key: cord-0803034-mt2xthda
authors: Kashima, Simone; Slavov, Svetoslav N.; Giovanetti, Marta; Rodrigues, Evandra S.; Patané, José S. L.; Viala, Vincent L.; Santos, Elaine V.; Evaristo, Mariane; de Lima, Loyze P. O.; Martins, Antonio J.; dos Santos Barros, Claudia R.; Marqueze, Elaine C.; Garibaldi, Pedro M. M.; Ferreira, Natasha N.; Moraes, Glenda R.; Brassaloti, Ricardo A.; Cassano, Raquel L. R. C.; Mariani, Pilar D. S. C.; Kitajima, João P.; Schlesinger, David; Bezerra, Rafael S.; Assato, Patricia A.; da Costa, Felipe A. S.; Poleti, Mirele Daiana; Lesbon, Jessika C. C.; Mattos, Elisangela C.; Banho, Cecilia A.; Sacchetto, Lívia; Grotto, Rejane M. T.; Souza‐Neto, Jayme A.; Fonseca, Vagner; de Alcantara, Luiz C. J.; Nogueira, Maurício L.; Fukumasu, Heidge; Coutinho, Luiz L.; Borges, Marcos; Calado, Rodrigo T.; Elias, Maria C.; Sampaio, Sandra C.; Covas, Dimas T.
title: Introduction of SARS‐CoV‐2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil
date: 2021-10-20
journal: J Med Virol
DOI: 10.1002/jmv.27389
sha: eb0fd5ef2c7eb108ab515aa5bde392a7415577e8
doc_id: 803034
cord_uid: mt2xthda

The Lambda variants of interest (VOI) (C37/GR/452Q.V1/21G) was initially reported in Lima, Peru but has gained rapid dissemination through other Latin American countries. Nevertheless, the dissemination and molecular epidemiology of the Lambda VOI in Brazil is unknown apart from a single case report. In this respect, we characterized the circulation of the SARS‐CoV‐2 Lambda VOI (C37/GR/452Q.V1/21G) in Sao Paulo State, Brazil. From March to June 2021, we identified seven Lambda isolates in a set of approximately 8000 newly sequenced genomes of the Network for Pandemic Alert of Emerging SARS‐CoV‐2 variants from Sao Paulo State. Interestingly, in three of the positive patients, the Lambda VOI infection was probably related to a contact transmission. These individuals were fully vaccinated to COVID‐19 and presented mild symptoms. The remaining positive for Lambda VOI individuals showed different levels of COVID‐19 symptoms and one of them needed hospitalization (score 5, WHO). In our study, we present a low level of Lambda VOI circulation in the Sao Paulo State. This reinforces the essential role of molecular surveillance for the effective SARS‐CoV‐2 pandemic response, especially in regard to circulating variants.

Currently, the State of Sao Paulo, located in southeastern Brazil harbors the highest number of reported COVID-19 cases in the country (4.4 million until October 3, 2021) . This high incidence (9515/100 000 inhabitants) has been linked to the circulation of several variants of concern (VOCs) and interest (VOIs) with an almost total predominance of the Gamma VOC (P.1/GR 5-1Y.V3/20J). 1 Despite the high frequency of Gamma VOC in the national and State scenario, the prompt detection of other circulating VOCs (Alpha, Beta, and Delta) and VOIs (Zeta and Lambda) is challenging and highly necessary, especially due to the ongoing vaccination process. In this respect, until now, 66% of the population in the Sao Paulo State have received their first vaccine application and about 26% are fully vaccinated according to the Health Surveillance Agency of the State (https://www.saopaulo.

sp.gov.br/). In early 2021, Sao Paulo implemented the Network for Pandemic Alert of Emerging SARS-CoV-2 Variants aiming to characterize the SARS-CoV-2 circulating variants. This Network contributes to the Brazilian SARS-CoV-2 genomic surveillance by random sequencing between 0.2% and 12.9% of positive cases per epidemiological week and nowadays the Sao Paulo State is the Brazilian Federal Unit, which provides the largest quantity of SARS-CoV-2 complete genomes deposited in GISAID. In view of this scenario, we described the circulation of an underestimated SARS-CoV-2 Lambda VOI (C.37/GR/452Q.V1/21G lineage) in the Sao Paulo State, providing a primary overview of its transmission dynamics. This VOI has been largely disseminated in many South American countries, including Chile, Peru, Argentina, Ecuador, and Colombia 2-6 but there is a unique report considering Brazil. 7 In total, we detected seven Lambda VOI isolates in a total of approximately 8000 sequenced SARS-CoV-2 genomes and therefore we describe their molecular epidemiology and mutational profile in the Sao Paulo State. 

The serological testing for the presence of anti-SARS-CoV-2 neutralizing antibodies was performed using the Liaison ® SARS-CoV-2 TrimericS IgG kit (DiaSorin) and Elecys ® Anti-SARS-CoV-2 Spike and Nucleocapsid (Roche) following the manufacturer's instructions. The serological results obtained by both tests have been shown to correlate positively with the titer of neutralizing antibodies. 8 

The raw sequence data were submitted to quality control analysis using the FastaQC 9 software v. 0.11.8. Trimming was performed using Trimmomatic 10 v. 0.3.9 to select the best quality sequences.

