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1.
Braz J Biol ; 83: e247219, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34468526

RESUMO

Military conflicts have been significant obstacles in detecting and treating infectious disease diseases due to the diminished public health infrastructure, resulting in malaria endemicity. A variety of violent and destructive incidents were experienced by FATA (Federally Administered Tribal Areas). It was a struggle to pursue an epidemiological analysis due to continuing conflict and Talibanization. Clinical isolates were collected from Bajaur, Mohmand, Khyber, Orakzai agencies from May 2017 to May 2018. For Giemsa staining, full blood EDTA blood samples have been collected from symptomatic participants. Malaria-positive microscopy isolates were spotted on filter papers for future Plasmodial molecular detection by nested polymerase chain reaction (nPCR) of small subunit ribosomal ribonucleic acid (ssrRNA) genes specific primers. Since reconfirming the nPCR, a malariometric study of 762 patients found 679 positive malaria cases. Plasmodium vivax was 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) were with mixed-species infection (P. vivax plus P. falciparum), and 83 were declared negative by PCR. Among the five agencies of FATA, Khyber agency has the highest malaria incidence (19%) with followed by P. vivax (19%) and P. falciparum (4.1%). In contrast, Kurram has about (14%), including (10.8%) P. vivax and (2.7%) P. falciparum cases, the lowest malaria epidemiology. Surprisingly, no significant differences in the distribution of mixed-species infection among all five agencies. P. falciparum and P. vivax were two prevalent FATA malaria species in Pakistan's war-torn area. To overcome this rising incidence of malaria, this study recommends that initiating malaria awareness campaigns in school should be supported by public health agencies and malaria-related education locally, targeting children and parents alike.


Assuntos
Plasmodium , Criança , Humanos , Epidemiologia Molecular , Paquistão/epidemiologia , Plasmodium/genética , Plasmodium falciparum/genética , Plasmodium vivax/genética
2.
Viruses ; 13(7)2021 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-34372500

RESUMO

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth-death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland.


Assuntos
COVID-19/epidemiologia , COVID-19/virologia , SARS-CoV-2/classificação , SARS-CoV-2/genética , Teorema de Bayes , Evolução Molecular , Variação Genética , Genoma Viral , Humanos , Epidemiologia Molecular , Mutação , Filogenia , Polônia/epidemiologia , Prevalência , Sequenciamento Completo do Genoma
3.
Viruses ; 13(7)2021 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-34372565

RESUMO

More than a year after the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of the 2019 coronavirus disease (COVID-19) in China, the emergence and spread of genomic variants of this virus through travel raise concerns regarding the introduction of lineages in previously unaffected regions, requiring adequate containment strategies. Concomitantly, such introductions fuel worries about a possible increase in transmissibility and disease severity, as well as a possible decrease in vaccine efficacy. Military personnel are frequently deployed on missions around the world. As part of a COVID-19 risk mitigation strategy, Belgian Armed Forces that engaged in missions and operations abroad were screened (7683 RT-qPCR tests), pre- and post-mission, for the presence of SARS-CoV-2, including the identification of viral lineages. Nine distinct viral genotypes were identified in soldiers returning from operations in Niger, the Democratic Republic of the Congo, Afghanistan, and Mali. The SARS-CoV-2 variants belonged to major clades 19B, 20A, and 20B (Nextstrain nomenclature), and included "variant of interest" B.1.525, "variant under monitoring" A.27, as well as lineages B.1.214, B.1, B.1.1.254, and A (pangolin nomenclature), some of which are internationally monitored due to the specific mutations they harbor. Through contact tracing and phylogenetic analysis, we show that isolation and testing policies implemented by the Belgian military command appear to have been successful in containing the influx and transmission of these distinct SARS-CoV-2 variants into military and civilian populations.


