key: cord-1022058-tik2qil7 authors: Slavov, Svetoslav N.; Patané, José S. L.; Bezerra, Rafael dos Santos; Giovanetti, Marta; Fonseca, Vagner; Martins, Antonio J.; Viala, Vincent L.; Rodrigues, Evandra S.; Santos, Elaine V.; Barros, Claudia R. S.; Marqueze, Elaine C.; Santos, Bibiana; Aburjaile, Flavia; Neto, Raul M.; Moretti, Debora B.; Haddad, Ricardo; Calado, Rodrigo T.; Kitajima, João P.; Freitas, Erika; Schlesinger, David; Junior de Alcantara, Luiz C.; Elias, Maria C.; Sampaio, Sandra C.; Kashima, Simone; Covas, Dimas T. title: Genomic monitoring unveil the early detection of the SARS‐CoV‐2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil date: 2021-07-19 journal: J Med Virol DOI: 10.1002/jmv.27190 sha: 88f6daba80be222a2184183af9c802828513da04 doc_id: 1022058 cord_uid: tik2qil7 Sao Paulo State, currently experiences a second COVID‐19 wave overwhelming the healthcare system. Due to the paucity of SARS‐CoV‐2 complete genome sequencing, we established a Network for Pandemic Alert of Emerging SARS‐CoV‐2 Variants to rapidly understand and monitor the spread of SARS‐CoV‐2 variants into the state. Through analysis of 210 SARS‐CoV‐2 complete genomes obtained from the largest regional health departments we identified cocirculation of multiple SARS‐CoV‐2 lineages such as B.1.1 (0.5%), B.1.1.28 (23.2%), B.1.1.7 (alpha variant, 6.2%), B.1.566 (1.4%), B.1.544 (0.5%), C.37 (0.5%) P.1 (gamma variant, 66.2%), and P.2 (zeta variant, 1.0%). Our analysis allowed also the detection, for the first time in Brazil, the South African B.1.351 (beta) variant of concern, B.1.351 (501Y.V2) (0.5%), characterized by the following mutations: ORF1ab: T265I, R724K, S1612L, K1655N, K3353R, SGF 3675_F3677del, P4715L, E5585D; spike: D80A, D215G, L242_L244del, A262D, K417N, E484K, N501Y, D614G, A701V, C1247F; ORF3a: Q57H, S171L, E: P71L; ORF7b: Y10F, N: T205I; ORF14: L52F. The most recent common ancestor of the identified strain was inferred to be mid‐October to late December 2020. Our analysis demonstrated the P.1 lineage predominance and allowed the early detection of the South African strain for the first time in Brazil. We highlight the importance of SARS‐CoV‐2 active monitoring to ensure the rapid detection of potential variants for pandemic control and vaccination strategies. Highlights Identification of B.1.351 (beta) variant of concern in the Sao Paulo State. Dissemination of SARS‐CoV‐2 variants of concern and interest in the Sao Paulo State. Mutational Profile of the circulating variants of concern and interest. The emergence of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage, namely P.1 (gamma variant), in the Brazilian city of Manaus 1 and its rapid dissemination despite the relatively high seroprevalence in the city, 2 demonstrated the importance of the SARS-CoV-2 genomic surveillance with the identification of mutation constellations which may impact viral infectivity, immunological evasion, and phenotypic characteristics. 1 Moreover, the importance of these lineages is related to the significant pressure which they exert on the healthcare system of the affected region due to the high morbidity and mortality leading to an overall collapse of the intensive care units, a situation which occurred when P.1 emerged in the Amazonian city of Manaus. Apart from data originating from the Brazilian Amazon, the cir- Regarding the SARS-CoV-2 genome obtained from the city of Sorocaba, raw files were basecalled using Guppy v4.4.2 (https:// nanoporetech.com/nanopore-sequencing-data-analysis) and barcode demultiplexing was performed using qcat v1.1.0 (https://github.com/ nanoporetech/qcat). We used Genome Detective 4 Typing Tool 5 to obtain consensus sequences by de novo assembling. For the remaining genomes, assembly against the SARS-CoV-2 reference (Genbank refseq NC_045512.2) was performed by a pipeline of BWA 6 for mapping, samtools for read indexing and to compile per base variation, bcftools for variant calling, 7 and seqtk for creation of consensus genome. 