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Article ; Online: SARS-CoV-2 testing among patients and healthcare professionals in an HIV outpatient clinic in Brazil.

Matsuda, Elaine Monteiro / Oliveira, Isabela Penteriche de / Campos, Ivana Barros de / Ahagon, Cintia Mayumi / Castejon, Marcia Jorge / Silva, Valeria Oliveira / Manzoni, Fernanda Matsuda / López-Lopes, Giselle Ibette / Brígido, Luís Fernando de Macedo

Revista do Instituto de Medicina Tropical de Sao Paulo

2022 Volume 64, Page(s) e3

Abstract: The COVID-19 pandemic in Brazil has been marked by high infection and death rates. The immune response generated by current vaccination might be influenced by previous natural infection, and baseline estimates may help in the evaluation of vaccine- ... ...

Abstract	The COVID-19 pandemic in Brazil has been marked by high infection and death rates. The immune response generated by current vaccination might be influenced by previous natural infection, and baseline estimates may help in the evaluation of vaccine-induced serological response. We evaluated previous SARS-CoV-2 testing (RT-PCR), and performed rapid diagnostic tests (RDT) and high throughput electrochemiluminescence immunoassay (ECLIA) before vaccination among people living with HIV (PLWH), users of antiretroviral prophylaxis (PrEP/PEP), and healthcare professionals in an HIV outpatient clinic (HCP-HC). RDT was positive in 25.7% (95% CI: 19-33%) overall, 31.3% (95% CI : 18-45%) among PLWH, 23.7% (95% CI : 14-34%) in PrEP/PEP users and 21.4% (95% CI : 05-28%) in HCP-HC (p=0.548). Diagnostic RT-PCR testing was very limited, even for symptomatic individuals, and whereas all HCP-HC had one test perfomed, only 35% of the patients (PREP/PEP/PLWH) were tested (p<0.0001). Adequate monitoring of post-vaccination humoral response and breakthrough infections including those in asymptomatic cases are warranted, especially in immunologically compromised individuals.
MeSH term(s)	Ambulatory Care Facilities ; Brazil ; COVID-19 ; COVID-19 Testing ; Delivery of Health Care ; HIV Infections ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2022-02-02
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	128928-7
ISSN	1678-9946 ; 0036-4665
ISSN (online)	1678-9946
ISSN	0036-4665
DOI	10.1590/S1678-9946202264003
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Article ; Online: Use of Sanger protocols to identify variants of concern, key mutations and track evolution of SARS-CoV-2

Cabral, Gabriela Bastos / Ahagon, Cintia Mayumi / de Souza Guimarães, Paula Morena / Silva Lopez-Lopes, Giselle Ibette / Hussein, Igor Mohamed / Cilli, Audrey / de Jesus Alves, Ivy / Coelho Bombonatte, Andréa Gobetti / do Carmo Sampaio Tavares Timenetsky, Maria / da Silva Santos, Jaqueline Helena / de Oliveira Santos, Katia Corrêa / dos Santos, Fabiana Cristina Pereira / de Macedo Brígido, Luís Fernando

Journal of Virological Methods. 2022 Feb., v. 300 p.114422-

2022

Abstract: Vaccination and the emergence of SARS-CoV-2 variants mark the second year of the pandemic. Variants have amino acid mutations at the spike region, a viral protein central in the understanding of COVID-19 pathogenesis and vaccine response. Variants may ... ...