Assuntos
COVID-19/virologia , Militares , SARS-CoV-2/classificação , SARS-CoV-2/genética , Afeganistão/epidemiologia , Bélgica , COVID-19/epidemiologia , China/epidemiologia , República Democrática do Congo/epidemiologia , Genoma Viral , Genômica , Humanos , Mali/epidemiologia , Epidemiologia Molecular , Mutação , Níger/epidemiologia , Filogenia , Viagem , Sequenciamento Completo do Genoma
4.
Viruses ; 13(8)2021 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-34452511

RESUMO

Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , SARS-CoV-2 , Análise de Sequência de RNA , Software , Águas Residuárias/virologia , Vigilância Epidemiológica Baseada em Águas Residuárias , Algoritmos , Missouri/epidemiologia , Epidemiologia Molecular , RNA Viral/genética , SARS-CoV-2/genética , SARS-CoV-2/fisiologia , Glicoproteína da Espícula de Coronavírus/genética
5.
Indian J Pharmacol ; 53(4): 310-316, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34414910

RESUMO

Knowledge of a new mutant strain of SARS-coronavirus (CoV-2) is enormously essential to identify a targeted drug and for the development of the vaccine. In this article, we systematically reviewed the different mutation strains (variant of concern [VOC] and variant of interest [VOI]) which were found in different countries such as the UK, Singapore, China, Germany, Vietnam, Western Africa, Dublin, Ireland, Brazil, Iran, Italy, France, America, and Philippines. We searched four literature databases (PubMed, EMBASE, NATURE, and Willey online library) with suitable keywords and the time filter was November 2019 to June 16, 2021. To understand the worldwide spread of variants of SARS-CoV-2, we included a total of 27 articles of case reports, clinical and observational studies in the systematic review. However, these variants mostly spread because of their ability to increase transmission, virulence, and escape immunity. So, in this paper is we found mutated strains of SARS-CoV-2 like VOCs that are found in different regions across the globe are ALPHA strain in the U.K, BETA strain in South Africa, GAMMA strain in Brazil, Gamma and Beta strains in European Countries, and some VOIs like Theta variant in the Philippines.


Assuntos
COVID-19/virologia , Mutação , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/epidemiologia , Genótipo , Interações Hospedeiro-Patógeno , Humanos , Epidemiologia Molecular , SARS-CoV-2/patogenicidade
6.
Viruses ; 13(7)2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34372586

RESUMO

Hepatitis B (HBV) and delta (HDV) viruses are endemic in the Amazon region, but vaccine coverage against HBV is still limited. People who use illicit drugs (PWUDs) represent a high-risk group due to common risk behavior and socioeconomic factors that facilitate the acquisition and transmission of pathogens. The present study assessed the presence of HBV and HBV-HDV co-infection, identified viral sub-genotypes, and verified the occurrence of mutations in coding regions for HBsAg and part of the polymerase in HBV-infected PWUDs in municipalities of the Brazilian states of Amapá and Pará, in the Amazon region. In total, 1074 PWUDs provided blood samples and personal data in 30 municipalities of the Brazilian Amazon. HBV and HDV were detected by enzyme-linked immunosorbent assay and polymerase chain reaction. Viral genotypes were identified by nucleotide sequencing followed by phylogenetic analysis, whereas viral mutations were analyzed by specialized software. High rates of serological (32.2%) and molecular (7.2%) markers for HBV were detected, including cases of occult HBV infection (2.5%). Sub-genotypes A1, A2, D4, and F2a were most frequently found. Escape mutations due to vaccine and antiviral resistance were identified. Among PWUDs with HBV DNA, serological (19.5%) and molecular (11.7%) HDV markers were detected, such as HDV genotypes 1 and 3. These are worrying findings, presenting clear implications for urgent prevention and treatment needs for the carriers of these viruses.


