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Article ; Online: Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023.

Arantes, Ighor / Gomes, Marcelo / Ito, Kimihito / Sarafim, Sharbilla / Gräf, Tiago / Miyajima, Fabio / Khouri, Ricardo / de Carvalho, Felipe Cotrim / de Almeida, Walquiria Aparecida Ferreira / Siqueira, Marilda Mendonça / Resende, Paola Cristina / Naveca, Felipe Gomes / Bello, Gonzalo

Microbiology spectrum

2024 Volume 12, Issue 3, Page(s) e0383123

Abstract: The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (: Importance: ... ...

Abstract	The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data ( Importance: Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.
MeSH term(s)	Humans ; Brazil/epidemiology ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03831-23
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Article ; Online: Seasonality, molecular epidemiology, and virulence of Respiratory Syncytial Virus (RSV): A perspective into the Brazilian Influenza Surveillance Program.

Vianna, Lucas A / Siqueira, Marilda M / Volpini, Lays P B / Louro, Iuri D / Resende, Paola C

PloS one

2021 Volume 16, Issue 5, Page(s) e0251361

Abstract: Background: Respiratory Syncytial Virus (RSV) is the main cause of pediatric morbidity and mortality. The complex evolution of RSV creates a need for worldwide surveillance, which may assist in the understanding of multiple viral aspects.: Objectives!# ...

Abstract	Background: Respiratory Syncytial Virus (RSV) is the main cause of pediatric morbidity and mortality. The complex evolution of RSV creates a need for worldwide surveillance, which may assist in the understanding of multiple viral aspects. Objectives: This study aimed to investigate RSV features under the Brazilian Influenza Surveillance Program, evaluating the role of viral load and genetic diversity in disease severity and the influence of climatic factors in viral seasonality. Methodology: We have investigated the prevalence of RSV in children up to 3 years of age with severe acute respiratory infection (SARI) in the state of Espirito Santo (ES), Brazil, from 2016 to 2018. RT-qPCR allowed for viral detection and viral load quantification, to evaluate association with clinical features and mapping of local viral seasonality. Gene G sequencing and phylogenetic reconstruction demonstrated local genetic diversity. Results: Of 632 evaluated cases, 56% were caused by RSV, with both subtypes A and B co-circulating throughout the years. A discrete inverse association between average temperature and viral circulation was observed. No correlation between viral load and disease severity was observed, but children infected with RSV-A presented a higher clinical severity score (CSS), stayed longer in the hospital, and required intensive care, and ventilatory support more frequently than those infected by RSV-B. Regarding RSV diversity, some local genetic groups were observed within the main genotypes circulation RSV-A ON1 and RSV-B BA, with strains showing modifications in the G gene amino acid chain. Conclusion: Local RSV studies using the Brazilian Influenza Surveillance Program are relevant as they can bring useful information to the global RSV surveillance. Understanding seasonality, virulence, and genetic diversity can aid in the development and suitability of antiviral drugs, vaccines, and assist in the administration of prophylactic strategies.
MeSH term(s)	Brazil/epidemiology ; Epidemiological Monitoring ; Female ; Genotype ; Humans ; Infant ; Influenza A virus/isolation & purification ; Influenza A virus/pathogenicity ; Influenza, Human/epidemiology ; Influenza, Human/pathology ; Influenza, Human/virology ; Male ; Molecular Epidemiology/methods ; Phylogeny ; RNA, Viral/genetics ; Respiratory Syncytial Virus Infections/epidemiology ; Respiratory Syncytial Virus Infections/pathology ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Human/genetics ; Respiratory Syncytial Virus, Human/isolation & purification ; Respiratory Syncytial Virus, Human/pathogenicity ; Seasons ; Viral Load/methods ; Virulence
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0251361
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Article ; Online: Resurgence of human respiratory syncytial virus during COVID-19 pandemic in Southern Brazil.

Fröhlich, Guilherme C / Gregianini, Tatiana S / Pinheiro, Felipe G / Nascimento, Rodrigo / Cezar, Thiago M / Pscheidt, Veridiane M / Selayaran, Tainá / Martins, Letícia G / Gomes, Marcelo Ferreira da Costa / Salvato, Richard S / Pereira, Elisa C / Guimarães-Ribeiro, Victor / Scalioni, Letícia de Paula / Siqueira, Marilda M / Resende, Paola C / Veiga, Ana B G

Journal of medical virology

2024 Volume 96, Issue 3, Page(s) e29551

Abstract: Respiratory Syncytial Virus (RSV) is an important cause of respiratory infection in humans. Severe cases are common in children ≤2 years old, immunocompromised individuals, and the elderly. In 2020, RSV infection reduced in Rio Grande do Sul (RS), ... ...

