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LIM/46 - Laboratório de Parasitologia Médica, Hospital das Clínicas, Faculdade de Medicina
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- Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2(2023) VOGELS, C. B. F.; BREBAN, M. I.; OTT, I. M.; ALPERT, T.; PETRONE, M. E.; WATKINS, A. E.; KALINICH, C. C.; EARNEST, R.; ROTHMAN, J. E.; JESUS, J. G. de; CLARO, I. M.; FERREIR, G. M.; CRISPIM, M. A. E.; SINGH, L.; TEGALLY, H.; ANYANEJI, U. J.; HODCROF, E. B.; MASON, C. E.; KHULLAR, G.; METTI, J.; DUDLEY, J. T.; MACKAY, M. J.; NASH, M.; WANG, J.; LIU, C.; HUI, P.; MURPHY, S.; NEAL, C.; LASZLO, E.; LANDRY, M. L.; MUYOMBWE, A.; DOWNING, R.; RAZEQ, J.; OLIVEIRA, T. de; FARIA, N. R.; SABINO, E. C.; NEHER, R. A.; FAUVER, J. R.; GRUBAUGH, N. D.Broadly accessible and inexpensive surveillance methods are needed to track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOC) around the world. While sequencing is the gold standard to identify circulating SARS-CoV-2 variants, routine genomic surveillance is not available in many locations primarily due to a lack of resources and expertise. The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples conducted in this study is not research involving human patients. Multiplex-PCR products were purified by using AmpureXP beads, and quantification was carried out using the Qubit dsDNA High Sensitivity assay on the Qubit 3.0. © 2023 Jenny Stanford Publishing Pte. Ltd.
- First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease(2020) DOMINGUES, Renan Barros; MENDES-CORREA, Maria Cassia; LEITE, Fernando Brunale Vilela de Moura; SABINO, Ester Cerdeira; SALARINI, Diego Zanotti; CLARO, Ingra; SANTOS, Daniel Wagner; JESUS, Jaqueline Goes de; FERREIRA, Noely Evangelista; ROMANO, Camila Malta; SOARES, Carlos Augusto SenneThe association between coronaviruses and central nervous system (CNS) demyelinating lesions has been previously shown. However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. SARS-COV-2 was previously detected in cerebrospinal fluid (CSF) sample of a patient with encephalitis. However, the virus identity was not confirmed by deep sequencing of SARS-COV-2 detected in the CSF. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with clinically isolated syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74-100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS-COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs.
- Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil(2021) FARIA, Nuno R.; MELLAN, Thomas A.; WHITTAKER, Charles; CLARO, Ingra M.; CANDIDO, Darlan da S.; MISHRA, Swapnil; CRISPIM, Myuki A. E.; SALES, Flavia C.; HAWRYLUK, Iwona; MCCRONE, John T.; HULSWIT, Ruben J. G.; FRANCO, Lucas A. M.; RAMUNDO, Mariana S.; JESUS, Jaqueline G. de; ANDRADE, Pamela S.; COLETTI, Thais M.; FERREIRA, Giulia M.; SILVA, Camila A. M.; MANULI, Erika R.; PEREIRA, Rafael H. M.; PEIXOTO, Pedro S.; KRAEMER, Moritz U.; GABURO JR., Nelson; CAMILO, Cecilia da C.; HOELTGEBAUM, Henrique; SOUZA, William M.; ROCHA, Esmenia C.; SOUZA, Leandro M. de; PINHO, Mariana C. de; ARAUJO, Leonardo J. T.; V, Frederico S. Malta; LIMA, Aline B. de; SILVA, Joice do P.; ZAULI, Danielle A. G.; FERREIRA, Alessandro C. de S.; SCHNEKENBERG, Ricardo P.; LAYDON, Daniel J.; WALKER, Patrick G. T.; SCHLUETER, Hannah M.; SANTOS, Ana L. P. dos; VIDAL, Maria S.; CARO, Valentina S. Del; FILHO, Rosinaldo M. F.; SANTOS, Helem M. dos; AGUIAR, Renato S.; PROENCA-MODENA, Jose L. P.; NELSON, Bruce; HAY, James A.; MONOD, Melodie; MISCOURIDOU, Xenia; COUPLAND, Helen; SONABEND, Raphael; VOLLMER, Michaela; GANDY, Axel; PRETE JR., Carlos A.; NASCIMENTO, Vitor H.; SUCHARD, Marc A.; BOWDEN, Thomas A.; POND, Sergei L. K.; WU, Chieh-Hsi; RATMANN, Oliver; FERGUSON, Neil M.; DYE, Christopher; LOMAN, Nick J.; LEMEY, Philippe; RAMBAUT, Andrew; FRAIJI, Nelson A.; CARVALHO, Maria do P. S. S.; PYBUS, Oliver G.; FLAXMAN, Seth; BHATT, Samir; SABINO, Ester C.Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
