A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

A novel coronavirus from patients with pneumonia in China, 2019

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

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Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

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A new coronavirus associated with human respiratory disease in China

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Ultrafast Approximation for Phylogenetic Bootstrap

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GISAID: Global initiative on sharing all influenza data – from vision to reality

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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.

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Untitled work

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Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource

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Mutational spectrum of SARS-CoV-2 during the global pandemic

Yi, K., Kim, S. Y., Bleazard, T., Kim, T., Youk, J., & Ju, Y. S. (2021) · Experimental & Molecular Medicine · doi:10.1038/s12276-021-00658-z · Cited by 70

One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

Benslimane, F. M., Al-Khatib, H. A., Al-Jamal, O., Albatesh, D., Boughattas, S., Ahmed, A. A., Bensaad, M., Younuskunju, S., Mohamoud, Y. A., Badr, M. A., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.768883 · Cited by 66

Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responsesPreprint

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Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing

Swadi, T., Geoghegan, J. L., Devine, T., McElnay, C., Sherwood, J., Shoemack, P., Ren, X., Storey, M., Jefferies, S., Smit, E., et al. (2021) · Emerging infectious diseases · doi:10.3201/eid2703.204714 · Cited by 67

Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

Makarenkov, V., Mazoure, B., Rabusseau, G., & Legendre, P. (2021) · BMC Ecology and Evolution · doi:10.1186/s12862-020-01732-2 · Cited by 67

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

Vega‐Magaña, N., Sánchez-Sánchez, R., Hernández‐Bello, J., Venancio-Landeros, A. A., Rodríguez, M. P., Vega-Zepeda, R. A., Galindo-Ornelas, B., Díaz-Sánchez, M., García‐Chagollán, M., Ojeda, G. M., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.672562 · Cited by 67

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

Lane, C. R., Sherry, N. L., Porter, A. F., Duchêne, S., Horan, K., Andersson, P., Wilmot, M., Turner, A., Dougall, S., Johnson, S. A. S., et al. (2021) · The Lancet Public Health · doi:10.1016/s2468-2667(21)00133-x · Cited by 68

Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway

Zhou, J., Peacock, T. P., Brown, J. C., Goldhill, D. H., Elrefaey, A. M. E., Penrice-Randal, R., Cowton, V. M., De Lorenzo, G., Furnon, W., Harvey, W. T., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110344 · Cited by 64

Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates

Addetia, A., Xie, H. J., Roychoudhury, P., Shrestha, L., Loprieno, M. A., Huang, M.-L. W., Jerome, K. R., & Greninger, A. L. (2020) · Journal of Clinical Virology · doi:10.1016/j.jcv.2020.104523 · Cited by 66

In silico discovery of antigenic proteins and epitopes of SARS-CoV-2 for the development of a vaccine or a diagnostic approach for COVID-19

Can, H., Köseoğlu, A. E., Alak, S. E., Güvendi, M., Döşkaya, M., Karakavuk, M., Gürüz, A. Y., & Ün, C. (2020) · Scientific Reports · doi:10.1038/s41598-020-79645-9 · Cited by 66

Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern

Shahhosseini, N., Babuadze, G. G., Wong, G., & Kobinger, G. (2021) · Microorganisms · doi:10.3390/microorganisms9050926 · Cited by 66

Impact of Delta Variant and Vaccination on SARS-CoV-2 Secondary Attack Rate Among Household Close Contacts

Ng, O. T., Koh, V. J. W., Chiew, C. J., Marimuthu, K., Thevasagayam, N. M., Mak, T. M., Chua, J. K., Ong, S. S. H., Lim, Y. K., Ferdous, Z., et al. (2021) · The Lancet Regional Health - Western Pacific · doi:10.1016/j.lanwpc.2021.100299 · Cited by 63

Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant

Ma, W., Yang, J., Fu, H., Su, C., Yu, C., Wang, Q., de Vasconcelos, A. T. R., Bazykin, G. A., Bào, Y., & Li, M. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.01.001 · Cited by 59