Assuntos
Hepatite B/genética , Hepatite D/genética , Transtornos Relacionados ao Uso de Substâncias/virologia , Adulto , Brasil/epidemiologia , Coinfecção , Estudos Transversais , DNA Viral/genética , Usuários de Drogas , Ensaio de Imunoadsorção Enzimática/métodos , Feminino , Genótipo , Hepatite B/diagnóstico , Antígenos de Superfície da Hepatite B/análise , Antígenos de Superfície da Hepatite B/sangue , Vírus da Hepatite B/genética , Vírus da Hepatite B/patogenicidade , Hepatite D/diagnóstico , Vírus Delta da Hepatite/genética , Vírus Delta da Hepatite/patogenicidade , Humanos , Drogas Ilícitas , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular/métodos , Filogenia , RNA Viral/genética , Análise de Sequência de DNA/métodos
7.
J Med Microbiol ; 70(8)2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34431760

RESUMO

Introduction. Staphylococcus coagulans (formerly Staphylococcus schleiferi subsp. coagulans) is a common commensal and opportunistic pathogen of companion dogs. It carries a range of antimicrobial resistance genes and is an occasional zoonotic pathogen.Hypothesis/Gap Statement. Despite the potential insight offered by genome sequencing into the biology of S. coagulans, few genomes are currently available for study.Aim. To sequence and analyse S. coagulans genomes to improve understanding of this organism's molecular epidemiology, antimicrobial resistance and bacterium-host interactions.Methodology. Twenty-five genomes of clinical isolates collected at a veterinary referral hospital in Scotland, UK, were sequenced with Illumina technology. These genomes were analysed by a series of bioinformatics tools along with 16 previously sequenced genomes.Results. Phylogenetic comparison of the 41 genomes shows that the current S. coagulans phylogeny is dominated by clades of closely related isolates, at least one of which has spread internationally. Ten of the 11 methicillin-resistant S. coagulans genomes in this collection of 41 encoded the mecA promoter and gene mutations that are predicted to render the isolates susceptible to penicillins in the presence of clavulanic acid, a feature only described to date in methicillin-resistant Staphylococcus aureus. Seven such isolates were from the current study and, in line with the genome-based prediction, all were susceptible to amoxicillin/clavulanic acid in vitro. S. coagulans shared very few highly conserved virulence-associated genes with Staphylococcus pseudintermedius, another common commensal and opportunistic canine pathogen.Conclusion. The availability of a further 25 genome sequences from clinical S. coagulans isolates will aid in better understanding the epidemiology, bacterial-host interactions and antimicrobial resistance of this opportunistic pathogen.


Assuntos
Doenças do Cão/epidemiologia , Doenças do Cão/microbiologia , Genoma Bacteriano , Genômica , Infecções Oportunistas , Infecções Estafilocócicas/veterinária , Staphylococcus/genética , Animais , Antibacterianos/farmacologia , Doenças do Cão/transmissão , Cães , Farmacorresistência Bacteriana , Genômica/métodos , Staphylococcus aureus Resistente à Meticilina , Epidemiologia Molecular , Animais de Estimação , Escócia/epidemiologia , Staphylococcus/efeitos dos fármacos
8.
Zhonghua Er Ke Za Zhi ; 59(8): 645-650, 2021 Aug 02.
Artigo em Chinês | MEDLINE | ID: mdl-34333916

