Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil

Nascimento, Valdinete Alves do; Corado, André de Lima Guerra; Nascimento, Fernanda; Costa, Ana Carolina Carioca da; Duarte, Débora; Luz, Sérgio Luíz Bessa; Fé-Gonçalves, Luciana Mara; Jesus, Michele Silva de; Costa, Cristiano Fernandes da; Delatorre, Edson; Naveca, Felipe Gomes

doi:10.1590/0074-02760200310

Cited by 49 publications

(42 citation statements)

References 26 publications

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“…1A), we focused ongoing SARS-CoV-2 genomic surveillance (2,(16)(17)(18)(19)(20) on recently collected samples from the city (see Materials and Methods). Prior to this, only seven SARS-CoV-2 genome sequences from Amazonas state were publicly available (SARS-CoV-2 was first detected in Manaus on 13 March 2020) (17,21). We sequenced SARS-CoV-2 genomes from 184 samples from patients seeking COVID-19 testing in two diagnostic laboratories in Manaus between November and December 2020, using the ARTIC V3 multiplexed amplicon scheme (22) and the MinION sequencing platform.…”

Section: Identification and Nomenclature Of A Novel P1 Lineage In Mamentioning

confidence: 99%

“…AmpureXP beads (Beckman Coulter, United Kingdom) were used for PCR product purification and fluorimetry-based quantification was carried out using the Qubit dsDNA High Sensitivity assay on the Qubit 3.0 (Life Technologies, USA). To ensure uniform sequencing of samples, equimolar normalisation of 10 ng per sample was performed followed by barcoding using the EXP-NBD104 (1-12) and EXP-NBD114 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) Native Barcoding Kits (Oxford Nanopore Technologies, UK). Finally, barcoded samples were pooled followed by library preparation using the SQK-LSK109 Kit (Oxford Nanopore Technologies, UK).…”

Section: Pcr Amplification and Virus Nanopore Sequencingmentioning

confidence: 99%

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Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

Faria

Mellan

Whittaker

et al. 2021

Preprint

214

232

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Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that 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 early 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 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with 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.One-Sentence SummaryWe report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.

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Section: Identification and Nomenclature Of A Novel P1 Lineage In Mamentioning

confidence: 99%

Section: Pcr Amplification and Virus Nanopore Sequencingmentioning

confidence: 99%

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

Faria

Mellan

Whittaker

et al. 2021

Preprint

214

232

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“…Coronavirus disease 2019 (COVID-19) was first documented in the UK at the end of January 2020, with possible community transmission likely to have started earlier [ 1 ]. On 11 March 2020, the World Health Organization classified COVID-19 as a global pandemic [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors

et al. 2021

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Most studies of severe/fatal COVID-19 risk have used routine/hospitalisation data without detailed pre-morbid characterisation. Using the community-based UK Biobank cohort, we investigate risk factors for COVID-19 mortality in comparison with non-COVID-19 mortality. We investigated demographic, social (education, income, housing, employment), lifestyle (smoking, drinking, body mass index), biological (lipids, cystatin C, vitamin D), medical (comorbidities, medications) and environmental (air pollution) data from UK Biobank (N = 473,550) in relation to 459 COVID-19 and 2626 non-COVID-19 deaths to 21 September 2020. We used univariate, multivariable and penalised regression models. Age (OR = 2.76 [2.18–3.49] per S.D. [8.1 years], p = 2.6 × 10–17), male sex (OR = 1.47 [1.26–1.73], p = 1.3 × 10–6) and Black versus White ethnicity (OR = 1.21 [1.12–1.29], p = 3.0 × 10–7) were independently associated with and jointly explanatory of (area under receiver operating characteristic curve, AUC = 0.79) increased risk of COVID-19 mortality. In multivariable regression, alongside demographic covariates, being a healthcare worker, current smoker, having cardiovascular disease, hypertension, diabetes, autoimmune disease, and oral steroid use at enrolment were independently associated with COVID-19 mortality. Penalised regression models selected income, cardiovascular disease, hypertension, diabetes, cystatin C, and oral steroid use as jointly contributing to COVID-19 mortality risk; Black ethnicity, hypertension and oral steroid use contributed to COVID-19 but not non-COVID-19 mortality. Age, male sex and Black ethnicity, as well as comorbidities and oral steroid use at enrolment were associated with increased risk of COVID-19 death. Our results suggest that previously reported associations of COVID-19 mortality with body mass index, low vitamin D, air pollutants, renin–angiotensin–aldosterone system inhibitors may be explained by the aforementioned factors.

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“…The first SARS-CoV-2 infection in Brazil was reported on 25 February 2020, and now (September 2020), Brazil is the third-most affected country in the world, with more than 5 million cases and 150 thousand deaths [ 9 ] ( — ). Recent publications based on the sequencing and characterization of SARS-CoV-2 genomes from Minas Gerais and São Paulo (southeast region of Brazil) revealed the introduction of different SARS-CoV-2 lineages from European countries, which were associated with recent travel history of the patients [ 9 , 10 , 11 ]. Resende et al 2020 [ 12 ], sequenced 95 SARS-CoV-2 genomes from 10 Brazilian states and Candido et al 2020 sequenced 427 genomes from 21 Brazilian states and both identified more than 100 independent introductions of SARS-CoV-2 in Brazil and the extensive community spread of prevailing lineages (B.1.1.28 and B.1.1.33) in some Southeast Brazilian states [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

Paiva

Guedes

Docena

et al. 2020

Viruses

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Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast region. Pernambuco state, located in the Northeast region, is the sixth most affected Brazilian state, but very few genomic sequences from the strains circulating in this region are available. We sequenced 101 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms that reside in Pernambuco. Phylogenetic reconstructions revealed that all genomes belong to the B lineage and most of the samples (88%) were classified as lineage B.1.1. We detected multiple viral introductions from abroad (likely from Europe) as well as six local B.1.1 clades composed by Pernambuco only strains. Local clades comprise sequences from the capital city (Recife) and other country-side cities, corroborating the community spread between different municipalities of the state. These findings demonstrate that different from Southeastern Brazilian states where the epidemics were majorly driven by one dominant lineage (B.1.1.28 or B.1.1.33), the early epidemic phase at the Pernambuco state was driven by multiple B.1.1 lineages seeded through both national and international traveling.

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Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil

Cited by 49 publications

References 26 publications

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

COVID-19 mortality in the UK Biobank cohort: revisiting and evaluating risk factors

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

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