camacho, J. R., Ávila-Carrasco, L., Martínez-Vázquez, M. C., Veloz, I. G., Zorrilla-Alfaro, S. M., Gutierrez-Camacho, V., & Martínez‐Fierro, M. L. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph191811383 · Cited by 22

High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection

Normandin, E., Rudy, M. A., Barkas, N., Schaffner, S. F., Levine, Z. C., Padera, R. F., Babadi, M., Mukerji, S. S., Park, D. J., MacInnis, B. L., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-34256-y · Cited by 21

Quantitative measures of within-host viral genetic diversity

Fuhrmann, L., Jablonski, K. P., & Beerenwinkel, N. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.06.002 · Cited by 19

COVID‐19 Pandemic and Periodontal Practice: The Immunological, Clinical, and Economic Points of View

Darestani, M. N., Akbari, A. A., Yaghobee, S., Taheri, M., & Akbari, S. (2022) · BioMed Research International · doi:10.1155/2022/3918980 · Cited by 18

Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection

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) · Scientific Reports · doi:10.1038/s41598-022-17542-z · Cited by 17

SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding

Dudouet, P., Colson, P., Aherfi, S., Levasseur, A., Beye, M., Delerce, J., Burel, E., Lavrard, P., Bader, W., Lagier, J., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-22060-z · Cited by 19

Periodontitis and COVID-19: Immunological Characteristics, Related Pathways, and Association

Qi, M., Sun, W., Wang, K., Li, W., Lin, J., Gong, J., & Wang, L. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24033012 · Cited by 22

Polymorphism of tmprss2 (rs12329760) but not ace2 (rs4240157), tmprss11a (rs353163) and cd147 (rs8259) is associated with the severity of COVID-19 in the Ukrainian population.

Кайдашев, І. П., Izmailova, O. V., Shlykova, O. A., Kabaliei, A., Vatsenko, A. I., Ivashchenko, D., Dudchenko, M., Volyansky, A. Y., Zelinskyy, G., Коваль, Т. І., et al. (2023) · Acta bio-medica dell'Ateneo parmense/Acta biomedica · doi:10.23750/abm.v94i1.13543 · Cited by 19

Potential interaction between the oral microbiota and COVID-19: a meta-analysis and bioinformatics prediction

Tan, L., Zhong, M., Liu, Q., Chen, Y., Zhao, Y., Zhao, J., Dusenge, M. A., Yao, F., Ye, Q., Hu, J., et al. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1193340 · Cited by 19

Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

Campos, G. S., Sardi, S. I., Falcão, M. B., Belitardo, E. M. M. D. A., Rocha, D. J. P. G., Rolo, C. D. A., Menezes, A. D. L., Pinheiro, C. S., Carvalho, R. H., de Almeida, J. P. P., et al. (2020) · Journal of Virological Methods · doi:10.1016/j.jviromet.2020.113888 · Cited by 22

Gut and airway microbiota and their role in COVID-19 infection and pathogenesis: a scoping review

Liu, T. F. D., Philippou, E., Kolokotroni, O., Siakallis, G., Rahima, K., & Constantinou, C. (2021) · Infection · doi:10.1007/s15010-021-01715-5 · Cited by 18

Compromised periodontal status could increase mortality for patients with COVID-19

Gupta, S., Saarikko, M., Pfützner, A., Räisänen, I. T., & Sorsa, T. (2022) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(22)00065-2 · Cited by 18

Possible Roles of Permafrost Melting, Atmospheric Transport, and Solar Irradiance in the Development of Major Coronavirus and Influenza Pandemics

Hofmeister, A. M., Seckler, J. M., & Criss, G. M. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph18063055 · Cited by 18

Cross-correlation of virome–bacteriome–host–metabolome to study respiratory health

Iorio, A., Biazzo, M., Gardini, S., Muda, A. O., Perno, C. F., Dallapiccola, B., & Putignani, L. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2021.04.011 · Cited by 21

Advancements in Testing Strategies for COVID-19

Asghar, R., Rasheed, M., Hassan, J. U., Rafique, M., Khan, M., & Deng, Y. (2022) · Biosensors · doi:10.3390/bios12060410 · Cited by 17

Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection

Lane, S., Hilliam, Y., & Bomberger, J. M. (2022) · Journal of Bacteriology · doi:10.1128/jb.00295-22 · Cited by 18

Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples

Terbot, J. W., Johri, P., Liphardt, S. W., Soni, V., Pfeifer, S. P., Cooper, B. S., Good, J. M., & Jensen, J. D. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011265 · Cited by 16

The COVID-19 Diagnostic Technology Landscape: Efficient Data Sharing Drives Diagnostic Development

Aguiar, E. R. G. R., Navas, J., & Pacheco, L. G. C. (2020) · Frontiers in Public Health · doi:10.3389/fpubh.2020.00309 · Cited by 17

Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

Sjaarda, C. P., Rustom, N., Evans, G. A., Huang, D., Pérez-Patrigeón, S., Hudson, M. L., Wong, H., Sun, Z., Guan, T. H., Ayub, M., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-83355-1 · Cited by 17

The microbiota-related coinfections in COVID-19 patients: a real challenge

Mohapatra, R. K., Dhama, K., Mishra, S., Sarangi, A. K., Kandi, V., Tiwari, R., & Pintilie, L. (2021) · Beni-Suef University Journal of Basic and Applied Sciences · doi:10.1186/s43088-021-00134-7 · Cited by 16

Beware of pharyngeal Fusobacterium nucleatum in COVID-19

Bao, L., Zhang, C., Lyu, J., Yan, C., Cao, R., Pan, M., & Li, Y. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02336-6 · Cited by 17

Characterization of SARS-CoV-2 viral diversity within and across hostsPreprint

Sashittal, P., Luo, Y., Peng, J., & El-Kebir, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.07.083410 · Cited by 18

Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2

Seibert, B., Cáceres, C. J., Carnaccini, S., Garcia, S. C., Gay, L. C., Ortiz, L., Geiger, G., Rajão, D. S., Ottesen, E. A., & Perez, D. R. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010734 · Cited by 14

Factors Influencing Microbiota in Modulating Vaccine Immune Response: A Long Way to Go

Ponziani, F. R., Coppola, G., Rio, P., Caldarelli, M., Borriello, R., Gambassi, G., Gasbarrini, A., & Cianci, R. (2023) · Vaccines · doi:10.3390/vaccines11101609 · Cited by 17

Laboratory-Based Resources for COVID-19 Diagnostics: Traditional Tools and Novel Technologies. A Perspective of Personalized Medicine

Andryukov, B. G., Besednova, N. N., Kuznetsova, T. A., & Fedyanina, L. N. (2021) · Journal of Personalized Medicine · doi:10.3390/jpm11010042 · Cited by 16

The administration of S. salivarius K12 to children may reduce the rate of SARS-CoV-2 infection

Pierro, F. D., & Colombo, M. D. H. P. (2021) · Minerva Medica · doi:10.23736/s0026-4806.21.07487-5 · Cited by 16

Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients

Sehli, S., Allali, I., Chahboune, R., Bakri, Y., Idrissi, N. A., Hamdi, S., Nejjari, C., Amzazi, S., & Ghazal, H. (2021) · Bioinformatics and Biology Insights · doi:10.1177/1177932221999428 · Cited by 16

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Song, S., Li, C., Kang, L., Tian, D., Badar, N., Ma, W., Zhao, S., Jiang, X., Wang, C., Sun, Y., et al. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.08.007 · Cited by 15

Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh

Saha, O., Islam, I., Shatadru, R. N., Rakhi, N. N., Hossain, M. S., & Rahaman, M. M. (2021) · Virus Genes · doi:10.1007/s11262-021-01860-x · Cited by 16

Microbiota and Its Impact on the Immune System in COVID-19—A Narrative Review

Jabczyk, M., Nowak, J., Hudzik, B., & Zubelewicz‐Szkodzińska, B. (2021) · Journal of Clinical Medicine · doi:10.3390/jcm10194537 · Cited by 17

Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy

Marco, C. D., Marascio, N., Veneziano, C., Biamonte, F., Trecarichi, E. M., Santamaria, G., Leviyang, S., Liberto, M. C., Mazzitelli, M., Quirino, A., et al. (2022) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2022.105253 · Cited by 16

Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants

Al-Khatib, H. A., Smatti, M. K., Ali, F. H., Zedan, H. T., Thomas, S., Ahmed, M. N., Kahlout, R. A. E., Bader, M. A. A., Elgakhlab, D., Coyle, P. V., et al. (2022) · iScience · doi:10.1016/j.isci.2022.105438 · Cited by 14

Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization

Xie, L., Chen, L., Li, X., Zhou, J., Tian, H., Zhao, J. X., Li, Z., & Li, Y. (2023) · Pathogens · doi:10.3390/pathogens12070944 · Cited by 15

Sampling and summarizing transmission trees with multi-strain infections

Sashittal, P., & El-Kebir, M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa438 · Cited by 15

A comparative phylogenomic analysis of SARS-CoV-2 strains reported from non-human mammalian species and environmental samples

Ul‐Rahman, A., Shabbir, M. A. B., Aziz, M. W., Yaqub, S., Mehmood, A., Raza, M. A., & Shabbir, M. Z. (2020) · Molecular Biology Reports · doi:10.1007/s11033-020-05879-5 · Cited by 15

SARS-CoV-2: Overview and Its Impact on Oral Health

Ting, M., & Suzuki, J. B. (2021) · Biomedicines · doi:10.3390/biomedicines9111690 · Cited by 16

SARS-CoV-2 infection threatening intestinal health: A review of potential mechanisms and treatment strategies

Liu, S., Zhao, Y., Feng, X., & Xu, H. (2022) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2022.2103090 · Cited by 16

Vaccination and Non-Pharmaceutical Interventions: When Can the UK Relax About COVID-19?Preprint

Moore, S., Hill, E. M., Tildesley, M. J., Dyson, L., & Keeling, M. J. (2021) · medRxiv · doi:10.1101/2020.12.27.20248896 · Cited by 15

Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia

Marimón, J. M., Sorarrain, A., Ercibengoa, M., Azcue, N., Alonso, M. M., & Vidaur, L. (2023) · Scientific Reports · doi:10.1038/s41598-023-45007-4 · Cited by 16

Severe acute respiratory syndrome coronavirus‐2 infection and the gut–liver axis

Mohandas, S., & Vairappan, B. (2020) · Journal of Digestive Diseases · doi:10.1111/1751-2980.12951 · Cited by 14

Annotation of miRNAs in COVID-19 coronavirus

Yu, T., Chen, M., & Wang, C. (2020) · Journal of Electronic Science and Technology · doi:10.1016/j.jnlest.2020.100060 · Cited by 14

Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components

Srivastava, M., Hall, D., Omoru, O. B., Gill, H. M., Smith, S., & Janga, S. C. (2021) · Microorganisms · doi:10.3390/microorganisms9091794 · Cited by 13

A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19

Zhu, Z., Zhang, S., Wang, P., Chen, X., Bi, J., Cheng, L., & Zhang, X. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab446 · Cited by 14

Pathogenic Connections in Post-COVID Conditions: What Do We Know in the Large Unknown? A Narrative Review

Stafie, C. S., Solomon, S. M., Șufaru, I.-G., Manaila, M., Stafie, I. I., Melinte, G., Simionescu, B., & Leuștean, L. (2022) · Viruses · doi:10.3390/v14081686 · Cited by 14

SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolutionPreprint

Siqueira, J. D., Goes, L. R., Alves, B. M., de Carvalho, P. S., Cicala, C., Arthos, J. A., Viola, J. P. B., de Melo, A. C., Soares, M. A., & on behalf of the INCA COVID-19 Task Force (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.26.267831 · Cited by 14

Streptococcus salivarius Role as a Probiotic in Children’s Health and Disease Prophylaxis—A Systematic Review

Al-Akel, C. F., Chiperi, L. E., Eszter, V. K., & Bacârea, A. (2024) · Life · doi:10.3390/life14121613 · Cited by 13

Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study

Xiao, Y., Shi, X., She, Q., Chen, Q., Pan, H., Jin, Z., Liu, X., Wu, H., Jin, W., Ke, G., et al. (2020) · Virulence · doi:10.1080/21505594.2020.1816076 · Cited by 13

Development and validation of a new triplex real-time quantitative reverse Transcriptase-PCR assay for the clinical detection of SARS-CoV-2

Gadkar, V. J., Goldfarb, D. A., Young, V., Watson, N., Al‐Rawahi, G. N., Srigley, J. A., & Tilley, P. A. G. (2021) · Molecular and Cellular Probes · doi:10.1016/j.mcp.2021.101744 · Cited by 13

Is increased mortality by multiple exposures to COVID-19 an overseen factor when aiming for herd immunity?