RESUMO

Objective: To investigate the molecular epidemiology of norovirus associated with pediatric acute gastroenteritis in Beijing under the Working Mechanism for Joint Prevention and Control of the Epidemic in 2020. Methods: This was a retrospective, repeated cross-sectional study. Fecal or vomit samples (1 213 cases) were collected from children visited the Capital Institute of Pediatrics Affiliated Children's Hospital for acute gastroenteritis from January 1 to December 31, 2020. First, real-time reverse PCR (RT-PCR) was used to screen the samples for norovirus, and then RdRp gene and capsid gene VP1 of norovirus-positive samples were amplified by conventional RT-PCR for genotyping based on the nucleotide sequence. The χ2 test was used to compare the positive rates and genotypes of norovirus among different specimen types, genders of children, and different age groups. Results: Among the 1 213 samples were collected, 215 samples were positive for norovirus, with a positivity rate of 17.7% for the whole year. The peak of norovirus infection observed mainly in the cold seasons, as the positive rates were 28.6% (18/63), 26.2% (16/61), 22.8% (77/338) and 17.1% (89/520) in January, October, November and December, respectively. The positive rate of norovirus in fecal sample was significantly higher than that in vomit sample (χ2 = 9.692, P<0.01). There was no significant difference between genders (χ2=0.041, P>0.05), but significant difference was found between age groups with the highest rate in the 6-48 months group (χ²=103.112, P<0.01). Three genogroups (GⅠ, GⅡ and GⅨ) of the circulating virus were detected by G-gene typing, and GⅡgenogroup was predominant, accounting for 98.5% (196/199). Among the GⅡ positive samples, genotype GⅡ.4 Sydney (55.1%, 108/196) was the most common, followed by GⅡ.2 (29.6%, 58/196), while the GⅡ.3 norovirus (10.2%, 20/196) which was common in previous years was not as much as before. Based on the P-type, GⅡ.P16 was predominant (61.5%, 96/156), followed by GII.P31 (19.9%, 31/156). The dual genotyping revealed that GⅡ.4 Sydney [P16] (36.4%, 56/154) and GⅡ.2 [P16] (24.7%, 38/154) were predominant. Conclusion: The prevalence of norovirus in children in 2020 in Beijing is not much different from those of the previous years, but the genotypes composition has changed significantly, and there are multiple genotypes circulating simultaneously.


Assuntos
Infecções por Caliciviridae , Gastroenterite , Norovirus , Pediatria , Pequim , Infecções por Caliciviridae/epidemiologia , Criança , Pré-Escolar , Estudos Transversais , Fezes , Feminino , Gastroenterite/epidemiologia , Genótipo , Humanos , Lactente , Masculino , Epidemiologia Molecular , Norovirus/genética , Filogenia , Estudos Retrospectivos
9.
Curr Issues Mol Biol ; 43(2): 845-867, 2021 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-34449545

RESUMO

This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.


Assuntos
COVID-19/virologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/epidemiologia , COVID-19/genética , Biologia Computacional/métodos , Humanos , Epidemiologia Molecular/métodos , Pandemias , Filogenia , SARS-CoV-2/isolamento & purificação
10.
Viruses ; 13(6)2021 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-34207617

RESUMO

We investigated an outbreak of acute gastroenteritis due to human astrovirus in a daycare center, describing the transmission mechanism, the most affected age groups, conditioning factors and the extent of the outbreak among household contacts of the daycare center attenders. Data were collected from persons exposed at the daycare center and their home contacts. Fecal samples from affected and non-affected daycare center attenders were analyzed for viruses causing acute gastroenteritis by RT-PCR. The percentage of households affected and the attack rates (AR) were calculated. The attack rates were compared using the rate ratio (RR) with 95% confidence intervals. Information was obtained from 245 people (76 attenders and 169 contacts) of whom 49 were clinical cases. Five HAstV-4, two HAstV-8 and three non-typable HAstV cases were identified (six from clinical cases and four from asymptomatic infected people). The global AR was 20% (41.2% in children aged < 2 years). Data were obtained from 67 households: 20 households of affected attenders and 47 of non-affected attendees. Household contacts of affected attenders had a higher AR (74.3%) than that of non-affected attendees (2.4%). We found asymptomatic infections amongst daycare attendees. The transmission of HAstV during the outbreak was not limited to the daycare center but extended to household contacts of both affected and non-affected attenders.


