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1.
Ann Lab Med ; 41(2): 129-138, 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33063674

RESUMO

Since its first report in December 2019, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly emerged as a pandemic affecting nearly all countries worldwide. As the COVID-19 pandemic progresses, the need to identify genetic risk factors for susceptibility to this serious illness has emerged. Host genetic factors, along with other risk factors may help determine susceptibility to respiratory tract infections. It is hypothesized that the ACE2 gene, encoding angiotensin-converting enzyme 2 (ACE2), is a genetic risk factor for SARS-CoV-2 infection and is required by the virus to enter cells. Together with ACE2, transmembrane protease serine 2 (TMPRSS2) and dipeptidyl peptidase-4 (DPP4) also play an important role in disease severity. Evaluating the role of genetic variants in determining the direction of respiratory infections will help identify potential drug target candidates for further study in COVID-19 patients. We have summarized the latest reports demonstrating that ACE2 variants, their expression, and epigenetic factors may influence an individual's susceptibility to SARS-CoV-2 infection and disease outcome.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/patologia , Variação Genética , Pneumonia Viral/patologia , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Dipeptidil Peptidase 4/genética , Dipeptidil Peptidase 4/metabolismo , Suscetibilidade a Doenças , Expressão Gênica , Humanos , Pandemias , Peptidil Dipeptidase A/química , Peptidil Dipeptidase A/genética , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral/virologia , Serina Endopeptidases/genética , Serina Endopeptidases/metabolismo , Índice de Gravidade de Doença
2.
Ann Lab Med ; 41(2): 225-229, 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33063685

RESUMO

In response to the ongoing coronavirus disease 2019 (COVID-19) pandemic, an online laboratory surveillance system was established to monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacities and results. SARS-CoV-2 rRT-PCR testing data were collected from 97 clinical laboratories, including 84 medical institutions and 13 independent clinical laboratories in Korea. We assessed the testing capacities to utilize SARS-CoV-2 rRT-PCR based on surveillance data obtained from February 7th to June 4th, 2020 and evaluated positive result characteristics according to the reagents used and sample types. A total of 1,890,319 SARS-CoV-2 rRT-PCR testing were performed, 2.3% of which were positive. Strong correlations were observed between the envelope (E) gene and RNA-dependent RNA polymerase (RdRp)/nucleocapsid (N) genes threshold cycle (Ct) values for each reagent. No statistically significant differences in gene Ct values were observed between the paired upper and lower respiratory tract samples, except in the N gene for nasopharyngeal swab and sputum samples. Our study showed that clinical laboratories in Korea have rapidly expanded their testing capacities in response to the COVID-19 outbreak, with a peak daily capacity of 34,193 tests. Rapid expansion in testing capacity is a critical component of the national response to the ongoing pandemic.


Assuntos
Betacoronavirus/genética , Serviços de Laboratório Clínico/estatística & dados numéricos , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Humanos , Laboratórios Hospitalares , Pandemias , Pneumonia Viral/virologia , RNA Replicase/genética , RNA Viral/genética , RNA Viral/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , República da Coreia , Proteínas do Envelope Viral/genética , Proteínas Virais/genética
3.
PLoS One ; 15(11): e0242124, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33166369

