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Article: Immune Evasion of SARS-CoV-2 Omicron Subvariants XBB.1.5, XBB.1.16 and EG.5.1 in a Cohort of Older Adults after ChAdOx1-S Vaccination and BA.4/5 Bivalent Booster.

Machado, Rafael Rahal Guaragna / Candido, Érika Donizetti / Aguiar, Andressa Simoes / Chalup, Vanessa Nascimento / Sanches, Patricia Romão / Dorlass, Erick Gustavo / Amgarten, Deyvid Emanuel / Pinho, João Renato Rebello / Durigon, Edison Luiz / Oliveira, Danielle Bruna Leal

Vaccines

2024 Volume 12, Issue 2

Abstract: The recently emerged SARS-CoV-2 Omicron sublineages, including the BA.2-derived XBB.1.5 (Kraken), XBB.1.16 (Arcturus), and EG.5.1 (Eris), have accumulated several spike mutations that may increase immune escape, affecting vaccine effectiveness. Older ... ...

Abstract	The recently emerged SARS-CoV-2 Omicron sublineages, including the BA.2-derived XBB.1.5 (Kraken), XBB.1.16 (Arcturus), and EG.5.1 (Eris), have accumulated several spike mutations that may increase immune escape, affecting vaccine effectiveness. Older adults are an understudied group at significantly increased risk of severe COVID-19. Here we report the neutralizing activities of 177 sera samples from 59 older adults, aged 62-97 years, 1 and 4 months after vaccination with a 4th dose of ChAdOx1-S (Oxford/AstraZeneca) and 3 months after a 5th dose of Comirnaty Bivalent Original/Omicron BA.4/BA.5 vaccine (Pfizer-BioNTech). The ChAdOx1-S vaccination-induced antibodies neutralized efficiently the ancestral D614G and BA.4/5 variants, but to a much lesser extent the XBB.1.5, XBB.1.16, and EG.5.1 variants. The results showed similar neutralization titers between XBB.1.16 and EG.5.1 and were lower compared to XBB.1.5. Sera from the same individuals boosted with the bivalent mRNA vaccine contained higher neutralizing antibody titers, providing a better cross-protection against Omicron XBB.1.5, XBB.1.16 and EG.5.1 variants. Previous history of infection during the epidemiological waves of BA.1/BA.2 and BA.4/BA.5, poorly enhanced neutralization activity of serum samples against XBBs and EG.5.1 variants. Our data highlight the continued immune evasion of recent Omicron subvariants and support the booster administration of BA.4/5 bivalent vaccine, as a continuous strategy of updating future vaccine booster doses to match newly emerged SARS-CoV-2 variants.
Language	English
Publishing date	2024-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines12020144
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Article ; Online: Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy.

Dorlass, Erick Gustavo / Lourenço, Karine Lima / Magalhães, Rubens Daniel Miserani / Sato, Hugo / Fiorini, Alex / Peixoto, Renata / Coelho, Helena Perez / Telezynski, Bruna Larotonda / Scagion, Guilherme Pereira / Ometto, Tatiana / Thomazelli, Luciano Matsumiya / Oliveira, Danielle Bruna Leal / Fernandes, Ana Paula / Durigon, Edison Luiz / Fonseca, Flavio Guimarães / Teixeira, Santuza Maria Ribeiro

Genomics

2021 Volume 113, Issue 6, Page(s) 4109–4115

Abstract: Genetic variants of SARS-CoV-2 have been emerging and circulating in many places across the world. Rapid detection of these variants is essential since their dissemination can impact transmission rates, diagnostic procedures, disease severity, response ... ...

Abstract	Genetic variants of SARS-CoV-2 have been emerging and circulating in many places across the world. Rapid detection of these variants is essential since their dissemination can impact transmission rates, diagnostic procedures, disease severity, response to vaccines or patient management. Sanger sequencing has been used as the preferred approach for variant detection among circulating human immunodeficiency and measles virus genotypes. Using primers to amplify a fragment of the SARS-CoV-2 genome encoding part of the Spike protein, we showed that Sanger sequencing allowed us to rapidly detect the introduction and spread of three distinct SARS-CoV-2 variants in two major Brazilian cities. In both cities, after the predominance of variants closely related to the virus first identified in China, the emergence of the P.2 variant was quickly followed by the detection of the P1 variant, which became dominant in less than one month after it was first detected.
MeSH term(s)	Brazil/epidemiology ; COVID-19/epidemiology ; COVID-19/virology ; China ; Cities ; Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation ; Phylogeny ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2021.10.015
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Article ; Online: Genetic diversity of adenovirus in neotropical bats from Brazil.

