key: cord-0282478-2f2uryle
authors: Padilha, D. A.; Benetti-Filho, V.; Moreira, R. S.; Soratto, T. S. T.; Maia, G. A.; Christoff, A. P.; Barazzetti, F. H.; Schorner, M. A.; Ferrari, F. L.; Martins, C. L.; Kawagoe, E. K.; Wachter, J. K.; Sacchet, P.; Baptistella, A.; Schlindwein, A. D.; Coelho, B. K.; Fernandes, S. B.; Rovaris, D. B.; dos Anjos, M. P. D.; Melo, F. R.; Bittencourt, B.; da Cunha, S.; Meneghetti, K. L.; Wendt, N.; Madaloz, T. Z.; Rodrigues, M. V. D.; Souza, D. S. M.; de Moraes, M. H.; Baptista, R. d. P.; Toledo-Silva, G.; Razzera, G.; Grisard, E. C.; Stoco, P. H.; de Oliveira, L. F. V.; Bazzo, M. L.; Fongaro, G.; Wa,
title: The emergence of two distinct SARS-CoV-2 Gamma related variants during the second wave of COVID-19 in Santa Catarina, Southern Brazil and the rapid spread of P.1-like-II SARS-CoV-2 variant transmission and a regionalization in the Western region
date: 2022-01-14
journal: nan
DOI: 10.1101/2022.01.13.22268697
sha: 6bdb6ea294ecabc23db2f5d4cd4a27dcfd817c5a
doc_id: 282478
cord_uid: 2f2uryle

COVID-19 has assumed significant and lasting proportions worldwide. Following initial cases in the Western mesoregion, the State of Santa Catarina (SC), southern Brazil, was heavily affected as a whole by the pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state through March 2020 to April 2021 using genomic surveillance. During this period, 23 distinct variants, including two VOCs (Beta and Gamma) were identified, among which, the Gamma and related lineages were predominant in the second pandemic wave within SC. However, a regionalization of P.1-like-II in the Western region was observed, concomitant to the increase in cases, mortality, and case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 transmission in the and highlight the importance of tracking variants, dispersion and their impact of SARS-CoV-2 on the public health system in Brazilian states.

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, is the world's most 45 significant public health challenge of the last 100 years. This virus has infected more than 270 46 million people, leading to more than 5,3 million deaths worldwide by December 2021(1). In the is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. Among several detected mutations for VOC Gamma the E484K mutation occurs in the 73 receptor binding domain (RBD) domain of the S protein and is believed to assist the evasion of 74 the virus from the immune system (10) and, therefore, may lead to lower vaccine efficacy (11). 75 Also present in the RBD domain, the N501Y mutation is associated with increased binding 76 specificity to the host cell angiotensin-converting enzyme 2 (ACE2) receptor. Subvariants of 77 VOC Gamma and related lineages (P.1-like-I and P.1-like-II), displaying distinct mutations, have 78 also emerged during 2021 (12). Among these, P. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. ; https://doi.org/10.1101/2022.01.13.22268697 doi: medRxiv preprint 6 obtained cDNA was amplified using 10 μM of 14 primer sets in individual reactions to amplify 109 different regions of the SARS-CoV-2 genome (approximately 2.5 Kb in each fragment) and 40 110 U/μL Platinum Taq DNA polymerase High Fidelity (Invitrogen, Waltham, MA, USA).

Amplicons were visualized on agarose 2% gel electrophoresis.

The amplicons were then pooled, purified using the AMPure XP (Beckman Coulter, is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. ; https://doi.org/10.1101/2022.01.13.22268697 doi: medRxiv preprint Mutations, deletions, and insertions were used to assess the dissimilarity of the genomes 131 using the vegan R package v. 2.5.6 (25) with the Jaccard index method. The multidimensional 132 scaling (MDS) and the distribution of variants in SC were plotted using the ggplot2 R package v. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. 

The mutations were represented over the 3D S protein structure PDB 6ZGG (resolution 3.8 Å). is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. ; https://doi.org/10.1101/2022.01.13.22268697 doi: medRxiv preprint 9 region. ( Figure 2B ). The Mountain Range was sampled only in February 2021. The VOC 174 Gamma was predominantly identified (n=10) and a single P.1-like-II was detected.

VOC Gamma and related lineages in Santa Catarina. 176 We inferred phylogenetic relationships between the SARS-CoV-2 genomes from SC and is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. ; https://doi.org/10.1101/2022.01.13.22268697 doi: medRxiv preprint beginning 2021 (39), except for the State of Amazonas were P.2 variant was first detected in 239 November 2020 but was overshadowed by P.1 since its early detection and thus never became (Figures 4C and 4D) . Also, as highlighted in Figure 5 and is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. ; https://doi.org/10.1101/2022.01.13.22268697 doi: medRxiv preprint the virus evasion mechanisms of the human immune system through mutations that hinder viral 262 recognition by the immune system. Most of these glycosylation sites are located in Asp residues 263 that contains N-glycosylation sites, or Ser and Thr residues that contain O-glycosylation sites.

Among these, the most frequent glycosylation sites were found in N+2, where Asp is followed 265 by a Ser/Thr residues (41). Remarkably, the herein reported T20N mutation at the NTD is is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. This work is dedicated to all SC citizens who suffered or passed away due to COVID-19. 336 We also are indebted to Hospital Universitário/HU/EBSERH from Federal University of Santa is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 14, 2022. ; https://doi.org/10.1101/2022.01.13.22268697 doi: medRxiv preprint

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and 464 P.1 emergence

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 467 lineage and diversification within P.2 clade in Brazil

Antibody evasion by the P.1 strain of SARS-CoV-2. Cell

O-glycosylation pattern of the 472 SARS-CoV-2 spike protein reveals an "O-Follow-N" rule

Alok Kumar Chakrabarti, Shanta Dutta. Pathogens. Covid-19

Comparative Analysis of the Second Wave with the First Wave. Pathogens. 476

On the association between SARS-478

COV-2 variants and COVID-19 mortality during the second wave of the pandemic in 479

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

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