RESUMO

BACKGROUND: In December 2019, the COVID-19 outbreak began in China and quickly spread throughout the world and was reclassified as a pandemic in March 2020. The first case of COVID-19 was declared in Togo on March 5. Two months later, few data were available to describe the circulation of the new coronavirus in the country. OBJECTIVE: This survey aimed to estimate the prevalence of SARS-CoV-2 in high-risk populations in Lomé. MATERIALS AND METHODS: From April 23, 2020, to May 8, 2020, we recruited a sample of participants from five sectors: health care, air transport, police, road transport and informal. We collected oropharyngeal swabs for direct detection through real-time reverse transcription polymerase chain reaction (rRT-PCR) and blood for antibody detection by serological tests. The overall prevalence (current and past) of infection was defined by positivity for both tests. RESULTS: A total of 955 participants with a median age of 36 (IQR 32-43) were included, and 71.6% (n = 684) were men. Approximately 22.1% (n = 212) were from the air transport sector, 20.5% (n = 196) were from the police sector, and 38.7% (n = 370) were from the health sector. Seven participants (0.7%, 95% CI: 0.3-1.6%) had a positive rRT-PCR test result at the time of recruitment, and nine (0.9%, 95% CI: 0.4-1.8%) were seropositive for IgM or IgG against SARS-CoV-2. We found an overall prevalence of 1.6% (n = 15), 95% CI: 0.9-2.6%. CONCLUSION: The prevalence of SARS-CoV-2 infection among high-risk populations in Lomé was relatively low and could be explained by the various measures taken by the Togolese government. Therefore, we recommend targeted screening.


Assuntos
Infecções por Coronavirus/patologia , Pneumonia Viral/patologia , Adulto , Anticorpos Antivirais/sangue , Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Estudos Transversais , Feminino , Humanos , Imunoensaio , Masculino , Pessoa de Meia-Idade , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Prevalência , RNA Viral/genética , RNA Viral/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Fatores de Risco , Togo/epidemiologia
4.
PLoS One ; 15(11): e0241959, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33166373

RESUMO

The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. In pooled sample testing, multiple samples are combined (or pooled) together and tested as a single unit. If the pool is positive, the individual samples can then be individually tested to identify the positive case(s). Here, we provide support for the adoption of sample pooling with the point-of-care Cepheid Xpert® Xpress SARS-CoV-2 molecular assay. Corroborating previous findings, the limit of detection of this assay was comparable to laboratory-developed reverse-transcription quantitative PCR SARS-CoV-2 tests, with observed detection below 100 copies/mL. The Xpert® Xpress assay detected SARS-CoV-2 after samples with minimum viral loads of 461 copies/mL were pooled in groups of six. Based on these data, we recommend the adoption of pooled testing with the Xpert® Xpress SARS-CoV-2 assay where warranted based on public health needs. The suggested number of samples per pool, or the pooling depth, is unique for each point-of-care testing site and can be determined by the positive test rates. To statistically determine appropriate pooling depth, we have calculated the pooling efficiency for numerous combinations of pool sizes and test rates. This information is included as a supplemental dataset that we encourage public health authorities to use as a guide to make recommendations that will maximize testing capacity and resource conservation.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , RNA Viral/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Humanos , Pandemias , Pneumonia Viral/virologia , Testes Imediatos , RNA Viral/genética , Kit de Reagentes para Diagnóstico , Manejo de Espécimes , Carga Viral
5.
BMC Infect Dis ; 20(1): 818, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33167900

RESUMO

BACKGROUND: To explore the kinetic changes in virology, specific antibody response and imaging during the clinical course of COVID-19. METHODS: This observational study enrolled 20 patients with COVID-19, who were hospitalized between January 20-April 6, 2020, in the two COVID-19 designated hospitals of Zhoushan, Zhejiang and Rushan, Shandong, China, The laboratory findings, imaging, serum response to viral infection, and viral RNA level in the throat and stool samples were assessed from onset to recovery phase in patients with COVID-19. RESULTS: SARS-COV-2 RNA was positive as early as day four. It remained positive until day 55 post-onset in the sputum-throat swabs and became negative in most cases (55%) within 14 days after onset. Lymphocytopenia occurred in 40% (8/20) of patients during the peak infection period and returned to normal at week five. The most severe inflammation in the lungs appeared in week 2 or 3 after onset, and this was completely absorbed between week 6 and 8 in 85.7% of patients. All patients had detectable antibodies to the receptor binding domain (RBD), and 95% of these patients had IgG to viral N proteins. The antibody titer peaked at week four. Anti-S IgM was positive in 7 of 20 patients after week three. CONCLUSIONS: All COVID-19 patients in this study were self-limiting and recovered well though it may take as long as 6-8 weeks. Our findings on the kinetic changes in imaging, serum response to viral infection and viral RNA level may help understand pathogenesis and define clinical course of COVID-19.