Assuntos
Infecções por Astroviridae/epidemiologia , Infecções por Astroviridae/virologia , Astroviridae , Creches , Surtos de Doenças , Adulto , Astroviridae/genética , Infecções por Astroviridae/diagnóstico , Infecções por Astroviridae/transmissão , Pré-Escolar , Características da Família , Feminino , Gastroenterite/epidemiologia , Gastroenterite/virologia , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , Reação em Cadeia da Polimerase , Vigilância da População , Espanha/epidemiologia
11.
Orphanet J Rare Dis ; 16(1): 300, 2021 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-34229749

RESUMO

BACKGROUND: Rhizomelic chondrodysplasia punctata (RCDP) is an inherited ultra-rare disease which results in severely impaired physical and mental development. Mutations in one of five genes involved in plasmalogen biosynthesis have been reported to drive disease pathology. Estimates of disease incidence have been extremely challenging due to the rarity of the disorder, preventing an understanding of the unmet medical need. To address this, we have prepared a disease incidence and prevalence model based on genetic epidemiology approaches to estimate the total number of RCDP patients affected, and their demographic characteristics. RESULTS: Extraction of allelic frequencies for known and predicted pathogenic variants in PEX7, GNPAT, AGPS, FAR1, PEX5 (limited to the PTS2 domain encoding region) genes, from large-scale human genetic diversity datasets (TopMed and gnomAD) revealed the mutational landscape contributing to the RCDP patient population in the US and Europe. We computed genetic prevalence to derive birth incidence for RCDP and modeled the impact to life expectancy to obtain high confidence estimates of disease prevalence. Our population genetics-based model indicates PEX7 variants are expected to contribute to the majority of RCDP cases in both the US and Europe; closely aligning with clinical reports. Furthermore, this model provides estimates for RCDP subtypes due to mutations in other genes, including exceedingly rare subtypes. CONCLUSION: In total, the estimated number of RCDP patients in the US and the five largest European countries (UK, Germany, France, Italy and Spain) is between 516 and 847 patients, all under the age of 35 years old. This model provides a quantitative framework for better understanding the unmet medical need in RCDP, to help guide disease awareness and diagnosis efforts for this specific patient group.


Assuntos
Condrodisplasia Punctata Rizomélica , Adulto , Condrodisplasia Punctata Rizomélica/epidemiologia , Condrodisplasia Punctata Rizomélica/genética , Europa (Continente) , França , Alemanha , Humanos , Incidência , Itália , Epidemiologia Molecular , Prevalência , Espanha
12.
Int J Infect Dis ; 109: 294-303, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34273514

RESUMO

OBJECTIVE: We conducted a cross-sectional study in the five administrative regions of Northern Ghana to determine the diversity of Mycobacterium tuberculosis complex (MTBC) sub/lineages and their susceptibility to isoniazid (INH) and rifampicin (RIF). METHODS: Sputum specimens were collected and cultured from 566 pulmonary tuberculosis patients reporting to 17 health facilities from 2015 to 2019. Mycobacterial isolates obtained from solid cultures were confirmed as members of the MTBC by PCR amplification of IS6110 and rpoß and assigned lineages and sub-lineages using spoligotyping. RESULTS: Of 294 mycobacterial isolates recovered, MTBC species identified were: M. tuberculosis sensu stricto (Mtbss) 241 (82.0%), M. africanum 41 (13.9%) and M. bovis four (1.4%) with eight (2.7%) unidentified. The human-adapted lineages (L) identified (N=279) were L1 (8/279, 2.9%), L2 (15/279, 5.4%), L3 (7/279, 2.5%), L4 (208/279, 74.5%), L5 (13/279, 4.7%) and L6 (28/279, 10.0%) with three unidentified lineages. Among the 208 L4, the dominant sub-lineages in the region were the Cameroon 120/208 (57.7%) and Ghana 50/208 (24.0%). We found 4.4% (13/294) and 0.7% (2/294) of the patients infected with MTBC isolates resistant to INH only and RIF only, respectively, with 2.4% (7/294) being infected with MDR strains. Whereas L6 was associated with the elderly, we identified that the Ghana sub-lineage of L4 was associated with both INH and MDR (p<0.05), making them important TB pathogens in Northern Ghana and a growing public health concern.


Assuntos
Mycobacterium tuberculosis , Preparações Farmacêuticas , Tuberculose Resistente a Múltiplos Medicamentos , Idoso , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , Estudos Transversais , Genótipo , Gana/epidemiologia , Humanos , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia
13.
PLoS One ; 16(7): e0248792, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34288921

RESUMO

Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.