Abstract	Vaccination and the emergence of SARS-CoV-2 variants mark the second year of the pandemic. Variants have amino acid mutations at the spike region, a viral protein central in the understanding of COVID-19 pathogenesis and vaccine response. Variants may dominate local epidemics, as Gamma (P.1) in Brazil, emerging in 2020 and prevailing until mid-2021. Different obstacles hinder a wider use of Next-Generation Sequencing for genomic surveillance. We describe Sanger based sequencing protocols: i) Semi-nested RT-PCR covering up to 3.684 kb (>96 %) spike gene; ii) One-Step RT-PCR for key Receptor Binding Domain (RBD) mutations (codons 417–501); iii) One-Step RT-PCR of partial N region to improve genomic capability. Protocols use leftovers of RNA extracted from nasopharyngeal swabs for quantitative RT-PCR diagnosis; with retro-transcribed DNA sequenced at ABI 3500 using dye termination chemistry. Analyses of sequences from 95 individuals (late 2020/early 2021) identified extensive amino acid variation, 57 % with at least one key mutation at the Receptor Binding Domain, with B.1.1.28 lineage most prevalent, followed by Gamma and Zeta variants, with no Delta variant observed. The relatively low cost and simplicity may provide an accessible tool to improve surveillance of SARS-CoV-2 evolution, monitor new variants and vaccinated breakthroughs.
Keywords	COVID-19 infection ; DNA ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; chemistry ; codons ; dyes ; evolution ; genomics ; monitoring ; mutation ; pandemic ; pathogenesis ; vaccination ; vaccines ; Brazil ; SARS-CoV-2 ; COVID-19 ; Variants ; Gamma ; Genomic surveillance
Language	English
Dates of publication	2022-02
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114422
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine (CoronaVac) in inadvertently vaccinated healthy children.

Fernandes, Eder Gatti / López-Lopes, Giselle Ibette Silva / Silva, Valeria Oliveira / Yamashiro, Rosemeire / Madureira, Karen Cristina Rolim / Gallo, Juliana Failde / Lindoso, José Angelo / Sato, Helena Keico / de Araujo, Núbia Virginia D'Avila Limeira / Nerger, Maria Ligia Bacciotte Ramos / Brigido, Luis Fernando Macedo

Revista do Instituto de Medicina Tropical de Sao Paulo

2021 Volume 63, Page(s) e83

Abstract: Twenty-seven children aged seven months to 5 years were inadvertently vaccinated with a COVID-19 vaccine, the CoronaVac (Sinovac, China), an inactivated SARS-CoV-2 vaccine, in two different cities of Sao Paulo State, Brazil. After the event, these ... ...

Abstract	Twenty-seven children aged seven months to 5 years were inadvertently vaccinated with a COVID-19 vaccine, the CoronaVac (Sinovac, China), an inactivated SARS-CoV-2 vaccine, in two different cities of Sao Paulo State, Brazil. After the event, these children were monitored by local pediatricians and serum samples were collected at the first visit and 30 days after vaccination and tested for SARS-CoV-2 S1 serology with Ortho total IgG anti-S1 protein and Cpass, an ACE2 receptor binding domain inhibition assay. Only one child had a mild symptom after vaccination, with no other adverse events documented up to the 30 days follow-up. Of 27 children tested 3-9 days after vaccination, 5 (19%) had positive serology suggesting a previous natural SARS-CoV-2 infection, with all 19 tested on day 30 after vaccination and presenting with positive tests, with an increment of antibody titers in those initially positive. A low Cpass binding inhibition was observed in the first collection in 11 seronegative cases, with high titers among those anti-S1 positive. All children showed an important increase in antibody titers on day 30. The event allowed the documentation of a robust serological response to one dose of CoronaVac in this small population of young children, with no major adverse effects. Although it was an unfortunate accident, this event may contribute with future vaccine strategies in this age group. The data suggest that CoronaVac is safe and immunogenic for children.
MeSH term(s)	Antibodies, Viral ; Brazil ; COVID-19 ; COVID-19 Vaccines ; Child ; Child, Preschool ; Humans ; SARS-CoV-2
Chemical Substances	Antibodies, Viral ; COVID-19 Vaccines
Language	English
Publishing date	2021-12-06
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	128928-7
ISSN	1678-9946 ; 0036-4665
ISSN (online)	1678-9946
ISSN	0036-4665
DOI	10.1590/S1678-9946202163083
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Article ; Online: Use of Sanger protocols to identify variants of concern, key mutations and track evolution of SARS-CoV-2.