Abstract	Respiratory Syncytial Virus (RSV) is an important cause of respiratory infection in humans. Severe cases are common in children ≤2 years old, immunocompromised individuals, and the elderly. In 2020, RSV infection reduced in Rio Grande do Sul (RS), southern Brazil; however, in 2021 resurgence of RSV was observed. This study analyzed epidemiological and genetic features of RSV infection cases reported in 2021 in RS. Nasopharyngeal samples collected from individuals with respiratory infection negative for SARS-CoV-2, Influenza A and B viruses were assessed for the presence of RSV by real time RT-qPCR. RSV-A and RSV-B genomic sequencing and phylogenetic reconstructions were performed for genotyping and clade characterization. Among 21,035 respiratory samples analyzed, 2,947 were positive for RSV, 947 of which were hospitalized patients. Positive cases were detected year-round, with the highest number in June-July (winter). Children <1 year comprised 56.28% (n = 533) of the hospitalized patients infected with RSV, whereas 14.46% (n = 137) were individuals >60 years. Of a total of 361 deaths, 14.68% (n = 53) were RSV positive, mostly patients >60 years old (73.58%, n = 39). Chronic kidney disease, cardiopathy, Down syndrome and neurological diseases were associated with RSV infection. RSV-A was identified in 58.5% (n = 117/200) of the patients, and RSV-B in 41.5% (n = 83/200). Of 95 RSV genomes recovered from SARI cases, 66 were RSV-A GA.2.3.5 genotype, while 29 were RSV-B GB.5.0.5a genotype. This study provides epidemiological and molecular data on RSV cases in RS during the COVID-19 pandemic and highlights that investigation of different respiratory viruses is essential for decision-making and disease prevention and control measures.
MeSH term(s)	Child ; Humans ; Infant ; Aged ; Child, Preschool ; Middle Aged ; Respiratory Syncytial Virus, Human/genetics ; Respiratory Syncytial Virus Infections/epidemiology ; Phylogeny ; Brazil/epidemiology ; Pandemics ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Influenza, Human/epidemiology ; Respiratory Tract Infections
Language	English
Publishing date	2024-03-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29551
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Article ; Online: SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil.

Lanzarini, Natália Maria / Mannarino, Camille Ferreira / Ribeiro, André Vinicius Costa / Prado, Tatiana / Vahia, Leonardo Saboia / Siqueira, Marilda Mendonça / Resende, Paola Cristina / Quintaes, Bianca Ramalho / Miagostovich, Marize Pereira

Environmental science and pollution research international

2023 Volume 30, Issue 25, Page(s) 67368–67377

Abstract: Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on ... ...

Abstract	Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log
MeSH term(s)	Humans ; Brazil ; COVID-19 ; SARS-CoV-2 ; Solid Waste
Chemical Substances	Solid Waste
Language	English
Publishing date	2023-04-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-27019-9
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Article ; Online: Reduced ability to neutralize the Omicron variant among adults after infection and complete vaccination with BNT162b2, ChAdOx1, or CoronaVac and heterologous boosting.

Espíndola, Otávio Melo / Fuller, Trevon L / de Araújo, Mia Ferreira / Tort, Luis Fernando Lopez / Guaraldo, Lusiele / Calvet, Guilherme / Resende, Paola / Bonaldo, Myrna / Whitworth, Jimmy / Smith, Chris / Siqueira, Marilda / Brasil, Patrícia

Scientific reports

2023 Volume 13, Issue 1, Page(s) 7437

Abstract: COVID-19 vaccines have dramatically reduced rates of severe infection requiring hospitalization. However, SARS-CoV-2 variants have reduced vaccine effectiveness at preventing any symptomatic infection. This real-world study analyzed binding and ... ...

Abstract	COVID-19 vaccines have dramatically reduced rates of severe infection requiring hospitalization. However, SARS-CoV-2 variants have reduced vaccine effectiveness at preventing any symptomatic infection. This real-world study analyzed binding and neutralizing antibodies generated after complete vaccination and boosting across three vaccine platforms. Binding antibodies decayed most slowly in people under 60 with hybrid immunity. Neutralizing antibodies against Omicron BA.1 were reduced compared to other variants. The anamnestic anti-spike IgG response to the first boost was more pronounced than after the second boost. Monitoring of the effects of SARS-CoV-2 mutations on disease severity and the effectiveness of therapeutics is warranted.
MeSH term(s)	Adult ; Humans ; COVID-19 Vaccines ; BNT162 Vaccine ; COVID-19/prevention & control ; SARS-CoV-2/genetics ; Vaccination ; Antibodies, Neutralizing ; Antibodies, Viral
Chemical Substances	sinovac COVID-19 vaccine ; COVID-19 Vaccines ; BNT162 Vaccine ; Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2023-05-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-34035-9
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Article ; Online: The Role of Children in Household Transmission of SARS-CoV-2 Across Four Waves of the Pandemic.