Rizotto, Laís Santos / Bueno, Larissa Mayumi / Corrêa, Thaís Camilo / Dos Santos de Moraes, Maria Vitória / de Oliveira Viana, Amanda / Silva, Laura Morais Nascimento / Benassi, Julia Cristina / Scagion, Guilherme Pereira / Lopes, Bruna Larotonda Telezynski / de Assis, Isabela Barbosa / Ometto, Tatiana / Dorlass, Erick Gustavo / Cunha, Irineu Noberto / Melinski, Ramiro Dário / Leitão, Gabriel Lins / Rodrigues, Roberta Costa / da Silva Pereira, Iolanda Maria / D'ark Nunes Dos Santos, Lilia / Hingst-Zaher, Erika /

de Azevedo Junior, Severino Mendes / Junior, Wallace Rodrigues Telino / de Araújo, Jansen / Durigon, Edison Luiz / Arns, Clarice Weis / Ferreira, Helena Lage

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology

2023 Volume 54, Issue 4, Page(s) 3221–3230

Abstract: Bats can harbor a diversity of viruses, such as adenovirus. Ten different species of bat adenoviruses (BtAdV A to J) have been previous described worlwide. In Brazil, BtAdV was described in three species of phyllostomid species: Artibeus lituratus, ... ...

Abstract	Bats can harbor a diversity of viruses, such as adenovirus. Ten different species of bat adenoviruses (BtAdV A to J) have been previous described worlwide. In Brazil, BtAdV was described in three species of phyllostomid species: Artibeus lituratus, Desmodus rotundus, and Sturnira lilium. There are around 180 bat species in Brazil, with 67% inhabiting the Atlantic Forest, with few information about the circulation of BtAdV in this biome. We aimed to describe the molecular detection and the phylogenetic characterization and suggest a classification of BtAdVs circulating in bats from the Brazilian Atlantic Forest. We collected 382 oral and rectal swabs from 208 bats between 2014-2015 and 2020-2021 from São Paulo, Pernambuco, and Santa Catarina Brazilian states. The adenovirus detection was done by a nested PCR targeting the DNA polymerase gene, and all positive samples were sequenced by the Sanger method. The phylogenetic analyses were based on the amino acid sequences using the MEGA 7 and BEAST software. We obtained 16 positive animals (detection rate 7.7%) belonging to seven bat species: Artibeus lituratus, Carollia perspicillata, Sturnira lilium, Molossus molossus, and the first record of Phyllostomus discolor, Eptesicus diminutus, and Myotis riparius. The phylogenetic analysis based on partial amino acid sequences showed that all obtained AdV sequences belong to the Mastadenovirus genus. We observed a high genetic diversity of BtAdV and identified eleven potential BtAdV species circulating in Brazil (BtAdV K to U). Our results contribute to the epidemiological surveillance of adenovirus, increasing the knowledge about the viral diversity and the distribution of AdV in bats from the Atlantic Forest.
MeSH term(s)	Animals ; Adenoviridae/genetics ; Brazil ; Chiroptera ; Phylogeny ; Adenoviridae Infections ; Mastadenovirus ; Genetic Variation
Language	English
Publishing date	2023-08-31
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	2017175-4
ISSN	1678-4405 ; 1517-8382
ISSN (online)	1678-4405
ISSN	1517-8382
DOI	10.1007/s42770-023-01109-9
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Article ; Online: Multisystem Inflammatory Syndrome Associated With COVID-19 With Neurologic Manifestations in a Child: A Brief Report.

