Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil

Sant’Anna, Fernando Hayashi; Varela, Ana Paula Muterle; Prichula, Janira; Comerlato, Juliana; Comerlato, Carolina Baldisserotto; Roglio, Vinícius Serafini; Pereira, Gérson Fernando Mendes; Moreno, Flávia; Seixas, Adriana; Wendland, Eliana Márcia

doi:10.1080/22221751.2021.1949948

Cited by 16 publications

(27 citation statements)

References 57 publications

(68 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additionally, in the present study three genomes (two in the second peak and one in third peak) classified as B.1.1.28 were shown to be VUI-NP13L, a potential new lineage [8,12]. VUI-NP13L was first reported in RS in August 2020, disseminating afterwards [12], and our results reinforce that this lineage continued to circulate at low frequency in RS.…”

Section: Discussionsupporting

confidence: 85%

“…Additionally, our study reveals the temporal frequency and divergence of SARS-CoV-2 lineages in RS over time. As observed in previous Brazilian studies, B.1.1.28 and B.1.1.33 predominated during the first epidemic peak (July and August 2020) [7,8,12,22]. Selection of these lineages over others might be explained by mutations associated with higher viral fitness and severe disease [26].…”

Section: Discussionsupporting

confidence: 65%

“…This lineage descends from B.1.1.28, carrying the lineage-defining mutations ORF1ab:L3468V, ORF1ab:synC11824U, N:A119S, and S:E484K [7]. According to our previous study, P.2 has been massively circulating in RS since October 2020 [12].…”

Section: Discussionmentioning

confidence: 90%

See 2 more Smart Citations

SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

Varela

Prichula

Mayer

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Genomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first case of each Regional Health Coordination and cases from three epidemic peaks. Methods: Ninety SARS-CoV-2 genomes from RS were sequenced and analyzed against SARS-CoV-2 datasets available in GISAID for phylogenetic inference and mutation analysis. Results: SARS-CoV-2 lineages among the first cases in RS were B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), evidencing SARS-CoV-2 introduction by both international origin and community-driven transmission. We found predominance of B.1.1.33 (50.0%) and B.1.1.28 (35.0%) during the first epidemic peak (July-August, 2020), emergence of P.2 (55.6%) in the second peak (November-December, 2020), and massive spread of P.1 and related sequences (78.4%), such as P.1-like-II, P.1.1 and P.1.2 in the third peak (February-April, 2021). Eighteen novel mutation combinations were found among P.1 genomes, and 22 different spike mutations and/or deletions among P.1 and related sequences. Conclusions: This study shows the dispersion of SARS-CoV-2 lineages in Southern Brazil, and describes SARS-CoV-2 diversity during three epidemic peaks, highlighting the spread of P.1 and the high genetic diversity of currently circulating lineages. Genomic monitoring of SARS-CoV-2 is essential to guide health authorities' decisions to control COVID-19 in Brazil.

show abstract

Section: Discussionsupporting

confidence: 85%

Section: Discussionsupporting

confidence: 65%

See 1 more Smart Citation

SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

Varela

Prichula

Mayer

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…We found a sharp increase of P.2 frequency in Rocha, with partial replacement of earlier circulating B.1.1.28 lineages, as previously reported in RS and many other Brazilian states [7,[15][16][17]. The dissemination of the VOI P.2 in Rocha may have been facilitated by the notorious increment in mobility and lax social distancing in that department (a popular holiday destination for Uruguayans) that occurred at the beginning of 2021.…”

Section: Discussionsupporting

confidence: 84%

“…The VOI P.2 reached the southernmost Brazilian state of Rio Grande do Sul (RS) in October, 2020 and then spread massively in that region [15][16][17][18]. Given the high viral flux between RS and Uruguay detected during 2020 [11], it is likely that the introduction of the VOI P.2 from Brazil could have been associated with the epidemic worsening in Uruguay by the end of 2020 and beginning of 2021.…”

Section: Introductionmentioning

confidence: 99%

Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with Brazil

Rego

Fernández-Calero

Arantes

et al. 2021

Preprint

View full text Add to dashboard Cite

During the first nine months of the SARS-CoV-2 pandemic, Uruguay successfully kept it under control, even when our previous studies support a recurrent viral flux across the Uruguayan-Brazilian border that sourced several local outbreaks in Uruguay. However, towards the end of 2020, a remarkable exponential growth was observed and the TETRIS strategy was lost. Here, we aimed to understand the factors that fueled SARS-CoV-2 viral dynamics during the first epidemic wave in the country. We recovered 84 whole viral genomes from patients diagnosed between November, 2020 and February, 2021 in Rocha, a sentinel eastern Uruguayan department bordering Brazil. The lineage B.1.1.28 was the most prevalent in Rocha during November-December 2020, P.2 became the dominant one during January-February 2021, while the first P.1 sequences corresponds to February, 2021. The lineage replacement process agrees with that observed in several Brazilian states, including Rio Grande do Sul (RS). We observed a one to three month delay between the appearance of P.2 and P.1 in RS and their subsequent detection in Rocha. The phylogenetic analysis detected two B.1.1.28 and one P.2 main Uruguayan SARS-CoV-2 clades, introduced from the southern and southeastern Brazilian regions into Rocha between early November and mid December, 2020. One synonymous mutation distinguishes the sequences of the main B.1.1.28 clade in Rocha from those widely distributed in RS. The minor B.1.1.28 cluster, distinguished by several mutations, harbours non-synonymous changes in the Spike protein: Q675H and Q677H, so far not concurrently reported. The convergent appearance of S:Q677H in different viral lineages and its proximity to the S1/S2 cleavage site raise concerns about its functional relevance. The observed S:E484K-VOI P.2 partial replacement of previously circulating lineages in Rocha might have increased transmissibility as suggested by the significant decrease in Ct values. Our study emphasizes the impact of Brazilian SARS-CoV-2 epidemics in Uruguay and the need of reinforcing real-time genomic surveillance on specific Uruguayan border locations, as one of the key elements for achieving long-term COVID-19 epidemic control.

show abstract

Genomic evidence of SARS-CoV-2 reinfection cases in southern Brazil

et al. 2023

Self Cite

View full text Add to dashboard Cite

Cases of reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported worldwide. We investigated reinfection cases in a set of more than 30,000 samples, and the SARS-CoV-2 genomes from selected samples from four patients with at least two positive diagnoses with an interval ≥ 45 days between tests were sequenced and analyzed. Comparative genomic and phylogenetic analysis confirmed three reinfection cases and suggested that the fourth one was caused by a virus of the same lineage. Viral sequencing is crucial for understanding the natural course of reinfections and for planning public health strategies for management of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s00705-022-05648-8.

show abstract

Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil

Abstract: 3 e art ent o hroni onditions and Se a y rans itted n e tions inistry o Hea th ras ia ra i

Cited by 16 publications

References 57 publications

SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with Brazil

Genomic evidence of SARS-CoV-2 reinfection cases in southern Brazil

Contact Info

Product

Resources

About