8 A representative subset of 3852 genomes obtained from GISAID 9 was obtained following the Nextstrain guidelines (https://nextstrain. github.io/ncov/customizing-analysis.html). These sequences were separated by downsampling as implied by Nextstrain using the most suitable parameters like space and sequence distribution. The 210 full-length new genomes were appended to this subset for further analyses. Sequence alignment was performed using MAFFT v7.475 10 and manually curated to remove artifacts using Aliview. 11 Approximate maximum likelihood phylogenetic trees were estimated using Mutational profile was investigated by using the Nextclade tool (https://clades.nextstrain.org/) to describe substitutions. Subsequently, we compared the set of nonsynonymous mutations with the profiles given in the PANGO lineages resource (https://cov-lineages. org/lineages.html) to attribute genomes to lineages. ORF3a: Q57H, S171L, E: P71L, ORF7b: Y10F, N: T205I, ORF14: L52F ( Figure 1D ). The dissemination of SARS-CoV-2 lineages in the State according to each region is shown in Figure 1A . We then explored the genetic relationship of the newly sequenced SARS-CoV-2 genomes to those of other isolates by phylogenetic inference. Figure 1B Other SARS-CoV-2 VOCs were also identified, including the UK variant, which shows that the SARS-CoV-2 lineages in the Sao Paulo State are presented as a complex mixture suggesting that more extensive genomic surveillance is urgently needed. In this respect, extensive VOC characterization and collaborative efforts are essential to evaluate the current SARS-CoV-2 scenario not only in the Sao Paulo State but also in Brazil due to the general worsening of the pandemic in a nationwide aspect. In conclusion, the performed study emphasizes the importance of the SARS-CoV-2 genomic surveillance to monitor the SARS-CoV-2 dissemination in the Brazilian regions and states. Given the vast extension of the country, a collaboration of different sequencing networks and combining SARS-CoV-2 genomic data will be of crucial importance to understand in more detail the nation-wide Brazilian SARS-CoV-2 pandemic, especially related to VOC emergence and improve the responsiveness to further possible waves and vaccination strategies to SARS-CoV-2. 2020/00694-6; 2013/08135-2; 2017/26950-6) and Hemocentro Marta Giovanetti is supported by Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ) Bioinformatic analysis Writing original draft Funding acquisition Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. medRxiv Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Genome Detective: an automated system for virus identification from high-throughput sequencing data Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Fast and accurate short read alignment with Burrows-Wheeler transform Twelve years of SAMtools and BCFtools SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation GISAID: global initiative on sharing all influenza data-from vision to reality MAFFT multiple sequence alignment software version 7: improvements in performance and usability AliView: a fast and lightweight alignment viewer and editor for large datasets FastTree 2-approximately maximumlikelihood trees for large alignments Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Smooth Skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics Time dependence of SARS-CoV-2 substitution rates. Virol Org Source Posterior summarization in bayesian phylogenetics using Tracer 1.7 Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil Evolution and epidemic spread of SARS-CoV-2 in Brazil Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England Sixteen novel lineages of SARS-CoV-2 in South Africa Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil The authors are grateful to all authors who have kindly deposited and shared genome data on GISAID. This study was supported by Butantan Foundation,Fundação de Amparo à Pesquisa do Estado de São Paulo(Grant nos.: 2018/15826-5; 2020/10127-1; 2020/05367- http://orcid.org/0000-0002-5849-7326Vagner Fonseca http://orcid.org/0000-0001-5521-6448