Cabral, Gabriela Bastos / Ahagon, Cintia Mayumi / de Souza Guimarães, Paula Morena / Silva Lopez-Lopes, Giselle Ibette / Hussein, Igor Mohamed / Cilli, Audrey / de Jesus Alves, Ivy / Coelho Bombonatte, Andréa Gobetti / do Carmo Sampaio Tavares Timenetsky, Maria / da Silva Santos, Jaqueline Helena / de Oliveira Santos, Katia Corrêa / Dos Santos, Fabiana Cristina Pereira / de Macedo Brígido, Luís Fernando

Journal of virological methods

2021 Volume 300, Page(s) 114422

Abstract	Vaccination and the emergence of SARS-CoV-2 variants mark the second year of the pandemic. Variants have amino acid mutations at the spike region, a viral protein central in the understanding of COVID-19 pathogenesis and vaccine response. Variants may dominate local epidemics, as Gamma (P.1) in Brazil, emerging in 2020 and prevailing until mid-2021. Different obstacles hinder a wider use of Next-Generation Sequencing for genomic surveillance. We describe Sanger based sequencing protocols: i) Semi-nested RT-PCR covering up to 3.684 kb (>96 %) spike gene; ii) One-Step RT-PCR for key Receptor Binding Domain (RBD) mutations (codons 417-501); iii) One-Step RT-PCR of partial N region to improve genomic capability. Protocols use leftovers of RNA extracted from nasopharyngeal swabs for quantitative RT-PCR diagnosis; with retro-transcribed DNA sequenced at ABI 3500 using dye termination chemistry. Analyses of sequences from 95 individuals (late 2020/early 2021) identified extensive amino acid variation, 57 % with at least one key mutation at the Receptor Binding Domain, with B.1.1.28 lineage most prevalent, followed by Gamma and Zeta variants, with no Delta variant observed. The relatively low cost and simplicity may provide an accessible tool to improve surveillance of SARS-CoV-2 evolution, monitor new variants and vaccinated breakthroughs.
MeSH term(s)	COVID-19/virology ; Evolution, Molecular ; Humans ; Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-12-13
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114422
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Article ; Online: P1 variant and amino acid mutations at Spike gene identified using Sanger protocol

Cabral, Gabriela Bastos / Ahagon, Cintia Mayumi / Lopez-Lopes, Giselle Ibette Silva / Hussein, Igor Mohamed / Guimaraes, Paula Morena / Cilli, Audrey / Silva, Valeria Oliveira / Timenetsky, Maria do Carmo ST / Alves, Ivy de Jesus / Bombonatte, Andrea GC / dos Santos, Fabiana C Pereira / Brigido, Luis Fernando de Macedo

medRxiv

Abstract: SARS-coV-2 variants, along with vaccination, mark the second year of the pandemic. The spike region is a focal point in COVID-19 pathogenesis, with different amino acid changes potentially modulating vaccine response and some being part of variant ... ...

Abstract	SARS-coV-2 variants, along with vaccination, mark the second year of the pandemic. The spike region is a focal point in COVID-19 pathogenesis, with different amino acid changes potentially modulating vaccine response and some being part of variant signatures. NGS is the standard tool to sequence the virus but limitations of different sources hinders expansion of genomic surveillance in many places. To improve surveillance capability we developed a Sanger based sequencing protocol to obtain coverage of most (>95%) spike gene. Eleven nasopharyngeal swabs collections had RNA extracted for real time PCR diagnosis and leftover RNA had up to 3785 bp sequenced at an ABI3500 using dye termination chemistry of nested PCR products of two reactions of one Step RT-PCR. P1 amino acid mutations signatures were present in 18% (2/11), with 82% (9/11) with three or more additional amino acid changes (GISAID CoVsurver list). Most sequences (86%, 7/8) from 2021 have the E484K, whereas the mutation was not present in samples collected in 2020 (0/4, p=0.015). The swiftness that favorable mutations to the virus may prevail and their potential impact in vaccines and other current interventions need broader surveillance and more public health attention.
Keywords	covid19
Language	English
Publishing date	2021-03-24
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.03.21.21253158
Database	COVID19

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Article ; Online: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19.