Assuntos
Anticorpos Antivirais/sangue , Betacoronavirus/imunologia , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico por imagem , Infecções por Coronavirus/imunologia , Pulmão/diagnóstico por imagem , Pneumonia Viral/diagnóstico por imagem , Pneumonia Viral/imunologia , Adolescente , Adulto , Idoso , Betacoronavirus/genética , Criança , China/epidemiologia , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Feminino , Humanos , Imunoglobulina G/sangue , Imunoglobulina M/sangue , Masculino , Pessoa de Meia-Idade , Proteínas do Nucleocapsídeo/imunologia , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Escarro/virologia , Tomografia Computadorizada por Raios X , Adulto Jovem
6.
Antimicrob Resist Infect Control ; 9(1): 185, 2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-33168097

RESUMO

BACKGROUND: Prehospital professionals such as emergency physicians or paramedics must be able to choose and adequately don and doff personal protective equipment (PPE) in order to avoid COVID-19 infection. Our aim was to evaluate the impact of a gamified e-learning module on adequacy of PPE in student paramedics. METHODS: This was a web-based, randomized 1:1, parallel-group, triple-blind controlled trial. Student paramedics from three Swiss schools were invited to participate. They were informed they would be presented with both an e-learning module and an abridged version of the current regional prehospital COVID-19 guidelines, albeit not in which order. After a set of 22 questions designed to assess baseline knowledge, the control group was shown the guidelines before answering a set of 14 post-intervention questions. The e-learning group was shown the gamified e-learning module right after the guidelines, and before answering post-intervention questions. The primary outcome was the difference in the percentage of adequate choices of PPE before and after the intervention. RESULTS: The participation rate was of 71% (98/138). A total of 90 answer sets was analyzed. Adequate choice of PPE increased significantly both in the control (50% [33;83] vs 25% [25;50], P = .013) and in the e-learning group (67% [50;83] vs 25% [25;50], P = .001) following the intervention. Though the median of the difference was higher in the e-learning group, there was no statistically significant superiority over the control (33% [0;58] vs 17% [- 17;42], P = .087). The e-learning module was of greatest benefit in the subgroup of student paramedics who were actively working in an ambulance company (42% [8;58] vs 25% [- 17;42], P = 0.021). There was no significant effect in student paramedics who were not actively working in an ambulance service (0% [- 25;33] vs 17% [- 8;50], P = .584). CONCLUSIONS: The use of a gamified e-learning module increases the rate of adequate choice of PPE only among student paramedics actively working in an ambulance service. In this subgroup, combining this teaching modality with other interventions might help spare PPE and efficiently protect against COVID-19 infection.


Assuntos
Betacoronavirus/fisiologia , Infecções por Coronavirus/prevenção & controle , Pessoal de Saúde/educação , Pandemias/prevenção & controle , Equipamento de Proteção Individual , Pneumonia Viral/prevenção & controle , Adulto , Pessoal Técnico de Saúde/educação , Pessoal Técnico de Saúde/normas , Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Educação a Distância/estatística & dados numéricos , Europa (Continente) , Feminino , Pessoal de Saúde/normas , Humanos , Transmissão de Doença Infecciosa do Paciente para o Profissional , Internet , Conhecimento , Aprendizagem , Masculino , Equipamento de Proteção Individual/normas , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Estudantes/psicologia , Adulto Jovem
7.
J Korean Med Sci ; 35(43): e391, 2020 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-33169560