De Paulis, Milena / Oliveira, Danielle Bruna Leal / Vieira, Rodolfo P / Pinto, Isabella Coutinho / Machado, Rafael Rahal Guaragna / Cavalcanti, Mariana Pauferro / Soares, Camila Pereira / de Araujo, Ananda Medeiros Pereira / Araujo, Danielle Bastos / Bachi, Andre Luis Lacerda / Leal, Fabyano Bruno / Dorlass, Erick Gustavo / Gilio, Alfredo Elias / Durigon, Edison Luiz / Barreira, Eliane Roseli

The Pediatric infectious disease journal

2020 Volume 39, Issue 10, Page(s) e321–e324

Abstract: Although first considered a benign infection, recent studies have disclosed severe and potentially lethal inflammatory manifestations of COVID-19 in children. We report the case of a 4-year-old child with a post-infectious multisystem inflammatory ... ...

Abstract	Although first considered a benign infection, recent studies have disclosed severe and potentially lethal inflammatory manifestations of COVID-19 in children. We report the case of a 4-year-old child with a post-infectious multisystem inflammatory syndrome associated with COVID-19, with a Kawasaki-like shock and prominent neurologic features, for whom a cytokine storm and reduced brain-derived neurotrophic factor were well documented.
MeSH term(s)	Antibodies, Viral/blood ; Betacoronavirus/immunology ; Brain-Derived Neurotrophic Factor/blood ; COVID-19 ; Child, Preschool ; Coronavirus Infections/complications ; Cytokines/blood ; Female ; Humans ; Immunoglobulin G/blood ; Inflammation ; Pandemics ; Pneumonia, Viral/complications ; SARS-CoV-2 ; Systemic Inflammatory Response Syndrome/complications ; Systemic Inflammatory Response Syndrome/pathology ; Systemic Inflammatory Response Syndrome/virology
Chemical Substances	Antibodies, Viral ; Brain-Derived Neurotrophic Factor ; Cytokines ; Immunoglobulin G
Keywords	covid19
Language	English
Publishing date	2020-09-12
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000002834
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Article: Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy

Genomics. 2021 Nov., v. 113, no. 6

2021

Abstract	Genetic variants of SARS-CoV-2 have been emerging and circulating in many places across the world. Rapid detection of these variants is essential since their dissemination can impact transmission rates, diagnostic procedures, disease severity, response to vaccines or patient management. Sanger sequencing has been used as the preferred approach for variant detection among circulating human immunodeficiency and measles virus genotypes. Using primers to amplify a fragment of the SARS-CoV-2 genome encoding part of the Spike protein, we showed that Sanger sequencing allowed us to rapidly detect the introduction and spread of three distinct SARS-CoV-2 variants in two major Brazilian cities. In both cities, after the predominance of variants closely related to the virus first identified in China, the emergence of the P.2 variant was quickly followed by the detection of the P1 variant, which became dominant in less than one month after it was first detected.
Keywords	Measles morbillivirus ; Severe acute respiratory syndrome coronavirus 2 ; disease severity ; genetic variation ; genome ; genomics ; humans ; immunosuppression ; patients ; rapid methods ; surveys ; viruses ; China
Language	English
Dates of publication	2021-11
Size	p. 4109-4115.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2021.10.015
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy.

Dorlass, Erick Gustavo / Lourenco, Karine Lima / Magalhaes, Rubens Daniel Miserani / Sato, Hugo / Fiorini, Alex / Peixoto, Renata / Coelho, Helena Perez / Telezynski, Bruna Larotonda / Scagion, Guilherme Pereira / Ometto, Tatiana / Thomazelli, Luciano Matsumiya / Oliveira, Danielle Bruna Leal / Fernandes, Ana Paula / Durigon, Edison Luiz / da Fonseca, Flavio Guimaraes / Teixeira, Santuza Maria Ribeiro

medRxiv

Abstract	Genetic variants of SARS-CoV-2 have been emerging and circulating in many places across the world. Rapid detection of these variants is essential since their dissemination can impact transmission rates, diagnostic procedures, disease severity, response to vaccines or patient management. Sanger sequencing has been used as the preferred approach for variant detection among circulating human immunodeficiency and measles virus genotypes. Using primers to amplify a fragment of the SARS-CoV-2 genome encoding part of the Spike protein, we showed that Sanger sequencing allowed us to rapidly detect the introduction and spread of three distinct SARS-CoV-2 variants in two major Brazilian cities. In both cities, after the predominance of variants closely related to the virus first identified in China, the emergence of the P.2 variant was quickly followed by the identification of the P1 variant, which became dominant in less than one month after it was first detected.
Keywords	covid19
Language	English
Publishing date	2021-07-05
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.07.02.21259802
Database	COVID19

