Automating the Integration of Viral Genomic Data: A Hierarchical Multi-Layered Approach for De-duplicating GenBank and GISAID Repositories

• Andrêza Leite de Alencar UFRPE
• Laise de Moraes Fiocruz / INCT DigiSaúde
• Ricardo Khouri Fiocruz / INCT DigiSaúde

DOI: https://doi.org/10.5753/sbcas_estendido.2026.25434

Resumo

The rapid expansion of viral genomic sequencing has led to data fragmentation across major repositories like GenBank and GISAID. The same isolate could be deposited in both databases without any cross-reference linking the two entries. Consequently, there is no systematic way to identify this redundancy, which compromises the compilation of representative, non redundant large scale datasets. For Neglected Tropical Diseases (NTDs), this redundancy complicates real time genomic surveillance. This paper presents a computational framework designed to de-duplicate and integrate these databases using a hierarchical strategy: sequence identity, fuzzy string matching of isolate identifiers, and metadata reconciliation. Our results demonstrate that the tool effectively identifies redundant records for CHIKV-ECSA lineage and filters out laboratory derived sequences, providing a high-quality dataset for phylogeographic analysis.

Referências

Benson, D. A., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2014). GenBank. Nucl. Acids Res., 42(D1):D32–D37.

Casper da Costa-Luis, Stephen Karl Larroque, K. A. H. M. r. M. K. N. R. I. I. M. B. and Rodrigues, N. (2026). tqdm: A fast, extensible progress bar for python and cli.

Cock PJA, Antao T, C. J. C. B. C. C. D. A. F. I. H. T. K. F. and B, W. (2009). Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics, 25:1422–1423.

Garamszegi, L. Z. and Møller, A. P. (2010). Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta-analytic review. Biological Reviews, 85(4):797–805.

Greninger, A. L., Chen, E. C., Sittler, T., Scheinerman, A., Roubinian, N., Yu, G., Kim, E., Pillai, D. R., Guyard, C., Mazzulli, T., Isa, P., Arias, C. F., Hackett, J., Schochetman, G., Miller, S., Tang, P., and Chiu, C. Y. (2010). A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America. PLoS ONE, 5(10):e13381.

He, C., Chen, M.-Y., and Zhu, H. (2025). Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection. Systematic Biology, page syaf085.

Khare S, Gurry C, F. L. S. M. B. G. D. A. A. N. H. J. L. R. Y. W. C. T. G. and S., M.-S. (2021). Gisaid’s role in pandemic response. China CDC Wkly, 3(3(49)):1049–1051.

Naveca, F. G., Almeida, T. A. P. D., Souza, V., Nascimento, V., Silva, D., Nascimento, F., Mejía, M., Oliveira, Y. S. D., Rocha, L., Xavier, N., Lopes, J., Maito, R., Meneses, C., Amorim, T., Fé, L., Camelo, F. S., Silva, S. C. D. A., Melo, A. X. D., Fernandes, L. G., Oliveira, M. A. A. D., Arcanjo, A. R., Araújo, G., André Júnior, W., Carvalho, R. L. C. D., Rodrigues, R., Albuquerque, S., Mattos, C., Silva, C., Linhares, A., Rodrigues, T., Mariscal, F., Morais, M. A., Presibella, M. M., Marques, N. F. Q., Paiva, A., Ribeiro, K., Vieira, D., Queiroz, J. A. D. S., Passos-Silva, A. M., Abdalla, L., Santos, J. H., Figueiredo, R. M. P. D., Cruz, A. C. R., Casseb, L. N., Chiang, J. O., Frutuoso, L. V., Rossi, A., Freitas, L., Campos, T. D. L., Wallau, G. L., Moreira, E., Lins Neto, R. D., Alexander, L. W., Sun, Y., Filippis, A. M. B. D., Gräf, T., Arantes, I., Bento, A. I., Delatorre, E., and Bello, G. (2024). Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region. Nat Med, 30(12):3509–3521.

Pekar, J. E., Lytras, S., Ghafari, M., Magee, A. F., Parker, E., Wang, Y., Ji, X., Havens, J. L., Katzourakis, A., Vasylyeva, T. I., Suchard, M. A., Hughes, A. C., Hughes, J., Rambaut, A., Robertson, D. L., Dellicour, S., Worobey, M., Wertheim, J. O., and Lemey, P. (2025). The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. Cell, 188(12):3167–3183.e18.

Santa Ardisson, J., Vedovatti Monfardini Sagrillo, M., Ramos Athaydes, B., Corredor Vargas, A. M., Torezani, R., Ribeiro-Rodrigues, R., Cruz Spano, L., Gaburro Paneto, G., Delatorre, E., Ventorin Von Zeidler, S., and Freire Bastos Filho, T. (2025). Comparative spatial–temporal analysis of SARS-CoV-2 lineages B.1.1.33 and BQ.1.1 Omicron variant across pandemic phases. Sci Rep, 15(1):10319.

Vakulenko, Y., Deviatkin, A., and Lukashev, A. (2019). The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses, 11(11):1032.

van, R. G. and FL, D. (2010). The Python language reference. Hampton, NH: Python Software Foundation, release 3.0.1 edition.

W, M. (2010). Data structures for statistical computing in python. page 56–61.

Weaver, S. C. (2014). Arrival of Chikungunya Virus in the New World: Prospects for Spread and Impact on Public Health. PLoS Negl Trop Dis, 8(6):e2921.

Worobey, M., Watts, T. D., McKay, R. A., Suchard, M. A., Granade, T., Teuwen, D. E., Koblin, B. A., Heneine, W., Lemey, P., and Jaffe, H. W. (2016). 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America. Nature, 539(7627):98–101.

Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., and Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798):265–269.

Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., Zheng, X.-S., Zhao, K., Chen, Q.-J., Deng, F., Liu, L.-L., Yan, B., Zhan, F.-X., Wang, Y.-Y., Xiao, G.-F., and Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798):270–273.