Fuller, Trevon L / Bastos, Leonardo / Carvalho, Marilia Sá / Resende, Paola Cristina / Damasceno, Luana / Cruz, Oswaldo Gonçalves / Medeiros, Fernando / Calvet, Guilherme / Guaraldo, Lusiele / Nielsen-Saines, Karin / Whitworth, James / Smith, Christopher / Siqueira, Marilda / Brasil, Patrícia

Journal of the Pediatric Infectious Diseases Society

2023 Volume 12, Issue 7, Page(s) 413–420

Abstract: Background: It is important to understand the dynamics of SARS-CoV-2 transmission in close-contact settings such as households. We hypothesized that children would most often acquire SARS-CoV-2 from a symptomatic adult caregiver.: Methods: This ... ...

Abstract	Background: It is important to understand the dynamics of SARS-CoV-2 transmission in close-contact settings such as households. We hypothesized that children would most often acquire SARS-CoV-2 from a symptomatic adult caregiver. Methods: This prospective cohort study was conducted from April 2020 to July 2022 in a low-resource, urban settlement in Brazil. We recruited families who brought their children to a public clinic. We collected nasopharyngeal and oral swabs from household members and tracked symptoms and vaccination. Results: In total, 1256 participants in 298 households were tested for SARS-CoV-2. A total of 4073 RT-PCR tests were run with 893 SARS-CoV-2 positive results (21.9%). SARS-CoV-2 cases were defined as isolated cases (N = 158) or well-defined transmission events (N = 175). The risk of household transmission was lower if the index case was a child (OR: 0.3 [95% CI: 0.16-0.55], P < .001) or was vaccinated (OR: 0.29 [95% CI: 0.1-0.85], P = .024), and higher if the index was symptomatic (OR: 2.53 [95% CI: 1.51-4.26], P < .001). The secondary attack rate for child index cases to child contacts was 0.29, whereas the secondary attack rate for adult index cases to child contacts was 0.47 (P = .08). Conclusions: In this community, children were significantly less infectious to their household contacts than adolescents or adults. Most children were infected by a symptomatic adult, usually their mother. There was a double benefit of vaccination as it protected the vaccine from severe illness and prevented onward transmission to household contacts. Our findings may also be valid for similar populations throughout Latin America.
MeSH term(s)	Adult ; Female ; Adolescent ; Child ; Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Prospective Studies ; Pandemics/prevention & control ; Family Characteristics
Language	English
Publishing date	2023-06-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2668791-4
ISSN	2048-7207 ; 2048-7193
ISSN (online)	2048-7207
ISSN	2048-7193
DOI	10.1093/jpids/piad044
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Article ; Online: Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean.

Nature communications

2024 Volume 15, Issue 1, Page(s) 1837

Abstract: Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic ... ...

Abstract	Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Latin America/epidemiology ; Pandemics ; Phylogeny ; COVID-19/epidemiology ; Caribbean Region/epidemiology
Language	English
Publishing date	2024-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46143-9
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Article ; Online: An Inexpensive and Accurate Reverse Transcription-PCR-Melting Temperature Analysis Assay for Real-Time Influenza Virus B Lineage Discrimination.

Motta, Fernando Couto / Born, Priscila Silva / Resende, Paola Cristina / Brown, David / Siqueira, Marilda Mendonça

Journal of clinical microbiology

2019 Volume 57, Issue 12

Abstract: In this work, we describe a SYBR-Green one-step reverse transcription-PCR protocol coupled with a melting temperature analysis (RT-PCR- ...

Abstract	In this work, we describe a SYBR-Green one-step reverse transcription-PCR protocol coupled with a melting temperature analysis (RT-PCR-
MeSH term(s)	Brazil ; Costs and Cost Analysis ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Humans ; Influenza B virus/classification ; Influenza B virus/genetics ; Influenza B virus/isolation & purification ; Influenza, Human/diagnosis ; Influenza, Human/virology ; Nucleic Acid Denaturation ; Real-Time Polymerase Chain Reaction/economics ; Real-Time Polymerase Chain Reaction/methods ; Reverse Transcriptase Polymerase Chain Reaction/economics ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Time Factors
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus
Language	English
Publishing date	2019-11-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.00602-19
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Article ; Online: Long COVID-19 syndrome associated with Omicron XBB.1.5 infection: a case report.