Lopez-Lopes, Giselle Ibette Silva / Ahagon, Cintia Mayumi / Bonega, Margarete Aparecida / Santos, Fabiana Pereira dos / Santos, Katia Correa de Oliveira / Cilli, Audrey / Prado, Lincoln Spinazola do / Silva, Daniela Bernardes Borges da / Luz, Nuria Borges da / Saraceni, Claudia Patara / Afonso, Ana Maria Sardinha / Timenetsky, Maria do Carmo / Brigido, Luis Fernando de Macedo

medRxiv

Abstract: Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA ... ...

Abstract	Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute. Methods: Consecutive volunteer testing of LWH and external household and close contacts were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea). Results: Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease. Over a third (38%) of asymptomatic cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease.
Keywords	covid19
Language	English
Publishing date	2020-08-01
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.07.29.20163998
Database	COVID19

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Article ; Online: PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL

Silva, Valeria Oliveira / de Oliveira, Elaine Lopes / Castejon, Marcia Jorge / Yamashiro, Rosemeire / Ahagon, Cintia Mayumi / Lopez-Lopes, Giselle Ibette / da Silveira, Edilene Peres Real / Hong, Marisa Ailin / Timenetsky, Maria do Carmo / Oliveira, Carmem aparecida de Freitas / Brigido, Luis Fernando de Macedo

medRxiv

Abstract: Background: Covid-19 Serology may document exposure and perhaps protection to the virus, and serological test may help understand epidemic dynamics. To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 ... ...

Abstract	Background: Covid-19 Serology may document exposure and perhaps protection to the virus, and serological test may help understand epidemic dynamics. To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 among HPs in Adolfo Lutz Institute, State of Sao Paulo, Brazil. Methods: This study was performed among professionals of Adolfo Lutz Institute in Sao Paulo, Brazil and some administrative areas of the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay and SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants. Results: A total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA.. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity. Conclusions: We documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, with higher rates among outsourced workers and those with referring cohabitation with COVID-19 patients. COVID samples handling was not related to increased seropositivity. Some symptoms how strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings.
Keywords	covid19
Language	English
Publishing date	2020-10-21
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.10.19.20213421
Database	COVID19

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Article ; Online: Discrepancies of HIV-1 reverse transcriptase resistance interpretation of insertions and deletions between two genotypic algorithms.

López-Lopes, Giselle Ibette Silva / Lança, André Minhoto / de Paula Ferreira, João Leandro / Souza, Luciana Oliveira / de Macedo Brígido, Luís Fernando

Intervirology

2013 Volume 56, Issue 4, Page(s) 217–223

Abstract: Background: Bioinformatics algorithms have been developed for the interpretation of resistance from sequence submission, which supports clinical decision making. This study evaluated divergences of the interpretation of the genotyping in two commonly ... ...