- Impact of COVID-19 RT-PCR testing of asymptomatic health care workers on absenteeism and hospital transmission during the pandemic(2023) MENDES, Elisa Teixeira; NETO, Danilo Glauco Pereira Villagelin; FERREIRA, Giulia Magalhaes; VALENCA, Ian Nunes; LIMA, Maria Patelli Juliani Souza; FREITAS, Maria Fernanda Marciano Barros de; DONALISIO, Maria Rita; MELO, Marcio Cristiano; LAZARI, Carolina; GOES, Jacqueline; MORALES, Ingra; JARDIM, Ana Carolina Gomes; SANTOS, Pamela Andrade dos; FRANCO, Lucas Augusto Moyses; SABINO, Ester Cerdeiro; COSTA, Silvia FigueiredoBackground: Reducing the transmission of SARS-CoV-2 from asymptomatic and pre-symptomatic patients is critical in controlling the circulation of the virus.Methods: This study evaluated the prevalence of Reverse transcription polymerase chain reaction (RT-PCR) positivity in serial tests in 429 asymptomatic health care workers (HCW) and its impact on absenteeism. HCW from a COVID-19 reference hospital were tested, screened, and placed on leave. A time-series seg-mented regression of weekly absenteeism rates was used, and cases of infection among hospitalized patients were analyzed. Viral gene sequencing and phylogenetic analysis were performed on samples from HCW who had a positive result.Results: A significant decrease in absenteeism was detected 3-4 weeks after the intervention at a time of increased transmission within the city. The prevalence of RT-PCR positivity among asymptomatic professio-nals was 17.3%. Phylogenetic analyses (59 samples) detected nine clusters, two of them strongly suggestive of intrahospital transmission with strains (75% B.1.1.28) circulating in the region during this period.Conclusions: Testing and placing asymptomatic professionals on leave contributed to control strategy for COVID-19 transmission in the hospital environment, and in reducing positivity and absenteeism, which directly influences the quality of care and exposes professionals to an extra load of stress.(c) 2022 Association for Professionals in Infection Control and Epidemiology, Inc.
- Molecular characterization and sequecing analysis of SARS-CoV-2 genome in Minas Gerais, Brazil(2022) FERREIRA, Giulia Magalhaes; CLARO, Ingra Morales; GROSCHE, Victoria Riquena; CANDIDO, Darlan; JOSE, Diego Pandelo; ROCHA, Esmenia Coelho; COLETTI, Thais de Moura; MANULI, Erika Regina; JR, Nelson Gaburo; FARIA, Nuno Rodrigues; SABINO, Ester Cerdeira; JESUS, Jaqueline Goes de; JARDIM, Ana Carolina GomesThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in Wuhan, China, is the causative agent of the coronavirus disease 2019 (COVID-19). Since its first notification in Sa similar to o Paulo state (SP) on 26th February 2020, more than 22,300,000 cases and 619,000 deaths were reported in Brazil. In early pandemic, SARS-CoV-2 spread locally, however, over time, this virus was disseminated to other regions of the country. Herein, we performed genomic sequencing and phylogenetic analysis of SARS-CoV-2 using 20 clinical samples of COVID-19 confirmed cases from 9 cities of Minas Gerais state (MG), in order to evaluate the molecular properties of circulating viral strains in this locality from March to May 2020. Our analyses demonstrated the circulation of B.1 lineage isolates in the investigated locations and nucleotide substitutions were observed into the genomic regions related to important viral structures. Additionally, sequences generated in this study clustered with isolates from SP, suggesting a dissemination route between these two states. Alternatively, monophyletic groups of sequences from MG and other states or country were observed, indicating independent events of virus introduction. These results reinforce the need of genomic surveillance for understand the ongoing spread of emerging viral pathogens.