RESUMO

Since mid-April 2020, cases of multisystem inflammatory syndrome in children (MIS-C) associated with coronavirus disease 2019 that mimics Kawasaki disease (KD) have been reported in Europe and North America. However, no cases have been reported in Korea. We describe an 11-year old boy with fever, abdominal pain, and diarrhea who developed hypotension requiring inotropes in intensive care unit. His blood test revealed elevated inflammatory markers, thrombocytopenia, hypoalbuminemia, and coagulopathy. Afterward, he developed signs of KD such as conjunctival injection, strawberry tongue, cracked lip, and coronary artery dilatation, and parenchymal consolidation without respiratory symptoms. Microbiological tests were all negative including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction. However, serum immunoglobulin G against SARS-CoV-2 was positive in repeated tests using enzyme-linked immunosorbent assay and fluorescent immunoassay. He was recovered well after intravenous immunoglobulin administration and discharged without complication on hospital day 13. We report the first Korean child who met all the criteria of MIS-C with features of incomplete KD or KD shock syndrome.


Assuntos
Infecções por Coronavirus/patologia , Pneumonia Viral/patologia , Síndrome de Resposta Inflamatória Sistêmica/diagnóstico , Abdome/diagnóstico por imagem , Anticorpos Antivirais/sangue , Betacoronavirus/genética , Betacoronavirus/imunologia , Criança , Infecções por Coronavirus/complicações , Infecções por Coronavirus/virologia , Humanos , Imunoglobulinas Intravenosas/administração & dosagem , Masculino , Síndrome de Linfonodos Mucocutâneos/patologia , Pandemias , Pneumonia Viral/complicações , Pneumonia Viral/virologia , Síndrome de Resposta Inflamatória Sistêmica/complicações , Tórax/diagnóstico por imagem , Tomografia Computadorizada por Raios X , Ultrassonografia
8.
PLoS One ; 15(11): e0240345, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33170902

RESUMO

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.


Assuntos
Betacoronavirus/genética , Variação Genética , Genoma Viral , Betacoronavirus/classificação , Betacoronavirus/isolamento & purificação , China , Infecções por Coronavirus/patologia , Infecções por Coronavirus/virologia , Evolução Molecular , Humanos , Pandemias , Filogenia , Pneumonia Viral/patologia , Pneumonia Viral/virologia , Estrutura Terciária de Proteína , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Proteínas Virais/química , Proteínas Virais/genética
9.
Virulence ; 11(1): 1569-1581, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33172355

RESUMO

A pandemic designated as Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading worldwide. Up to date, there is no efficient biomarker for the timely prediction of the disease progression in patients. To analyze the inflammatory profiles of COVID-19 patients and demonstrate their implications for the illness progression of COVID-19. Retrospective analysis of 3,265 confirmed COVID-19 cases hospitalized between 10 January 2020, and 26 March 2020 in three medical centers in Wuhan, China. Patients were diagnosed as COVID-19 and hospitalized in Leishenshan Hospital, Zhongnan Hospital of Wuhan University and The Seventh Hospital of Wuhan, China. Univariable and multivariable logistic regression models were used to determine the possible risk factors for disease progression. Moreover, cutoff values, the sensitivity and specificity of inflammatory parameters for disease progression were determined by MedCalc Version 19.2.0. Age (95%CI, 1.017 to 1.048; P < 0.001), serum amyloid A protein (SAA) (95%CI, 1.216 to 1.396; P < 0.001) and erythrocyte sedimentation rate (ESR) (95%CI, 1.006 to 1.045; P < 0.001) were likely the risk factors for the disease progression. The Area under the curve (AUC) of SAA for the progression of COVID-19 was 0.923, with the best predictive cutoff value of SAA of 12.4 mg/L, with a sensitivity of 83.9% and a specificity of 97.67%. SAA-containing parameters are novel promising ones for predicting disease progression in COVID-19.


Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Idoso , Área Sob a Curva , Betacoronavirus/genética , Biomarcadores , Sedimentação Sanguínea , Proteína C-Reativa/análise , China , Estudos de Coortes , Progressão da Doença , Feminino , Humanos , Laringe/virologia , Contagem de Leucócitos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Pandemias , Valor Preditivo dos Testes , RNA Viral/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Estudos Retrospectivos , Fatores de Risco , Sensibilidade e Especificidade , Proteína Amiloide A Sérica/análise
10.
Br J Community Nurs ; 25(11): 562-566, 2020 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-33161739

RESUMO

In December 2019, a new species of coronavirus (SARS-CoV-2) was identified in a number of patients presenting with pneumonias of unknown aetiology in WuHan Province, China. Early epidemiological indications were of a zoonotic origin: many of the initial patients confirmed contact with a local wet market and the genomic sequencing showed similar characteristics with coronaviruses known to be carried by bats. The theory of subsequent human to human transmission became evident once global epidemiological reporting of COVID infection was established. Confirmation of the origins of infections caused by SARS-CoV-2 was enabled by the early sharing of the initial genomic sequence by China in January 2020 and since developed collaboratively on a globally accessible database, supported by the World Health Organization (https://tinyurl.com/rj32fp3).


Assuntos
Betacoronavirus/genética , Evolução Biológica , Infecções por Coronavirus/genética , Infecções por Coronavirus/transmissão , Genômica , Pneumonia Viral/genética , Pneumonia Viral/transmissão , Zoonoses/genética , Zoonoses/transmissão , Animais , China/epidemiologia , Infecções por Coronavirus/epidemiologia , Transmissão de Doença Infecciosa , Humanos , Pandemias , Pneumonia Viral/epidemiologia
11.
Sci Rep ; 10(1): 18899, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144632

RESUMO

Severe acute respiratory coronavirus 2 (SARS-CoV-2) testing reagents are expected to become scarce worldwide. However, little is known regarding whether pooling of samples accurately detects SARS-CoV-2. To validate the feasibility of pooling samples, serial dilution analysis and spike-in experiments were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2-positive and -negative patients. Furthermore, we studied 1000 individuals, 667 of whom were "healthy" individuals (195 healthcare workers and 472 hospitalized patients with disorders other than COVID-19 infection), and 333 infection-suspected patients with cough and fever. Serial dilution analysis showed a limit of detection of around 10-100 viral genome copies according to the protocol of the National Institute of Infectious Diseases, Japan. Spike-in experiments demonstrated that RT-qPCR detected positive signals in pooled samples with SARS-CoV-2-negative and -positive patients at 5-, 10-, 20-fold dilutions. By screening with this pooling strategy, by the end of April 2020 there were 12 SARS-CoV-2-positive patients in 333 infection-suspected patients (3.6%) and zero in 667 "healthy" controls. We obtained these results with a total of 538 runs using the pooling strategy, compared with 1000 standard runs. In a prospective study, we successfully detected SARS-CoV-2 using 10- to 20-fold diluted samples of nasopharyngeal swabs from eighteen COVID-19 patients with wide ranges of viral load. Pooling sample is feasible for conserving test reagents and detecting SARS-CoV-2 in clinical settings. This strategy will help us to research the prevalence infected individuals and provide infected-status information to prevent the spread of the virus and nosocomial transmission.


Assuntos
Técnicas de Laboratório Clínico/métodos , Programas de Rastreamento/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Técnicas de Laboratório Clínico/normas , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/epidemiologia , Humanos , Limite de Detecção , Programas de Rastreamento/normas , Reprodutibilidade dos Testes , Mucosa Respiratória/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas
12.
J Perinat Med ; 48(9): 883-891, 2020 Nov 26.
Artigo em Inglês | MEDLINE | ID: mdl-33151180