Helle, K. B., Sadiku, A., Zelleke, G. M., Bouba, A., Ibrahim, T. B., Obama, H. C. J. T., Appiah, V., Ngwa, G. A., Teboh-Ewungkem, M. I., & Schneider, K. A. (2021) · PLoS ONE · doi:10.1371/journal.pone.0253758 · Cited by 12

COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity

Naumov, V., Lane, E., Pushkov, S., Kozlova, E., Romantsov, K., Kalashnikov, A., Galkin, F., Tihonova, N., Shneyderman, A., Galkin, E. G., et al. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009183 · Cited by 13

Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution

Poelvoorde, L. A. E. V., Gand, M., Fraiture, M., Keersmaecker, S. C. J. D., Verhaegen, B., Hoorde, K. V., Cay, A. B., Balmelle, N., Herman, P., & Roosens, N. H. C. (2021) · Current Issues in Molecular Biology · doi:10.3390/cimb43030134 · Cited by 14

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters

Gallego‐García, P., Varela, N., Estévez‐Gómez, N., Chiara, L. D., Fernández-Silva, I., Valverde, D., Sapoval, N., Treangen, T. J., Regueiro, B. J., Cabrera, J. J., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac008 · Cited by 12

Population genomics insights into the recent evolution of SARS-CoV-2Preprint

Vasilarou, M., Alachiotis, N., Garefalaki, J., Beloukas, A. I., & Pavlidis, P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.21.054122 · Cited by 13

Metatranscriptomic analysis revealed Prevotella as a potential biomarker of oropharyngeal microbiomes in SARS-CoV-2 infection

Lu, S., Zhou, Y., Hu, Y., Wang, J., Li, H., Lin, Y., Wang, D., Xian, J., Zhao, S., Ma, J., et al. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1161763 · Cited by 12

Lack of skin manifestations in COVID‐19 hospitalized patients during the second epidemic wave in Spain: a possible association with a novel SARS‐CoV‐2 variant – a cross‐sectional study

Fernández‐Nieto, D., Ortega-Quijano, D., Suárez‐Valle, A., ­Jimenez‐Cauhe, J., Jaén‐Olasolo, P., & Fernández-Guarino, M. (2020) · Journal of the European Academy of Dermatology and Venereology · doi:10.1111/jdv.17051 · Cited by 12

Jumper enables discontinuous transcript assembly in coronaviruses

Sashittal, P., Zhang, C., Peng, J., & El-Kebir, M. (2021) · Nature Communications · doi:10.1038/s41467-021-26944-y · Cited by 12

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients

Wang, Y., Wang, D., Zhang, L., Sun, W., Zhang, Z., Chen, W., Zhu, A., Huang, Y., Xiao, F., Yao, J., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00847-5 · Cited by 124

Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa

San, J. E., Ngcapu, S., Kanzi, A. M., Tegally, H., Fonseca, V., Giandhari, J., Wilkinson, E., Nelson, C. W., Smidt, W., Kiran, A. M., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab041 · Cited by 49

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

Valesano, A. L., Rumfelt, K. E., Dimcheff, D. E., Blair, C. N., Fitzsimmons, W. J., Petrie, J. G., Martin, E. T., & Lauring, A. S. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009499 · Cited by 95

SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort

Cavalli, L., Taylor, B. P., Schaeffer, B., Turcinovic, J., Connor, J. H., & Hanage, W. P. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001784

Persistence of SARS‐CoV‐2 infection and viral intra ‐ and inter ‐host evolution in COVID‐19 hospitalized patients

Pavia, G., Quirino, A., Marascio, N., Veneziano, C., Longhini, F., Bruni, A., Garofalo, E., Pantanella, M., Manno, M., Gigliotti, S., et al. (2024) · Journal of Medical Virology · doi:10.1002/jmv.29708 · Cited by 18