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Tsui, J. L.-H., McCrone, J. T., Lambert, B., Bajaj, S., Inward, R. P. D., Bosetti, P., Pena, R. E., Tegally, H., Hill, V., Zarebski, A. E., et al. (2023) · Science · doi:10.1126/science.adg6605 · Cited by 60

2023/24 mid-season influenza and Omicron XBB.1.5 vaccine effectiveness estimates from the Canadian Sentinel Practitioner Surveillance Network (SPSN)

Skowronski, D. M., Zhan, Y., Kaweski, S. E., Sabaiduc, S., Khalid, A., Olsha, R., Carazo, S., Dickinson, J. A., Mather, R. G., Charest, H., et al. (2024) · Eurosurveillance · doi:10.2807/1560-7917.es.2024.29.7.2400076 · Cited by 65

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

Gónzález‐Candelas, F., Shaw, M., Phan, T. G., Kulkarni‐Kale, U., Paraskevis, D. N., Luciani, F., Kimura, H., & Sironi, M. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.104869 · Cited by 65

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

IMPACC Manuscript Writing Team, Rouphael, N., Maecker, H. T., Montgomery, R. R., Diray‐Arce, J., Kleinstein, S. H., Altman, M. C., Bosinger, S. E., Eckalbar, W. L., Guan, L., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abf3733 · Cited by 58

Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil

do Nascimento, V. A., Corado, A. D. L. G., Nascimento, F., Costa, Á., Duarte, D., Luz, S. L. B., Gonçalves, L. M. F., de Jesus, M. S., da Costa, C. F., Delatorre, E. O., et al. (2020) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760200310 · Cited by 64

Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients

Carreño, J. M., Alshammary, H., Singh, G., Raskin, A. J., Amanat, F., Amoako, A. A., Gonzalez-Reiche, A. S., van de Guchte, A., PARIS study group, Awawda, M. H., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103626 · Cited by 61

SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa

Koeppel, K. N., Mendes, A., Strydom, A., Rotherham, L. S., Mulumba, M., & Venter, M. (2022) · Viruses · doi:10.3390/v14010120 · Cited by 70

Targeting SARS‐CoV‐2 viral proteases as a therapeutic strategy to treat COVID‐19

Anirudhan, V., Lee, H., Cheng, H., Cooper, L. M., & Rong, L. (2021) · Journal of Medical Virology · doi:10.1002/jmv.26814 · Cited by 63

Discovery of a SARS-CoV-2 variant from the P.1 lineage harboring K417T/E484K/N501Y mutations in Kofu, Japan

Hirotsu, Y., & Omata, M. (2021) · Journal of Infection · doi:10.1016/j.jinf.2021.03.013 · Cited by 64

A single intranasal dose of a live-attenuated parainfluenza virus-vectored SARS-CoV-2 vaccine is protective in hamsters

Liu, X.-Q., Luongo, C., Matsuoka, Y., Park, H.-S., Santos, C., Yang, L.-J., Moore, I. N., Afroz, S., Johnson, R. F., Lafont, B., et al. (2021) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2109744118 · Cited by 60

Humoral immune response after different SARS-CoV-2 vaccination regimens

Rose, R., Neumann, F., Grobe, O., Lorentz, T., Fickenscher, H., & Krumbholz, A. (2022) · BMC Medicine · doi:10.1186/s12916-021-02231-x · Cited by 62

Unlocking capacities of genomics for the COVID-19 response and future pandemics

Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Baykal, P. I., Comarova, Z., Lu, A., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01444-z · Cited by 61

Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Brizzi, A., Whittaker, C., Servo, L. M. S., Hawryluk, I., Junior, C. A. P., de Souza, W. M., Aguiar, R. S., de Araújo, L. J. T., Bastos, L. S., Blenkinsop, A., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01807-1 · Cited by 74

Contributions of adaptation and purifying selection to SARS-CoV-2 evolution

Neher, R. A. (2022) · Virus Evolution · doi:10.1093/ve/veac113 · Cited by 58

Sensitive Recovery of Complete SARS-CoV-2 Genomes from Clinical Samples by Use of Swift Biosciences’ SARS-CoV-2 Multiplex Amplicon Sequencing Panel