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Article ; Online: Multisystem Inflammatory Syndrome Associated With COVID-19 With Neurologic Manifestations in a Child

De Paulis, Milena / Oliveira, Danielle Bruna Leal / Vieira, Rodolfo P. / Pinto, Isabella Coutinho / Machado, Rafael Rahal Guaragna / Cavalcanti, Mariana Pauferro / Soares, Camila Pereira / de Araujo, Ananda Medeiros Pereira / Araujo, Danielle Bastos / Bachi, Andre Luis Lacerda / Leal, Fabyano Bruno / Dorlass, Erick Gustavo / Gilio, Alfredo Elias / Durigon, Edison Luiz / Barreira, Eliane Roseli

Pediatric Infectious Disease Journal

A Brief Report

2020 Volume 39, Issue 10, Page(s) e321–e324

Keywords	Pediatrics, Perinatology, and Child Health ; Microbiology (medical) ; Infectious Diseases ; covid19
Language	English
Publisher	Ovid Technologies (Wolters Kluwer Health)
Publishing country	us
Document type	Article ; Online
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/inf.0000000000002834
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Multisystem Inflammatory Syndrome Associated With COVID-19 With Neurologic Manifestations in a Child: A Brief Report

Pediatr Infect Dis J

Abstract	Although first considered a benign infection, recent studies have disclosed severe and potentially lethal inflammatory manifestations of COVID-19 in children. We report the case of a 4-year-old child with a post-infectious multisystem inflammatory syndrome associated with COVID-19, with a Kawasaki-like shock and prominent neurologic features, for whom a cytokine storm and reduced brain-derived neurotrophic factor were well documented.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #766876
Database	COVID19

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Article ; Online: High genetic diversity of alphacoronaviruses in bat species (Mammalia: Chiroptera) from the Atlantic Forest in Brazil.

Bueno, Larissa Mayumi / Rizotto, Laís Santos / Viana, Amanda de Oliveira / Silva, Laura Morais Nascimento / de Moraes, Maria Vitória Dos Santos / Benassi, Julia Cristina / Scagion, Guilherme Pereira / Dorlass, Erick Gustavo / Lopes, Bruna Larotonda Telezynski / Cunha, Irineu Noberto / Melinski, Ramiro / de Alvarenga, Igor Ferreira / Leitão, Gabriel Lins / Rodrigues, Roberta Costa / Pereira, Iolanda Maria da Silva / Dos Santos, Lilia D'ark Nunes / Fisch, Fabiane / Rocha, Alana Drielle / Port, Dagoberto /

Pereira, Gabriela Stahelin / Greatti, Alessandra / Barnabé, Ana Caroline de Souza / Tsukamoto, Junko / Hingst-Zaher, Erika / de Azevedo, Severino Mendes / Telino, Wallace Rodrigues / Branco, Joaquim Olinto / Ometto, Tatiana / de Araujo, Jansen / Arns, Clarice Weis / Ferreira, Helena Lage / Durigon, Edison Luiz

Transboundary and emerging diseases

2022 Volume 69, Issue 5, Page(s) e2863–e2875

Abstract: Bat coronaviruses (Bat-CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat-CoV surveillance programmes were carried out in ... ...

