Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020

Claro, Ingra Morales; Sales, Flavia Cristina da Silva; Ramundo, Mariana Severo; Cândido, Darlan da Silva; Silva, Camila A. M.; Jesus, Jaqueline Góes de; Manuli, Erika R.; Oliveira, Cristina Mendes de; Scarpelli, Luciano Cesar; Campana, Gustavo; Pybus, Oliver G.; Sabino, Éster Cerdeira; Faria, Nuno Rodrigues; Levi, José Eduardo

doi:10.3201/eid2703.210038

Cited by 60 publications

(52 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The results indicated that the first infection in September 2020 was caused by a non-VOC virus. This is expected as the two currently circulating VOCs in Brazil (B.1.1.7 and P.1) had not emerged yet 6 , 9 . However, the RT-qPCR results suggested that the second episode was caused by a VOC, that could be either B.1.1.7 or P.1.…”

Section: Case Descriptionmentioning

confidence: 87%

SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil

Romano

Félix

et al. 2021

Rev. Inst. Med. trop. S. Paulo

Self Cite

View full text Add to dashboard Cite

Section: Case Descriptionmentioning

confidence: 87%

SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil

Romano

Félix

et al. 2021

Rev. Inst. Med. trop. S. Paulo

Self Cite

View full text Add to dashboard Cite

“…After a rapid increase in hospitalizations in Manaus caused by severe acute respiratory infection (SARI) in December 2020 ( Fig. 1A ), we focused ongoing SARS-CoV-2 genomic surveillance ( 2 , 18 22 ) on recently collected samples from the city (supplementary materials, materials and methods, and table S2). Before this, only seven SARS-CoV-2 genome sequences from Amazonas were publicly available (SARS-CoV-2 was first detected in Manaus on 13 March 2020) ( 19 , 23 ).…”

Section: Identification and Nomenclature Of The P1 Lineage In Manausmentioning

confidence: 99%

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Faria

Mellan

Whittaker

et al. 2021

Science

Self Cite

1,256

1,110

View full text Add to dashboard Cite

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

show abstract

“…B and B.1 lineages have presented a relatively low time of spread, while several B.1.1 derived lineages probably have spreaded for a longer period ( e. g, B.1.1.143, B.1.1.28, B.1.1.314, B.1.1.33, B.1.1.74, B.1.1.94) ( Figure S2). B.1.1.7 (UK-associated lineage) was firstly detected in the country in mid-December (Claro et al 2021) , while P.1 was found in November in Manaus (Amazonas, Brazil) and Japan (Faria et al 2021a) . P.2 was discovered in mid-April 2020, but has been increasing rapidly in frequency since August 2020 ( Figure 3A, Figure S2).…”

Section: Regarding Distribution Between the Five Different Brazilian mentioning

confidence: 99%

Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021: insights and limitations from uneven sequencing efforts

Pag

et al. 2021

Preprint

View full text Add to dashboard Cite

The COVID-19 pandemic has already reached approximately 110 million people and it is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. Unprecedented international efforts have been established in order to share information about epidemiology, viral evolution and transmission dynamics. However, sequencing facilities and research investments are very heterogeneous across different regions and countries across the globe. The understanding of the SARS-CoV-2 biology is a vital part for the development of effective strategies for public health care and disease management. This work aims to analyze the available genomes sequenced in Brazil between February 2020 and February 2021, in order to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in the Brazilian territory by using phylogenetics and phylodynamics analyses from high-quality genomes. We describe heterogeneous and episodic sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of novel and specific lineages across different Brazilian regions. We found at least seven major (1-7) and two minor clades (4.2 and 5.3) related to the six most prevalent Brazilian lineages and described its distribution across the Brazilian territory. The emergence and recent frequency shift of lineages (P.1 and P.2) containing mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers and enable precise evidence-based decisions to fight the COVID-19 pandemic.

show abstract

Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020

Cited by 60 publications

References 7 publications

SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil

SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021: insights and limitations from uneven sequencing efforts

Contact Info

Product

Resources

About