Addetia, A., Lin, M. J., Peddu, V., Roychoudhury, P., Jerome, K. R., & Greninger, A. L. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.02226-20 · Cited by 59

SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021

Alkhatib, M., Svicher, V., Salpini, R., Ambrosio, F. A., Bellocchi, M. C., Carioti, L., Piermatteo, L., Scutari, R., Costa, G., Artese, A., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.01096-21 · Cited by 62

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

Colson, P., Fournier, P., Chaudet, H., Delerce, J., Giraud‐Gatineau, A., Houhamdi, L., Andrieu, C., Bréchard, L., Bedotto, M., Prudent, E., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.786233 · Cited by 64

Limit of Detection for Rapid Antigen Testing of the SARS-CoV-2 Omicron and Delta Variants of Concern Using Live-Virus Culture

Stanley, S., Hamel, D. J., Wolf, I. D., Riedel, S. F., Dutta, S., Contreras, E., Callahan, C. J., Cheng, A., Arnaout, R., Kirby, J. E., et al. (2022) · Journal of Clinical Microbiology · doi:10.1128/jcm.00140-22 · Cited by 61

First case of monkeypox virus, SARS-CoV-2 and HIV co-infection

Nolasco, S., Vitale, F. M., Geremia, A., Tramuto, F., Maida, C. M., Sciuto, A., Coco, C., Manuele, R., Frasca, E., Frasca, M., et al. (2022) · Journal of Infection · doi:10.1016/j.jinf.2022.08.014 · Cited by 61

A nidovirus perspective on SARS-CoV-2

Gulyaeva, A. A., & Gorbalenya, A. E. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.11.015 · Cited by 59

Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2

Kissler, S. M., Fauver, J. R., Mack, C. D., Tai, C. G.-L., Breban, M. I., Watkins, A. E., Samant, R. M., Anderson, D. J., Ho, D. D., Grubaugh, N. D., et al. (2021) · Digital Access to Scholarship at Harvard (DASH) (Harvard University) · Cited by 60

Detecting SARS-CoV-2 variants with SNP genotyping

Harper, H., Burridge, A. J., Winfield, M., Finn, A. H. R., Davidson, A. D., Matthews, D. A., Hutchings, S., Vipond, B. B., Jain, N., Edwards, K. J., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0243185 · Cited by 60

A Narrative Review of COVID-19 Vaccines

Eroglu, B., Nuwarda, R. F., Ramzan, I. M., & Kayser, V. (2021) · Vaccines · doi:10.3390/vaccines10010062 · Cited by 59

Transmission of SARS-CoV-2 from humans to animals and potential host adaptationPreprint

Tan, C. C. S., Lam, S. D., Richard, D., Owen, C. J., Berchtold, D., Orengo, C. A., Nair, M. S., Kuchipudi, S. V., Kapur, V., van Dorp, L., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.16.384743 · Cited by 62

SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19

Stanevich, O. V., Alekseeva, E. I., Sergeeva, M. V., Fadeev, A. V., Komissarova, K., Ivanova, A. A., Simakova, T., Vasilyev, K., Shurygina, A.-P. S., Stukova, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-34033-x · Cited by 60

Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

Tiwari, A., Adhikari, S., Zhang, S., Solomon, T. B., Lipponen, A., Islam, M. A., Thakali, O., Sangkham, S., Shaheen, M. N. F., Jiang, G., et al. (2023) · Water · doi:10.3390/w15061018 · Cited by 61

SARS-CoV-2 variants reveal features critical for replication in primary human cells

Pohl, M. O., Busnadiego, I., Kufner, V., Glas, I., Karakus, U., Schmutz, S., Zaheri, M., Abela, I. A., Trkola, A., Huber, M., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001006 · Cited by 55

Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein

Colson, P., Delerce, J., Burel, E., Dahan, J., Jouffret, A., Fenollar, F., Yahi, N., Fantini, J., Scola, B. L., & Raoult, D. (2022) · Archives of Virology · doi:10.1007/s00705-022-05385-y · Cited by 21

Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF

Nikolaidis, M., Papakyriakou, A., Chlichlia, K., Markoulatos, P., Oliver, S. G., & Amoutzias, G. D. (2022) · Viruses · doi:10.3390/v14040707 · Cited by 57

Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges

Yang, J., Gong, Y., Zhang, C., Sun, J., Wong, G., Shi, W., Liu, W., Gao, G. F., & Bi, Y. (2022) · The Innovation · doi:10.1016/j.xinn.2022.100306 · Cited by 58

Global SNP analysis of 11,183 SARS‐CoV‐2 strains reveals high genetic diversity

Yuan, F., Wang, L., Fāng, Y., & Wang, L. (2020) · Transboundary and Emerging Diseases · doi:10.1111/tbed.13931 · Cited by 55

Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences

Ali, S., & Patterson, M. (2021) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata52589.2021.9671848 · Cited by 59

The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant

López, M. G., Chiner‐Oms, Á., de Viedma, D. G., Ruiz-Rodríguez, P., Bracho, M. A., Cancino‐Muñoz, I., D’Auria, G., Marco, G. D., García‐González, N., Goig, G. A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00936-6 · Cited by 56

Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2

Ringlander, J., Fingal, J., Kann, H., Prakash, K., Rydell, G. E., Andersson, M., Martner, A., Lindh, M., Horal, P., Hellstrand, K., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2112663119 · Cited by 57

Emerging SARS-CoV-2 variants: Why, how, and what's next?

Chen, Y. Z., Liu, Q., Zhou, L., Zhou, Y., Yan, H., & Lan, K. (2022) · Cell Insight · doi:10.1016/j.cellin.2022.100029 · Cited by 58

Recent insights into SARS‐CoV‐2 omicron variant

da Silva, S. J. R., Kohl, A., Pena, L., & Pardee, K. (2022) · Reviews in Medical Virology · doi:10.1002/rmv.2373 · Cited by 56

Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era

Ling-Hu, T., Rios-Guzman, E., Lorenzo-Redondo, R., Ozer, E. A., & Hultquist, J. F. (2022) · Viruses · doi:10.3390/v14112532 · Cited by 60

The emergence of SARS-CoV-2 in Europe and the USPreprint

Worobey, M., Pekar, J. E., Larsen, B. B., Nelson, M. I., Hill, V., Joy, J. B., Rambaut, A., Suchard, M. A., Wertheim, J. O., & Lemey, P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.21.109322 · Cited by 60

A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual

Caccuri, F., Zani, A., Messali, S., Giovanetti, M., Bugatti, A., Campisi, G., Filippini, F., Scaltriti, E., Ciccozzi, M., Fiorentini, S., et al. (2020) · Journal of Translational Medicine · doi:10.1186/s12967-020-02535-1 · Cited by 55

Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission

Borges, V., Isidro, J., Macedo, F., Neves, J., Silva, L. R., Paiva, M., Barata, J., Catarino, J., Ciobanu, L. G., Duarte, S., et al. (2021) · Viruses · doi:10.3390/v13040604 · Cited by 56

Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New YorkPreprint

West, A. P., Wertheim, J. O., Wang, J. C., Vasylyeva, T. I., Havens, J. L., Chowdhury, M. A., Gonzalez, E., Fang, C. E., Lonardo, S. S. D., Hughes, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.14.431043 · Cited by 74

Pathogen-sugar interactions revealed by universal saturation transfer analysis

Buchanan, C. J., Gaunt, B., Harrison, P. J., Yang, Y., Liu, J., Khan, A., Giltrap, A. M., Bas, A. L., Ward, P. N., Gupta, K., et al. (2022) · Science · doi:10.1126/science.abm3125 · Cited by 55

Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections and Incidence of the Presumptive B.1.427/B.1.429 Variant Among Healthcare Personnel at a Northern California Academic Medical Center

Jacobson, K. B., Pinsky, B. A., Montez Rath, M. E., Wang, H., Miller, J. A., Skhiri, M., Shepard, J., Mathew, R., Lee, G., Bohman, B., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab554 · Cited by 62

