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Article ; Online: Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America.

Gutierrez, Bernardo / Castelán Sánchez, Hugo G / Candido, Darlan da Silva / Jackson, Ben / Fleishon, Shay / Houzet, Renaud / Ruis, Christopher / Delaye, Luis / Faria, Nuno R / Rambaut, Andrew / Pybus, Oliver G / Escalera-Zamudio, Marina

Cell host & microbe

2022 Volume 30, Issue 8, Page(s) 1112–1123.e3

Abstract: ... viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames ... By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now ...

Abstract	Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation thus far. Here, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages to investigate the possibility of virus recombination among them. Our analyses reveal well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames. By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now designated as lineage XB, originated from a recombination event between viruses of B.1.631 and B.1.634 lineages. This scenario is supported by the spatiotemporal distribution of these lineages across the USA and Mexico during 2021, suggesting that the recombination event originated in this geographical region. This event raises important questions regarding the role and potential effects of recombination on SARS-CoV-2 evolution.
MeSH term(s)	COVID-19/epidemiology ; Genome, Viral ; Humans ; Phylogeny ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-06-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2022.06.010
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Article ; Online: Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern.

Cell

2023 Volume 186, Issue 15, Page(s) 3277–3290.e16

Abstract: The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in ... ...

Abstract	The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
MeSH term(s)	Humans ; Air Travel ; COVID-19 ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2023-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.06.001
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Article ; Online: Routes for COVID-19 importation in Brazil.

Candido, Darlan Da S / Watts, Alexander / Abade, Leandro / Kraemer, Moritz U G / Pybus, Oliver G / Croda, Julio / de Oliveira, Wanderson / Khan, Kamran / Sabino, Ester C / Faria, Nuno R

Journal of travel medicine

2020 Volume 27, Issue 3

MeSH term(s)	Aircraft ; Betacoronavirus ; Brazil/epidemiology ; COVID-19 ; Communicable Diseases, Imported/epidemiology ; Coronavirus Infections/epidemiology ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; SARS-CoV-2 ; Travel
Keywords	covid19
Language	English
Publishing date	2020-03-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1212504-0
ISSN	1708-8305 ; 1195-1982
ISSN (online)	1708-8305
ISSN	1195-1982
DOI	10.1093/jtm/taaa042
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Article ; Online: Clinical markers of post-Chikungunya chronic inflammatory joint disease: A Brazilian cohort.

Lázari, Carolina Dos Santos / Ramundo, Mariana Severo / Ten-Caten, Felipe / Bressan, Clarisse S / de Filippis, Ana Maria Bispo / Manuli, Erika Regina / de Moraes, Isabella / Pereira, Geovana Maria / Côrtes, Marina Farrel / Candido, Darlan da Silva / Gerber, Alexandra L / Guimarães, Ana Paula / Faria, Nuno Rodrigues / Nakaya, Helder I / Vasconcelos, Ana Tereza R / Brasil, Patrícia / Paranhos-Baccalà, Gláucia / Sabino, Ester Cerdeira

PLoS neglected tropical diseases

2023 Volume 17, Issue 1, Page(s) e0011037

Abstract: Background: Chikungunya-fever (CHIKF) remains a public health major issue. It is clinically divided into three phases: acute, post-acute and chronic. Chronic cases correspond to 25-40% individuals and, though most of them are characterized by long- ... ...