RESUMO

The outbreak of the SARS-CoV-2 elicited a surge in publications. Obstetric reports were with few exceptions characterized by small sample sizes with potentially limited generalizability. In this review, evidence suggests increased susceptibility to COVID-19 in pregnancy; common pregnancy comorbidities may help explain worse outcomes. While the risk of death is low, pregnancy may be associated with increased need for ventilation. Prematurity rates seem to be increased but may be accounted for in part by higher cesarean rates, to a large degree accounted for by elective decision to shorten the course of the labor. Though fetal/neonatal complication rates may be higher in the presence of COVID-19 infection, survival rates seem unaffected and vertical transmission is rare. As the outbreak continues in the USA with resurgence in many other western countries that achieved initial success in suppressing the virus, much remains to be learned. For example, the question related to the degree to pregnancy modifying symptomatology remains open. Currently, routine polymerase chain reaction testing remains limited by supply shortages possibly delaying diagnosis until later in the course of the disorder and thus altering the symptom complex at presentation. To add to the knowledge base, we initiated a regional COVID-19 in pregnancy collaborative observational study with a coordinating center, standardized data collection and a shared database. This was facilitated by a longstanding tradition of collaboration among regional obstetric services. Over an anticipated two-year study duration, we expect to study 400 documented and suspected COVID-19 pregnancies with time and site of services controls for cohort effect and high power to detect several adverse maternal/infant outcomes. We include a complete listing of variables in our database, which, along with our experience in setting up our regional collaborative, we hope and believe will be of use in other settings.


Assuntos
Betacoronavirus , Infecções por Coronavirus/complicações , Colaboração Intersetorial , Pneumonia Viral/complicações , Complicações Infecciosas na Gravidez/virologia , Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/terapia , Suscetibilidade a Doenças , Feminino , Humanos , Metanálise como Assunto , Michigan/epidemiologia , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/terapia , Gravidez , Complicações Infecciosas na Gravidez/diagnóstico , Complicações Infecciosas na Gravidez/terapia , Resultado da Gravidez , Nascimento Prematuro/epidemiologia , Sistema de Registros , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Sensibilidade e Especificidade , Revisões Sistemáticas como Assunto , Resultado do Tratamento
13.
Biomedica ; 40(Supl. 2): 148-158, 2020 10 30.
Artigo em Inglês, Espanhol | MEDLINE | ID: mdl-33152198

RESUMO

Introduction: SARS-CoV-2 has been identified as the new coronavirus causing an outbreak of acute respiratory disease in China in December, 2019. This disease, currently named COVID-19, has been declared as a pandemic by the World Health Organization (WHO). The first case of COVID-19 in Colombia was reported on March 6, 2020. Here we characterize an early SARS-CoV-2 isolate from the pandemic recovered in April, 2020. Objective: To describe the isolation and characterization of an early SARS-CoV-2 isolate from the epidemic in Colombia. Materials and methods: A nasopharyngeal specimen from a COVID-19 positive patient was inoculated on different cell lines. To confirm the presence of SARS-CoV-2 on cultures we used qRT-PCR, indirect immunofluorescence assay, transmission and scanning electron microscopy, and next-generation sequencing. Results: We determined the isolation of SARS-CoV-2 in Vero-E6 cells by the appearance of the cytopathic effect three days post-infection and confirmed it by the positive results in the qRT-PCR and the immunofluorescence with convalescent serum. Transmission and scanning electron microscopy images obtained from infected cells showed the presence of structures compatible with SARS-CoV-2. Finally, a complete genome sequence obtained by next-generation sequencing allowed classifying the isolate as B.1.5 lineage. Conclusion: The evidence presented in this article confirms the first isolation of SARSCoV-2 in Colombia. In addition, it shows that this strain behaves in cell culture in a similar way to that reported in the literature for other isolates and that its genetic composition is consistent with the predominant variant in the world. Finally, points out the importance of viral isolation for the detection of neutralizing antibodies, for the genotypic and phenotypic characterization of the strain and for testing compounds with antiviral potential.


Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Pandemias , Pneumonia Viral/virologia , RNA Viral/genética , Animais , Betacoronavirus/genética , Betacoronavirus/fisiologia , Betacoronavirus/ultraestrutura , Chlorocebus aethiops , Colômbia/epidemiologia , Convalescença , Infecções por Coronavirus/epidemiologia , Efeito Citopatogênico Viral , Técnica Indireta de Fluorescência para Anticorpo , Genoma Viral , Humanos , Microscopia Eletrônica , Tipagem Molecular , Nasofaringe/virologia , Pneumonia Viral/epidemiologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência de RNA , Especificidade da Espécie , Células Vero , Vírion/ultraestrutura , Cultura de Vírus
14.
Biomedica ; 40(Supl. 2): 166-172, 2020 10 30.
Artigo em Inglês, Espanhol | MEDLINE | ID: mdl-33152200

RESUMO

Introduction: The 2019 coronavirus pandemic (COVID-19) has caused around 25 million cases worldwide. Asymptomatic patients have been described as potential sources of transmission. However, there are difficulties to detect them and to establish their role in the dynamics of virus transmission, which hinders the implementation of prevention strategies. Objective: To describe the behavior of asymptomatic SARS-CoV-2 virus infection in a cohort of workers at the El Dorado "Luis Carlos Galán Sarmiento" International Airport in Bogotá, Colombia. Materials and methods: A prospective cohort of 212 workers from the El Dorado airport was designed. The follow-up began in June, 2020. A survey was used to characterize health and work conditions. Every 21 day, a nasopharyngeal swab was taken to identify the presence of SARS-CoV-2 using RT-PCR. We analyzed the behavior of the cycle threshold (ORF1ab and N genes) according to the day of follow-up. Results: In the first three follow-ups of the cohort, we found an incidence of SARS-CoV-2 infection of 16.51%. The proportion of positive contacts was 14.08%. The median threshold for cycle threshold was 33.53. Conclusion: We characterized the asymptomatic SARS-CoV-2 infection in a cohort of workers. The identification of asymptomatic infected persons continues to be a challenge for epidemiological surveillance systems.


Assuntos
Aeroportos , Infecções Assintomáticas , Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Nasofaringe/virologia , Pandemias , Pneumonia Viral/diagnóstico , Adulto , Infecções Assintomáticas/epidemiologia , Betacoronavirus/genética , Betacoronavirus/fisiologia , Colômbia , Busca de Comunicante , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Proteínas do Nucleocapsídeo/genética , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Estudos Prospectivos , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Inquéritos e Questionários , Proteínas Virais/genética , Replicação Viral/genética , Local de Trabalho
15.
Biomedica ; 40(Supl. 2): 188-197, 2020 10 30.
Artigo em Inglês, Espanhol | MEDLINE | ID: mdl-33152203

RESUMO

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Genoma Viral , Disseminação de Informação , Epidemiologia Molecular/tendências , Pandemias , Pneumonia Viral/epidemiologia , Vigilância da População , RNA Viral/genética , Análise de Sequência de RNA , Sequência de Bases , Região do Caribe , Doenças Transmissíveis Emergentes , Infecções por Coronavirus/prevenção & controle , Infecções por Coronavirus/virologia , Planejamento em Desastres , Surtos de Doenças , Humanos , América Latina/epidemiologia , Epidemiologia Molecular/métodos , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Pneumonia Viral/virologia , Utilização de Procedimentos e Técnicas , Saúde Pública , RNA-Seq , Desenvolvimento Sustentável , Viroses/epidemiologia
16.
J Mol Model ; 26(12): 338, 2020 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-33175236