- Prolonged presence of replication-competent SARS-CoV-2 in mildly symptomatic individuals: A report of two cases(2021) CORREA, Maria C. Mendes; LEAL, Fabio E.; BOAS, Lucy S. Villas; WITKIN, Steven S.; PAULA, Anderson de; MENDONZA, Tania R. Tozetto; FERREIRA, Noely E.; CURTY, Gislaine; CARVALHO, Pedro S. de; BUSS, Lewis F.; COSTA, Silvia F.; CARVALHO, Flavia M. da Cunha; KAWAKAMI, Joyce; TANIWAKI, Noemi N.; PAIAO, Heuder; BIZARIO, Joao C. da Silva; JESUS, Jaqueline G. de; SABINO, Ester C.; ROMANO, Camila M.; GREPAN, Regina M. Z.; SESSO, AntonioIt has been estimated that individuals with COVID-19 can shed replication-competent virus up to a maximum of 20 days after initiation of symptoms. The majority of studies that addressed this situation involved hospitalized individuals and those with severe disease. Studies to address the possible presence of SARS-CoV-2 during the different phases of COVID-19 disease in mildly infected individuals, and utilization of viral culture techniques to identify replication-competent viruses, have been limited. This report describes two patients with mild forms of the disease who shed replication-competent virus for 24 and 37 days, respectively, after symptom onset.
- Y Interacting Epidemics in Amazonian Brazil: Prior Dengue Infection Associated With Increased Coronavirus Disease 2019 (COVID-19) Risk in a Population-Based Cohort Study(2021) NICOLETE, Vanessa C.; RODRIGUES, Priscila T.; JOHANSEN, Igor C.; CORDER, Rodrigo M.; TONINI, Juliana; CARDOSO, Marly A.; JESUS, Jaqueline G. de; CLARO, Ingra M.; FARIA, Nuno R.; SABINO, Ester C.; CASTRO, Marcia C.; FERREIRA, Marcelo U.Background. Immunity after dengue virus (DENV) infection has been suggested to cross-protect from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality. Methods. We tested whether serologically proven prior DENV infection diagnosed in September-October 2019, before the coronavirus disease 2019 (COVID-19) pandemic, reduced the risk of SARS-CoV-2 infection and clinically apparent COVID-19 over the next 13 months in a population-based cohort in Amazonian Brazil. Mixed-effects multiple logistic regression analysis was used to identify predictors of infection and disease, adjusting for potential individual and household-level confounders. Virus genomes from 14 local SARS-CoV-2 isolates were obtained using whole-genome sequencing. Results. Anti-DENV immunoglobulin G (IgG) was found in 37.0% of 1285 cohort participants (95% confidence interval [CI]: 34.3% to 39.7%) in 2019, with 10.4 (95% CI: 6.7-15.5) seroconversion events per 100 person-years during the follow-up. In 2020, 35.2% of the participants (95% CI: 32.6% to 37.8%) had anti-SARS-CoV-2 IgG and 57.1% of the 448 SARS-CoV-2 seropositives (95% CI: 52.4% to 61.8%) reported clinical manifestations at the time of infection. Participants aged >60 years were twice more likely to have symptomatic COVID-19 than children under 5 years. Locally circulating SARS-CoV-2 isolates were assigned to the B.1.1.33 lineage. Contrary to the cross-protection hypothesis, prior DENV infection was associated with twice the risk of clinically apparent COVID-19 upon SARS-CoV-2 infection, with P values between .025 and .039 after adjustment for identified confounders. Conclusions. Higher risk of clinically apparent COVID-19 among individuals with prior dengue has important public health implications for communities sequentially exposed to DENV and SARS-CoV-2 epidemics.
- Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil(2021) IANI, Felipe C. M.; GIOVANETTI, Marta; FONSECA, Vagner; SOUZA, William M.; ADELINO, Talita E. R.; XAVIER, Joilson; JESUS, Jaqueline G.; PEREIRA, Maira A.; SILVA, Marcos V. F.; COSTA, Alana V. B.; SILVA, Erniria C.; MENDES, Marcia C. O.; FILIPPIS, Ana M. B.; ALBUQUERQUE, Carlos F. C.; ABREU, Andre L.; OLIVEIRA, Marluce A. A.; ALCANTARA, Luiz C. J.; FARIA, Nuno R.Autochthonous Zika virus (ZIKV) transmission in Brazil was first identified in April 2015 in Brazil, with the first ZIKV-associated microcephaly cases detected in October 2015. Despite efforts on understanding ZIKV transmission in Brazil, little is known about the virus epidemiology and genetic diversity in Minas Gerais (MG), the second most populous state in the country. We report molecular and genomic findings from the main public health laboratory in MG. Until January 2020, 26,817 ZIKV suspected infections and 86 congenital syndrome cases were reported in MG state. We tested 8552 ZIKV and microcephaly suspected cases. Ten genomes were generated on-site directly from clinical samples. A total of 1723 confirmed cases were detected in Minas Gerais, with two main epidemic waves; the first and larger epidemic wave peaked in March 2016, with the second smaller wave that peaked in March 2017. Dated molecular clock analysis revealed that multiple introductions occurred in Minas Gerais between 2014 and 2015, suggesting that the virus was circulating unnoticed for at least 16 months before the first confirmed laboratory case that we retrospectively identified in December 2015. Our findings highlight the importance of continued genomic surveillance strategies combined with traditional epidemiology to assist public health laboratories in monitoring and understanding the diversity of circulating arboviruses, which might help attenuate the public health impact of infectious diseases.
- Genetic differences of dengue virus 2 in patients with distinct clinical outcome(2023) MARQUES, Beatriz de Carvalho; SACCHETTO, Livia; BANHO, Cecilia Artico; ESTOFOLETE, Cassia Fernanda; DOURADO, Fernanda Simoes; CANDIDO, Darlan da Silva; DUTRA, Karina Rocha; SALLES, Flavia Cristina da Silva; JESUS, Jaqueline Goes de; SABINO, Ester Cerdeira; FARIA, Nuno Rodrigues; NOGUEIRA, Mauricio LacerdaThe genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the virus is essential to identify lineages responsible for an epidemic and understanding the processes of virus spread and virulence. Here, we characterize, using portable nanopore genomic sequencing, different lineages of dengue virus 2 (DENV-2) detected in 22 serum samples from patients with and without dengue warning signs attended at Hospital de Base of Sao Jose do Rio Preto (SJRP) in 2019, during a DENV-2 outbreak. Demographic, epidemiological, and clinical data were also analyzed. The phylogenetic reconstruction and the clinical data showed that two lineages belonging to the American/Asian genotype of DENV-2-BR3 and BR4 (BR4L1 and BR4L2)-were co-circulating in SJRP. Although preliminary, these results indicate no specific association between clinical form and phylogenetic clustering at the virus consensus sequence level. Studies with larger sample sizes and which explore single nucleotide variants are needed. Therefore, we showed that portable nanopore genome sequencing could generate quick and reliable sequences for genomic surveillance to monitor viral diversity and its association with disease severity as an epidemic unfolds.
- Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis(2023) CASTRO, Thais Regina y; PICCOLI, Bruna C.; VIEIRA, Andressa A.; CASARIN, Bruna C.; TESSELE, Luiza F.; SALVATO, Richard S.; GREGIANINI, Tatiana S.; MARTINS, Leticia G.; RESENDE, Paola Cristina; PEREIRA, Elisa C.; MOREIRA, Filipe R. R.; JESUS, Jaqueline G. de; SEERIG, Ana Paula; LOBATO, Marcos Antonio O.; CAMPOS, Marli M. A. de; GOULARTE, Juliana S.; SILVA, Mariana S. da; DEMOLINER, Meriane; FILIPPI, Micheli; PEREIRA, Vyctoria M. A. Goes; SCHWARZBOLD, Alexandre V.; SPILKI, Fernando R.; TRINDADE, Priscila A.Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 x 10-4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.