Abstract	Background: Chikungunya-fever (CHIKF) remains a public health major issue. It is clinically divided into three phases: acute, post-acute and chronic. Chronic cases correspond to 25-40% individuals and, though most of them are characterized by long-lasting arthralgia alone, many of them exhibit persistent or recurrent inflammatory signs that define post-Chikungunya chronic inflammatory joint disease (pCHIKV-CIJD). We aimed to identify early clinical markers of evolution to pCHIKV-CIJD during acute and post-acute phases. Methodology/principal findings: We studied a prospective cohort of CHIKF-confirmed volunteers with longitudinal clinical data collection from symptoms onset up to 90 days, including a 21-day visit (D21). Of 169 patients with CHIKF, 86 (50.9%) completed the follow-up, from whom 39 met clinical criteria for pCHIKV-CIJD (45.3%). The relative risk of chronification was higher in women compared to men (RR = 1.52; 95% CI = 1.15-1.99; FDR = 0.03). None of the symptoms or signs presented at D0 behaved as an early predictor of pCHIKV-CIJD, while being symptomatic at D21 was a risk factor for chronification (RR = 1.31; 95% CI = 1.09-1.55; FDR = 0.03). Significance was also observed for joint pain (RR = 1.35; 95% CI = 1.12-1.61; FDR = 0.02), reported edema (RR = 3.61; 95% CI = 1.44-9.06; FDR = 0.03), reported hand and/or feet small joints edema (RR = 4.22; 95% CI = 1.51-11.78; FDR = 0.02), and peri-articular edema observed during physical examination (RR = 2.89; 95% CI = 1.58-5.28; FDR = 0.002). Furthermore, patients with no findings in physical examination at D21 were at lower risk of chronic evolution (RR = 0.41, 95% CI = 0.24-0.70, FDR = 0.01). Twenty-nine pCHIKV-CIJD patients had abnormal articular ultrasonography (90.6% of the examined). The most common findings were synovitis (65.5%) and joint effusion (58.6%). Conclusion: This cohort has provided important insights into the prognostic evaluation of CHIKF. Symptomatic sub-acute disease is a relevant predictor of evolution to chronic arthritis with synovitis, drawing attention to joint pain, edema, multiple articular involvement including small hand and feet joints as risk factors for chronification beyond three months, especially in women. Future studies are needed to accomplish the identification of accurate and early biomarkers of poor clinical prognosis, which would allow better understanding of the disease's evolution and improve patients' management, modifying CHIKF burden on global public health.
MeSH term(s)	Male ; Humans ; Female ; Chikungunya Fever/complications ; Chikungunya Fever/diagnosis ; Chikungunya Fever/epidemiology ; Prospective Studies ; Brazil/epidemiology ; Arthritis ; Synovitis ; Arthralgia/epidemiology ; Arthralgia/etiology ; Biomarkers ; Chronic Disease
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0011037
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern

Cell. 20232023 July 07, June 07, v. 186, no. 15 p.3277-3290.e16

2023

Abstract	The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%–2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; air transportation ; genomics ; monitoring ; phylogeny ; phylogeography ; India ; South Africa ; mobility ; travel ; SARS-CoV-2 ; global dispersal ; phylogenetics ; variants
Language	English
Dates of publication	2023-0607
Size	p. 3277-3290.e16.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.06.001
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Article ; Online: Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020.

Claro, Ingra Morales / da Silva Sales, Flavia Cristina / Ramundo, Mariana Severo / Candido, Darlan S / Silva, Camila A M / de Jesus, Jaqueline Goes / Manuli, Erika R / de Oliveira, Cristina Mendes / Scarpelli, Luciano / Campana, Gustavo / Pybus, Oliver G / Sabino, Ester Cerdeira / Faria, Nuno Rodrigues / Levi, José Eduardo

Emerging infectious diseases

2021 Volume 27, Issue 3, Page(s) 970–972

Abstract: In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient ...

Abstract	In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.
MeSH term(s)	Adult ; Brazil ; COVID-19/epidemiology ; COVID-19/virology ; Female ; Genome, Viral ; Humans ; Male ; Phylogeny ; SARS-CoV-2/isolation & purification ; Travel ; Young Adult
Language	English
Publishing date	2021-01-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2703.210038
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Article: Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.

Wellcome open research

2023 Volume 6, Page(s) 241

Abstract: Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic ... ...

Abstract	Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.
Language	English
Publishing date	2023-04-24
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.17170.2
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Article ; Online: Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

Claro, Ingra Morales / Romano, Camila Malta / Candido, Darlan da Silva / Lima, Evelyn Lepka de / Lindoso, José Angelo Lauletta / Ramundo, Mariana Severo / Moreira, Filipe Romero Rebello / Barra, Luiz Alberto Costa / Borges, Luciana Marques Sansão / Medeiros, Lucas Alberto / Tomishige, Marcia Y S / Moutinho, Tomas / Silva, Anderson José Dias da / Rodrigues, Camila Cristina Martini / Azevedo, Luiz Cesar Fernandes de / Villas-Boas, Lucy Santos / Silva, Camila Alves Maia da / Coletti, Thaís Moura / Manuli, Erika R /

O'Toole, Aine / Quick, Joshua / Loman, Nicholas / Rambaut, Andrew / Faria, Nuno R / Figueiredo-Mello, Claudia / Sabino, Ester Cerdeira

Revista do Instituto de Medicina Tropical de Sao Paulo

2022 Volume 64, Page(s) e48

Abstract: Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was ...