RESUMO

A novel coronavirus (SARS-CoV-2) identified in Wuhan state of China in 2019 is the causative agent of deadly disease COVID-19. It has spread across the globe (more than 210 countries) within a short period. Coronaviruses pose serious health threats to both humans and animals. A recent publication reported an experimental 3D complex structure of the S protein of SARS-CoV-2 showed that the ectodomain of the SARS-CoV-2 S protein binds to the peptidase domain (PD) of human ACE2 with a dissociation constant (Kd) of ~ 15 nM. In this study, we focused on inhibitors for ACE2: S protein complex using virtual screening and inhibition studies through molecular docking for over 200,000 natural compounds. Toxicity analysis was also performed for the best hits, and the final complex structures for four complexes were subjected to 400 ns molecular dynamics simulations for stability testing. We found two natural origin inhibitors for the S protein: human ACE2 complex (Andrographolide and Pterostilbene) which displayed better inhibition potential for ACE2 receptor and its binding with the S protein of SARS-CoV-2. Comparative studies were also performed to test and verify that these two drug candidates are also better than hydroxychloroquine which is known to inhibit this complex. However, we needed better potential drug candidates to overcome the side effects of hydroxychloroquine. Supplementary experimental studies need to be carried forward to corroborate the viability of these two new inhibitors for ACE2: S protein complex so as to curb down COVID-19.


Assuntos
Betacoronavirus/fisiologia , Infecções por Coronavirus/epidemiologia , Peptídeo Hidrolases/metabolismo , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral/epidemiologia , Glicoproteína da Espícula de Coronavírus/metabolismo , Betacoronavirus/genética , Infecções por Coronavirus/virologia , Reposicionamento de Medicamentos , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Pandemias , Peptídeo Hidrolases/genética , Peptidil Dipeptidase A/genética , Pneumonia Viral/virologia , Domínios Proteicos , Glicoproteína da Espícula de Coronavírus/genética
17.
Comput Biol Med ; 126: 104051, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33131530

RESUMO

SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs, including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, plasma components, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management.


Assuntos
Antivirais , Betacoronavirus , Infecções por Coronavirus , Bases de Dados Genéticas , Descoberta de Drogas , Modelos Biológicos , Pandemias , Pneumonia Viral , Antivirais/química , Antivirais/farmacocinética , Antivirais/uso terapêutico , Betacoronavirus/genética , Betacoronavirus/metabolismo , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/genética , Infecções por Coronavirus/metabolismo , Humanos , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/genética , Pneumonia Viral/metabolismo , Proteômica
18.
Nat Commun ; 11(1): 5518, 2020 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-33139704

RESUMO

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.


Assuntos
Betacoronavirus/genética , Doenças Transmissíveis Importadas/virologia , Infecções por Coronavirus/transmissão , Genoma Viral/genética , Pneumonia Viral/transmissão , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Sequência de Bases , Número Básico de Reprodução/estatística & dados numéricos , Criança , Pré-Escolar , Doenças Transmissíveis Importadas/epidemiologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/prevenção & controle , Feminino , Humanos , Lactente , Recém-Nascido , Israel/epidemiologia , Masculino , Pessoa de Meia-Idade , Pandemias/prevenção & controle , Filogenia , Pneumonia Viral/epidemiologia , Pneumonia Viral/prevenção & controle , RNA Viral/genética , Análise de Sequência de RNA , Distância Social , Estados Unidos , Adulto Jovem
19.
BMC Med ; 18(1): 346, 2020 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-33143712

RESUMO

BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv, and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS-2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites. RESULTS: Of 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from - 6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 and 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post-symptom onset. CONCLUSIONS: RT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond 10 days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias, so the positivity rates are probably overestimated.


Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , Betacoronavirus/genética , Técnicas de Laboratório Clínico , Infecções por Coronavirus/genética , Humanos , Estudos Longitudinais , Pandemias , Pneumonia Viral/genética
20.
Nat Commun ; 11(1): 5558, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144575

RESUMO

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Genoma Viral/genética , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Infecções por Coronavirus/prevenção & controle , Geografia , Humanos , Programas de Rastreamento/métodos , Epidemiologia Molecular/métodos , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Dispositivos de Proteção Respiratória , Distância Social , Estados Unidos/epidemiologia , Wisconsin/epidemiologia
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