Espíndola, Otávio / Resende, Paola C / Guaraldo, Lusiele / Calvet, Guilherme Amaral / Fuller, Trevon L / Penetra, Stephanie Lema Suarez / Santos, Heloisa Ferreira Pinto / Pina-Costa, Anielle / da Silva, Michele Fernanda Borges / Moraes, Isabella Campos Vargas / Medeiros, Fernando / Whitworth, Jimmy / Smith, Christopher / Nielsen-Saines, Karin / Siqueira, Marilda M / Brasil, Patrícia

Memorias do Instituto Oswaldo Cruz

2023 Volume 118, Page(s) e230069

Abstract: Background: There is interest in lingering non-specific symptoms after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, referred to as Long coronavirus disease 2019 (Long COVID-19). It remains unknown whether the risk of Long ... ...

Abstract	Background: There is interest in lingering non-specific symptoms after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, referred to as Long coronavirus disease 2019 (Long COVID-19). It remains unknown whether the risk of Long COVID-19 is associated with pre-existing comorbidities or initial COVID-19 severity, including infections due to new Omicron lineages which predominated in 2023. Objectives: The aim of this case report was to characterize the clinical features of acute XBB.1.5 infection followed by Long COVID-19. Methods: We followed a 73-year old female resident of Rio de Janeiro with laboratory-confirmed SARS-CoV-2 during acute infection and subsequent months. The SARS-CoV-2 lineage was determined by genome sequencing. Findings: The participant denied comorbidities and had completed a two-dose vaccination schedule followed by two booster doses eight months prior to SARS-CoV-2 infection. Primary infection by viral lineage XBB.1.5. was clinically mild, but the participant subsequently reported persistent fatigue. Main conclusions: This case demonstrates that Long COVID-19 may develop even after mild disease due to SARS-CoV-2 in fully vaccinated and boosted individuals without comorbidities. Continued monitoring of new SARS-CoV-2 lineages and associated clinical outcomes is warranted. Measures to prevent infection should continue to be implemented including development of new vaccines and antivirals effective against novel variants.
MeSH term(s)	Female ; Humans ; Aged ; COVID-19/complications ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; Brazil ; Chromosome Mapping
Language	English
Publishing date	2023-10-13
Publishing country	Brazil
Document type	Case Reports ; Journal Article
ZDB-ID	953293-6
ISSN	1678-8060 ; 0074-0276
ISSN (online)	1678-8060
ISSN	0074-0276
DOI	10.1590/0074-02760230069
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Article ; Online: Cohort-profile: Household transmission of SARS-CoV-2 in a low-resource community in Rio de Janeiro, Brazil.

Brasil, Patrícia / Damasceno, Luana / Fuller, Trevon / Bastos, Leonardo S / Cruz, Oswaldo G / Medeiros, Fernando / Calvet, Guilherme Amaral / Resende, Paola / Whitworth, Jimmy / Smith, Chris / Siqueira, Marilda M / Carvalho, Marilia

BMJ open

2022 Volume 12, Issue 12, Page(s) e067212

Abstract: Purpose: To better understand the household transmission of SARS-COV-2 in a low-resource community in Rio de Janeiro during the COVID-19 pandemic (2020-2022).: Participants: This is an open prospective cohort study of children ≤12 years old and their ...

Abstract	Purpose: To better understand the household transmission of SARS-COV-2 in a low-resource community in Rio de Janeiro during the COVID-19 pandemic (2020-2022). Participants: This is an open prospective cohort study of children ≤12 years old and their household contacts. During home visits over 24 months, we collected data on sociodemographic characteristics, behavioural data, clinical manifestations of SARS-CoV-2, vaccination status, SARS-CoV-2 (reverse transcription-polymerase chain reaction) RT-PCR and anti-S antibody tests. Among adults, the majority of participants were women (62%). Findings to date: We enrolled 845 families from May 2020 to May 2022. The median number of residents per household was four. The median household density, defined as the number of persons per room, was 0.95. The risk of SARS-CoV-2 occurrence was higher in households with a high number of persons per room. Children were not the principal source of SARS-CoV-2 infections in their households during the first wave of the pandemic. Future plans: Future studies will investigate cellular and humoral immune responses to locally circulating SARS-CoV-2 variants, which is relevant for the design of vaccines, antivirals and monoclonal antibodies. We will also engage in outreach to encourage vaccination as a means of limiting the transmission of novel SARS-CoV-2 variants and other emerging pathogens.
MeSH term(s)	Adult ; Child ; Humans ; Female ; Male ; SARS-CoV-2 ; COVID-19/epidemiology ; Prospective Studies ; Pandemics/prevention & control ; Brazil/epidemiology ; Antibodies
Chemical Substances	Antibodies
Language	English
Publishing date	2022-12-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2022-067212
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