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Giallonardo, F. D., Duchêne, S., Puglia, I., Curini, V., Profeta, F., Cammà, C., Marcacci, M., Calistri, P., Holmes, E. C., & Lorusso, A. (2020) · Viruses · doi:10.3390/v12121438 · Cited by 56

Insights into SARS-CoV-2 Persistence and Its Relevance

Desimmie, B. A., Raru, Y., Awadh, H., He, P., Teka, S., & Willenburg, K. S. (2021) · Viruses · doi:10.3390/v13061025 · Cited by 58

The Rise of SARS-CoV-2 Variants and the Role of Convalescent Plasma Therapy for Management of Infections

Moubarak, M., Kasozi, K. I., Hetta, ‏. F., Shaheen, H. M., Rauf, A., Al-Kuraishy, H. M., Qusti, S. Y., Alshammari, E. M., Ayikobua, E. T., Ssempijja, F., et al. (2021) · Life · doi:10.3390/life11080734 · Cited by 57

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

Gupta, D., Sharma, P., Singh, M., Kumar, M., Ethayathulla, A. S., & Kaur, P. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04008-0 · Cited by 56

SARS-CoV-2 transmission dynamics in Belarus in 2020 revealed by genomic and incidence data analysis

Nemira, A., Adeniyi, A. E., Леонидовна, Г. Е., Bulda, K. Y., Valentovich, L. N., Kras’ko, A. G., Glebova, O., Kirpich, A., & Skums, P. (2021) · Communications Medicine · doi:10.1038/s43856-021-00031-1 · Cited by 55

Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny

Pipes, L., Wang, H., Huelsenbeck, J. P., & Nielsen, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa316 · Cited by 55

Bioinformatics resources for SARS-CoV-2 discovery and surveillance

Hu, T., Li, J., Zhou, H., Li, C., Holmes, E. C., & Shi, W. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa386 · Cited by 57

Genome Sequencing of Wastewater Confirms the Arrival of the SARS-CoV-2 Omicron Variant at Frankfurt Airport but Limited Spread in the City of Frankfurt, Germany, in November 2021

Agrawal, S., Orschler, L., Tavazzi, S., Greither, R., Gawlik, B. M., & Lackner, S. (2022) · Microbiology Resource Announcements · doi:10.1128/mra.01229-21 · Cited by 54

COVID-19 at a Glance: An Up-to-Date Overview on Variants, Drug Design and Therapies

Iacopetta, D., Ceramella, J., Catalano, A. A., Saturnino, C., PELLEGRINO, M. A., Mariconda, A., Longo, P., Sinicropi, M. S., & Aquaro, S. (2022) · Viruses · doi:10.3390/v14030573 · Cited by 54

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

Diray‐Arce, J., Fourati, S., Jayavelu, N. D., Patel, R. K., Maguire, C. P., Chang, A. C., Dandekar, R., Qi, J., Lee, B. H., van Zalm, P., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101079 · Cited by 49

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

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SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater – a longitudinal study in Bengaluru, India

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The Antibody Response to SARS-CoV-2 Infection

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A review on favipiravir: the properties, function, and usefulness to treat COVID-19

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A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

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TBEV Subtyping in Terms of Genetic Distance

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Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

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SARS-CoV-2 Lineages and Sub-Lineages Circulating Worldwide: A Dynamic Overview

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Novavax NVX-COV2373 triggers neutralization of Omicron sub-lineages

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A mixture model for determining SARS-Cov-2 variant composition in pooled samplesPreprint

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COVID-19, the first pandemic in the post-genomic era

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Broadly directed SARS-CoV-2-specific CD4+ T cell response includes frequently detected peptide specificities within the membrane and nucleoprotein in patients with acute and resolved COVID-19

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The twin-beginnings of COVID-19 in Asia and Europe—one prevails quickly

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PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny

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Fitness, growth and transmissibility of SARS-CoV-2 genetic variants

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SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs

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Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021

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A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiologyPreprint

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A framework for automated scalable designation of viral pathogen lineages from genomic data

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Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

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