Abstract	Background: Bioinformatics algorithms have been developed for the interpretation of resistance from sequence submission, which supports clinical decision making. This study evaluated divergences of the interpretation of the genotyping in two commonly used algorithms, using sequences with indels of reverse transcriptase genes. Methods: Sequences were obtained from virus RNA of patients failing highly active antiretroviral therapy from 2004 to 2011. Alignments were obtained using Clustal W including subtype B consensus and HXB2. Sequences with evidence of indels were submitted to the Stanford Resistance Database and to the Geno2Pheno to locate indel positioning and determine the resistance profile. Results: A total of 1,959 partial reverse transcriptase sequences were assessed, mostly subtype B (74%). Insertions and deletions were observed in 0.9 and 0.6% of sequences, respectively. Discordant insert positioning was assigned for most (90%) insertion sequences, with 27% discordances for deletions. Susceptibility differed for some antiretroviral drugs, predominantly for TDF, d4T and ETV, when sequences with deletions were evaluated. Conclusion: Both indel positioning and its impact on drug susceptibility varies depending on the algorithm, a fact that might influence the clinical decision. Critical analysis of indel sequences with manual alignments is important, and its use alongside different algorithms may be important to better understand the outcomes of genotypic resistance prediction.
MeSH term(s)	Adolescent ; Adult ; Algorithms ; Child ; Computational Biology/methods ; Drug Resistance, Viral ; Female ; Genotype ; HIV Infections/virology ; HIV Reverse Transcriptase/genetics ; HIV-1/drug effects ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; INDEL Mutation ; Male ; Microbial Sensitivity Tests/methods ; Middle Aged ; RNA, Viral/genetics ; Reverse Transcriptase Inhibitors/pharmacology ; Young Adult
Chemical Substances	RNA, Viral ; Reverse Transcriptase Inhibitors ; reverse transcriptase, Human immunodeficiency virus 1 (EC 2.7.7.-) ; HIV Reverse Transcriptase (EC 2.7.7.49)
Language	English
Publishing date	2013
Publishing country	Switzerland
Document type	Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184545-7
ISSN	1423-0100 ; 0300-5526
ISSN (online)	1423-0100
ISSN	0300-5526
DOI	10.1159/000348511
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Discrepancies of HIV-1 Reverse Transcriptase Resistance Interpretation of Insertions and Deletions between Two Genotypic Algorithms

López-Lopes, Giselle Ibette Silva / Lança, André Minhoto / de Paula Ferreira, João Leandro / Souza, Luciana Oliveira / de Macedo Brígido, Luís Fernando

Intervirology

2013 Volume 56, Issue 4, Page(s) 217–223

Institution	Laboratório de Retrovírus, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, Brazil
Abstract	Background: Bioinformatics algorithms have been developed for the interpretation of resistance from sequence submission, which supports clinical decision making. This study evaluated divergences of the interpretation of the genotyping in two commonly used algorithms, using sequences with indels of reverse transcriptase genes. Methods: Sequences were obtained from virus RNA of patients failing highly active antiretroviral therapy from 2004 to 2011. Alignments were obtained using Clustal W including subtype B consensus and HXB2. Sequences with evidence of indels were submitted to the Stanford Resistance Database and to the Geno2Pheno to locate indel positioning and determine the resistance profile. Results: A total of 1,959 partial reverse transcriptase sequences were assessed, mostly subtype B (74%). Insertions and deletions were observed in 0.9 and 0.6% of sequences, respectively. Discordant insert positioning was assigned for most (90%) insertion sequences, with 27% discordances for deletions. Susceptibility differed for some antiretroviral drugs, predominantly for TDF, d4T and ETV, when sequences with deletions were evaluated. Conclusion: Both indel positioning and its impact on drug susceptibility varies depending on the algorithm, a fact that might influence the clinical decision. Critical analysis of indel sequences with manual alignments is important, and its use alongside different algorithms may be important to better understand the outcomes of genotypic resistance prediction.
Keywords	Highly active antiretroviral therapy ; HIV-1 antiretroviral drugs ; HIV Stanford Resistance Database ; Geno2Pheno
Language	English
Publishing date	2013-05-09
Publisher	S. Karger AG
Publishing place	Basel, Switzerland
Document type	Article
Note	Original Paper
ZDB-ID	184545-7
ISSN	1423-0100 ; 0300-5526
ISSN (online)	1423-0100
ISSN	0300-5526
DOI	10.1159/000348511
Database	Karger publisher's database

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