We mapped the trimmed sequences against the SARS-CoV-2 reference (Genbank refseq NC_045512.2) using BWA 11 software and samtools 12 for read indexing. The mapped files were submitted to refinement with the software Pilon 13 to obtain the indels and insertions in the most correct way possible. Finally, we used bcftools 14 for variant calling and seqtk 15 for the creation of consensus genomes.

For performing phylogenetic analysis, we used a dataset containing 630 Lambda VOI genomes obtained from GISAID up to September 26, 2021 . Only genomes >29 000 bp and <1% of ambiguities were retrieved, low-quality genomes (>10% of ambiguous positions) were excluded. Sequence alignment was performed using MAFFT v7.475 16 and manually curated to remove artifacts using Aliview. 17 severity with a score of 5 (WHO). 21 We also characterized the mutational profile of this VOI, which harbored the following mutations: 

In this report, we provide more detailed information about the Lambda VOI circulation in Sao Paulo State, which was detected as part of a wide program for SARS-CoV-2 genomic surveillance in this part of Brazil. The mutation profile of this VOI 2 was also characterized. In the first place, the performed genomic surveillance for the period of 8th to 31st epidemiological week demonstrated a very low circulation of the Lambda VOI in the State of Sao Paulo, despite the intensive presence of this VOI in the neighboring countries, and principally Peru, where it accounts almost approximately 97% of the identified genomes by April 2021. 22 reference Lambda SARS-CoV-2 complete genomes obtained from GISAID (https://www.gisaid.org) until September 2021. We also represented on the right side, zoom of the sequences obtained from the inner São Paulo State with the bootstrap support of this branch recent study. 25 Of particular interest is the L452Q mutation, which has been related to increased viral transmission 26 that may contribute to the higher morbidity of this VOI in the countries in which it initially emerged.

Detailed epidemiological information of the positive for Lambda VOI patients demonstrated that three of them have been fully vaccinated against COVID-19. In addition, these individuals worked together and on the phylogenetic tree, the samples clustered with high bootstrap support (Figure 1 ). On one hand, the presence of the mutation L452Q 26 and D614G 27 was related to high replication and antiviral immunity fitness of the Lambda VOI, which can be explained by the reduced neutralizing activity of the vaccine-induced antibodies to this VOI. 28 In addition, Lambda VOI has demonstrated higher vaccine escape compared to the Delta VOC, which also demonstrates high rates of infectivity. 29 

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

Nextstrain: real-time tracking of pathogen evolution

Geographical distribution of genetic variants and lineages of SARS-CoV-2 in Chile

Genomic sequences and analysis of five SARS-CoV-2 variants obtained from patients in Lambayeque

Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern

First identification of SARS-CoV-2 lambda (C.37) variant in Southern Brazil

SARS-CoV-2 specific antibody and neutralization assays reveal the wide range of the humoral immune response to virus

quality control tool for high throughput sequence data

Trimmomatic: a flexible trimmer for Illumina sequence data

Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv

The sequence alignment/map format and SAMtools

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

MAFFT multiple sequence alignment software version 7: improvements in performance and usability

AliView: a fast and lightweight alignment viewer and editor for large datasets

IQ-TREE: a fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies

Temporal signal and the phylodynamic threshold of SARS-CoV-2

TreeTime: maximum-likelihood phylodynamic analysis

WHO Working Group on the Clinical Characterisation and Management of COVID-19 infection. A minimal common outcome measure set for COVID-19 clinical research

The emergence of SARS-CoV-2 variant lambda (C.37) in South America

Multiple introduction of SARS-CoV-2 C.37 lambda lineage in the southern Brazilian region

Infectivity and immune escape of the new SARS-CoV-2 variant of interest lambda. medRxiv

SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance

Spike mutation D614G alters SARS-CoV-2 fitness

Reduced neutralizing activity of post-SARS-CoV-2 vaccination serum against variants B.1.617.2, B.1.351, B.1.1.7+E484K and a sub-variant of C

The Lambda variant of SARS-CoV-2 has a better chance than the Delta variant to escape vaccines

SARS-CoV-2 Lambda variant remains susceptible to neutralization by mRNA vaccine-elicited antibodies and convalescent serum

Introduction of SARS-CoV-2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil

The authors declare that there are no conflict of interests. 

The Lambda VOI sequences generated in this study were deposited under the following Gisaid accession numbers: EPI_ISL_2928137, EPI_ISL_4681968, EPI_ISL_4684266, EPI_ISL_4685838, EPI_ISL_4687 192, EPI_ISL_1966094, EPI_ISL_1445272.

http://orcid.org/0000-0002-1487-0141Vagner Fonseca http://orcid.org/0000-0001-5521-6448Maurício L. Nogueira https://orcid.org/0000-0003-1102-2419