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A call for a more comprehensive SARS-CoV-2 sequence database for Brazil

2021; Elsevier BV; Volume: 5; Linguagem: Inglês

10.1016/j.lana.2021.100095

2667-193X

Adriano Abbud, Euclides Ayres de Castilho,

COVID-19 diagnosis using AI

Genomics can bring valuable information for tracking transmission and evolution of pathogens, and COVID-19 is showing that it is a tool for rapid response to overcome the SARS-CoV-2.1Lo SW Jamrozy D. Genomics and epidemiological surveillance.Nat Rev Microbiol. 2020; 18: 478Crossref PubMed Scopus (23) Google Scholar By the end of August 2021, more than 3·1 million sequences have been shared through the Global Initiative on Sharing Avian Influenza Data (GISAID), in an effort towards open data sharing.2Shu Y McCauley J. GISAID: Global initiative on sharing all influenza data – from vision to reality.EuroSurveillance. 2017; 22: 13Crossref Scopus (1686) Google Scholar GISAID is the leading SARS-CoV-2 database and requires that users confirm their identity and agree not to republish genomes without permission from the submitter, meaning that studies building on GISAID data cannot publish full data so that others can easily check their analyses or further build on their data set, and they must direct readers back to the GISAID site.3Noorden RV. Scientists call for fully open sharing of coronavirus genome data.Nature. 2021; 590 (2021): 195-196Crossref PubMed Scopus (34) Google Scholar Those policies benefit those who share incentivize genomic surveillance, once GISAID boosts sharing by negating researchers' reluctance to rapidly deposit anonymously.4Kamil JP. Virus variants: GISAID policies incentivize surveillance in global south.Nature. 2021; 593: 341Crossref PubMed Scopus (3) Google Scholar Additionally, the World Health Organization (WHO) recommends sequence sharing for public health impact, hence continued genome sequencing supports monitoring of COVID-19 spread and virus evolution, and integration of sequencing into practices of the global health community is required to be prepared for future threats.5World Health Organization (Geneva). Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. https://www.who.int/publications/i/item/9789240018440. Jan 8, 2021.Google Scholar An effective genomic surveillance system requires not only sequencing SARS-CoV-2 strains from patients, but also rapid submission to platforms like GISAID, once this enables researchers to track the evolved variants and their mutations, epidemiological studies, and biological consequences.6Kalia K Saberwal G Sharma G. The lag in SARS-CoV-2 genome submissions to GISAID.Nat Biotechnol. 2021; Crossref PubMed Scopus (37) Google Scholar SARS-CoV-2 sequencing began from the first cases in Brazil, which lies today in 18th place in the number of sequences. As the pandemics evolved, new institutions started sequencing, increasing submissions to GISAID, allowing others, as Fundação Oswaldo Cruz (FIOCRUZ), in Rio de Janeiro, to share information about the detection and circulation of lineages in Brazil, or projects like Covariants, that provides an overview of SARS-CoV-2 variants and mutations of interest to the community.7Fundação Oswaldo Cruz (Brazil). Rede Genômica Fiocruz. http://www.genomahcov.fiocruz.br/dashboard. 2020.Google Scholar,8Hodcroft EB. CoVariants: SARS-CoV-2 Mutations and Variants of Interest. https://covariants.org 2021.Google Scholar Although this increases in submissions, some institutions may be holding their data, sharing only a fraction of their sequences. One example we could identify is of Instituto Butantan (IB), from the Secretary of Health of São Paulo (SES-SP). According to data from GISAID, that institution submitted 6,528 sequences to the database up to last August 26. When this number is compared to an epidemiological bulletin on their site, where it is stated that until the 32nd epidemiological week 19,185 samples were sequenced, we observe almost 2/3 of their sequences have not been submitted to GISAID.9Instituto Butantan (São Paulo, Brazil). Boletim Epidemiológico da Rede de Alerta das Variantes do SARS-CoV-2. https://butantan.gov.br/assets/arquivos/Covid/Boletim_epidemiologico/SaoPaulo/14_8_21_Relat%C3%B3rio_Sequenciamento.pdf. Aug 14 2021.Google Scholar Considering Brazil has submitted 31,826 sequences, something like 40% of Brazilian sequences are not on the platform, and it could be possible that other institutions may do the same. If we consider São Paulo State's reality, which sequences more than 1/3 of samples in Brazil, it causes a severe impact to the country, although there is state regulation from SES-SP that demands the GISAID accession number for the confirmation of variant cases in the territory.10Secretaria de Estado da Saúde (São Paulo, Brazil). Resolução SS-28, de 18-2-2021 – Dispõe sobre a confirmação da investigação epigenômica do SARS-CoV-2 para fins de vigilância em saúde no Estado de São Paulo. Diário Oficial do Estado de São Paulo. No 34 – DOE –19/02/2021 – seção 1 – p. 28.Google Scholar From a public health point of view, these differences are not only about numbers. It is possible to observe that submissions to GISAID could be biased, leading to false information on the prevalence of variants in Brazil. For instance, 251 out of 9,679 sequences (2·59%) are classified as Delta variant, but when this is confronted to the bulletin from IB, up to August 14, 706 out of 19,185 (3·68%) lie on that classification, imprinting a 42% rise in the frequency of Delta variant. Considering organizations from all around the world, including the WHO, look for data on GISAID, this may lead to miscomprehension of COVID-19 dynamics, as observed on data from Covariants, showing the frequency of Gamma, Delta, and other lineages (like B.1.621 and P.4) as of 55%, 43%, and 2%, respectively, in Brazil from July 26 to August 9. We acknowledge that researchers affiliated with institutions not in surveillance systems may not be aware they are responsible to provide data for public health responses, or could not see the importance of sharing information during health events, as stated in International Health Regulations, but the lack of reliable information in a huge and diverse country as Brazil may cause considerable impacts to the understanding of the pandemics and could be seen as lack of transparency from Brazilian scientists and authorities regarding the situation of COVID-19.11World Health Organization (Geneva)International health regulations (2005). World Health Assembly, 2006https://www.who.int/publications/i/item/9789241580496Google Scholar Although COVID-19 pandemics is an unprecedented event, we believe it can leave a legacy to surveillance systems if matters like fast and reliable data sharing are debated. Should the immediate submission be mandatory? Would it be possible that health organizations could reach institutions so they can provide vital data to fight the pandemics? These questions, among others related to epigenomics, should be addressed if we want to be prepared for the next events. AA: conceptualisation, data curation, writing – original draft, writing – review & editing; EAC: conceptualisation, supervision, writing – review & editing. The authors declare no competing interests.