Abstract	Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.
MeSH term(s)	Brazil ; Humans ; Metagenomics ; Mpox (monkeypox)/diagnosis ; Mpox (monkeypox)/epidemiology ; Monkeypox virus/genetics
Language	English
Publishing date	2022-06-24
Publishing country	Brazil
Document type	Case Reports ; Journal Article
ZDB-ID	128928-7
ISSN	1678-9946 ; 0036-4665
ISSN (online)	1678-9946
ISSN	0036-4665
DOI	10.1590/S1678-9946202264048
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Article: Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel.

medRxiv : the preprint server for health sciences

2022

Abstract: In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third ... ...

Abstract	In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance. Highlights: Global phylogenetic analysis reveals relationship between air travel and speed of dispersal of SARS-CoV-2 variants of concern (VOCs)Omicron VOC spread to 5x more countries within 100 days of its emergence compared to all other VOCsOnward transmission and dissemination of VOCs Delta and Omicron was primarily from secondary hubs rather than initial country of detection during a time of increased global air travelAnalysis highlights highly connected countries identified as major global and regional exporters of VOCs.
Language	English
Publishing date	2022-11-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.11.22.22282629
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Article ; Online: Pathophysiology of chikungunya virus infection associated with fatal outcomes.

de Souza, William M / Fumagalli, Marcilio J / de Lima, Shirlene T S / Parise, Pierina L / Carvalho, Deyse C M / Hernandez, Cristian / de Jesus, Ronaldo / Delafiori, Jeany / Candido, Darlan S / Carregari, Victor C / Muraro, Stefanie P / Souza, Gabriela F / Simões Mello, Leda M / Claro, Ingra M / Díaz, Yamilka / Kato, Rodrigo B / Trentin, Lucas N / Costa, Clauber H S / Maximo, Ana Carolina B M /

Cavalcante, Karene F / Fiuza, Tayna S / Viana, Vânia A F / Melo, Maria Elisabeth L / Ferraz, Clarissa P M / Silva, Débora B / Duarte, Larissa M F / Barbosa, Priscilla P / Amorim, Mariene R / Judice, Carla C / Toledo-Teixeira, Daniel A / Ramundo, Mariana S / Aguilar, Patricia V / Araújo, Emerson L L / Costa, Fabio T M / Cerqueira-Silva, Thiago / Khouri, Ricardo / Boaventura, Viviane S / Figueiredo, Luiz Tadeu M / Fang, Rong / Moreno, Brechla / López-Vergès, Sandra / Mello, Liana Perdigão / Skaf, Munir S / Catharino, Rodrigo R / Granja, Fabiana / Martins-de-Souza, Daniel / Plante, Jessica A / Plante, Kenneth S / Sabino, Ester C / Diamond, Michael S / Eugenin, Eliseo / Proença-Módena, José Luiz / Faria, Nuno R / Weaver, Scott C

Cell host & microbe

2024 Volume 32, Issue 4, Page(s) 606–622.e8

Abstract: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, ... ...

Abstract	Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, histopathological, cytokine, molecular dynamics, metabolomic, proteomic, and genomic analyses to investigate viral and host factors that contribute to chikungunya-associated (CHIK) death. Our results indicate that CHIK deaths are associated with multi-organ infection, central nervous system damage, and elevated serum levels of pro-inflammatory cytokines and chemokines compared with survivors. The histopathologic, metabolite, and proteomic signatures of CHIK deaths reveal hemodynamic disorders and dysregulated immune responses. The CHIKV East-Central-South-African lineage infecting our study population causes both fatal and survival cases. Additionally, CHIKV infection impairs the integrity of the blood-brain barrier, as evidenced by an increase in permeability and altered tight junction protein expression. Overall, our findings improve the understanding of CHIK pathophysiology and the causes of fatal infections.
MeSH term(s)	Animals ; Humans ; Chikungunya Fever/complications ; Proteomics ; Chikungunya virus/genetics ; Cytokines/metabolism
Chemical Substances	Cytokines
Language	English
Publishing date	2024-03-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2024.02.011
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