Abstract	Bat coronaviruses (Bat-CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat-CoV surveillance programmes were carried out in the country. Thus, our aim was to jevaluate the Bat-CoV diversity in the Atlantic Forest, the second biome with the highest number of bat species in Brazil. We analysed 456 oral and rectal swabs and 22 tissue samples from Atlantic Forest bats, detecting Alphacoronavirus in 44 swab samples (9.6%) targeting the RdRp gene from seven different bat species, three of which have never been described as Bat-CoV hosts. Phylogenetic analysis of the amino acid (aa) sequences coding the RdRp gene grouped the sequences obtained in our study with Bat-CoV previously detected in identical or congeneric bat species, belonging to four subgenera, with high aa identity (over 90%). The RdRp gene was also detected in three tissue samples from Diphylla ecaudata and Sturnira lilium, and the partial S gene was successfully sequenced in five tissues and swab samples of D. ecaudata. The phylogenetic analysis based on the partial S gene obtained here grouped the sequence of D. ecaudata with CoV from Desmodus rotundus previously detected in Peru and Brazil, belonging to the Amalacovirus subgenus, with aa identity ranging from 73.6% to 88.8%. Our data reinforce the wide distribution of Coronaviruses in bats from Brazil and the novelty of three bats species as Bat-CoV hosts and the co-circulation of four Alphacoronavirus subgenera in Brazil.
MeSH term(s)	Alphacoronavirus/genetics ; Amino Acids/genetics ; Animals ; Brazil/epidemiology ; Chiroptera ; Coronavirus/genetics ; Coronavirus Infections/veterinary ; Forests ; Genetic Variation ; Genome, Viral ; Phylogeny ; RNA-Dependent RNA Polymerase
Chemical Substances	Amino Acids ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2022-07-12
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14636
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Article: High genetic diversity of alphacoronaviruses in bat species (Mammalia: Chiroptera) from the Atlantic Forest in Brazil

Bueno, Larissa Mayumi / Rizotto, Laís Santos / Viana, Amanda de Oliveira / Silva, Laura Morais Nascimento / de Moraes, Maria Vitória dos Santos / Benassi, Julia Cristina / Scagion, Guilherme Pereira / Dorlass, Erick Gustavo / Lopes, Bruna Larotonda Telezynski / Cunha, Irineu Noberto / Melinski, Ramiro / de Alvarenga, Igor Ferreira / Leitão, Gabriel Lins / Rodrigues, Roberta Costa / Pereira, Iolanda Maria da Silva / dos Santos, Lilia D'ark Nunes / Fisch, Fabiane / Rocha, Alana Drielle / Port, Dagoberto /

Pereira, Gabriela Stahelin / Greatti, Alessandra / Barnabé, Ana Caroline de Souza / Tsukamoto, Junko / Hingst‐Zaher, Erika / de Azevedo, Severino Mendes, Jr / Telino, Wallace Rodrigues, Jr / Branco, Joaquim Olinto / Ometto, Tatiana / de Araujo, Jansen / Arns, Clarice Weis / Ferreira, Helena Lage / Durigon, Edison Luiz

Transboundary and emerging diseases. 2022 Sept., v. 69, no. 5

2022

Abstract: Bat coronaviruses (Bat‐CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat‐CoV surveillance programmes were carried out in ... ...

Abstract	Bat coronaviruses (Bat‐CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat‐CoV surveillance programmes were carried out in the country. Thus, our aim was to jevaluate the Bat‐CoV diversity in the Atlantic Forest, the second biome with the highest number of bat species in Brazil. We analysed 456 oral and rectal swabs and 22 tissue samples from Atlantic Forest bats, detecting Alphacoronavirus in 44 swab samples (9.6%) targeting the RdRp gene from seven different bat species, three of which have never been described as Bat‐CoV hosts. Phylogenetic analysis of the amino acid (aa) sequences coding the RdRp gene grouped the sequences obtained in our study with Bat‐CoV previously detected in identical or congeneric bat species, belonging to four subgenera, with high aa identity (over 90%). The RdRp gene was also detected in three tissue samples from Diphylla ecaudata and Sturnira lilium, and the partial S gene was successfully sequenced in five tissues and swab samples of D. ecaudata. The phylogenetic analysis based on the partial S gene obtained here grouped the sequence of D. ecaudata with CoV from Desmodus rotundus previously detected in Peru and Brazil, belonging to the Amalacovirus subgenus, with aa identity ranging from 73.6% to 88.8%. Our data reinforce the wide distribution of Coronaviruses in bats from Brazil and the novelty of three bats species as Bat‐CoV hosts and the co‐circulation of four Alphacoronavirus subgenera in Brazil.
Keywords	Alphacoronavirus ; Desmodus ; amino acids ; ecosystems ; forests ; genes ; genetic variation ; mammals ; monitoring ; phylogeny ; species diversity ; viruses ; Brazil ; Peru
Language	English
Dates of publication	2022-09
Size	p. e2863-e2875.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14636
Database	NAL-Catalogue (AGRICOLA)

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