Assuntos
COVID-19/epidemiologia , SARS-CoV-2/genética , Chipre/epidemiologia , Humanos , Epidemiologia Molecular , Filogenia , SARS-CoV-2/fisiologia
14.
Front Public Health ; 9: 667337, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34235130

RESUMO

Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis Transmission (LITT) algorithm to systematize the integration and analysis of whole-genome sequencing, clinical, and epidemiological data. Based on the work typically performed by hand during a cluster investigation, LITT identifies and ranks potential source cases for each case in a TB cluster. We evaluated LITT using a diverse dataset of 534 cases in 56 clusters (size range: 2-69 cases), which were investigated locally in three different U.S. jurisdictions. Investigators and LITT agreed on the most likely source case for 145 (80%) of 181 cases. By reviewing discrepancies, we found that many of the remaining differences resulted from errors in the dataset used for the LITT algorithm. In addition, we developed a graphical user interface, user's manual, and training resources to improve LITT accessibility for frontline staff. While LITT cannot replace thorough field investigation, the algorithm can help investigators systematically analyze and interpret complex data over the course of a TB cluster investigation. Code available at: https://github.com/CDCgov/TB_molecular_epidemiology/tree/1.0; https://zenodo.org/badge/latestdoi/166261171.


Assuntos
Mycobacterium tuberculosis , Tuberculose , Algoritmos , Humanos , Epidemiologia Molecular , Mycobacterium tuberculosis/genética , Tuberculose/epidemiologia , Sequenciamento Completo do Genoma
15.
Arch Virol ; 166(9): 2479-2486, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34218319

RESUMO

Rotaviruses are important causative agents of acute gastroenteritis in children. In China, rotavirus infection has a prevalence rate of 30% and is therefore considered a serious public health problem. This study was carried out to investigate the clinical and molecular epidemiological characteristics of rotavirus infections in children under 5 years old with acute diarrhea in Shandong province, China. From July 2017 to June 2018, a total of 1211 fecal specimens were tested, and the prevalence of rotavirus infection was 32.12%. The mean age of the infected children was 12.2 ± 10.9 months, and the highest infection rate was observed in children aged 7-12 months, with a rate of 41.64%. G9P[8] (76.61%) was the most prevalent genotype combination, followed by G2P[4] (7.20%), G3P[8] (3.60%), and G9P[4] (2.06%). In addition to diarrhea, vomiting, fever, and dehydration were the most common clinical signs. In general, there was no significant difference in clinical manifestations among different age groups. However, the clinical manifestations differed significantly between vaccinated and unvaccinated children. Vaccinated children showed lower incidence and frequency of vomiting, lower incidence and degree of dehydration, and lower incidence of severe cases than unvaccinated children. These findings suggest that it is necessary to continuously monitor changes in the characteristics of rotavirus infections. Moreover, the introduction of vaccines into the national immunization program to prevent and control rotavirus infection is needed in China.


Assuntos
Epidemiologia Molecular , Infecções por Rotavirus/epidemiologia , Infecções por Rotavirus/virologia , Rotavirus/genética , Pré-Escolar , China/epidemiologia , Diarreia/virologia , Feminino , Gastroenterite/virologia , Genótipo , Humanos , Programas de Imunização , Incidência , Lactente , Masculino , Prevalência , Infecções por Rotavirus/fisiopatologia , Infecções por Rotavirus/prevenção & controle , Vacinas contra Rotavirus , Vacinação
16.
BMC Infect Dis ; 21(1): 704, 2021 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-34303348

RESUMO

BACKGROUND: The co-circulation of types of arbovirus in areas where they are endemic increased the risk of outbreaks and limited the diagnostic methods available. Here, we analyze the epidemiological profile of DENV, CHIKV and ZIKV at the serological and molecular level in patients with suspected infection with these arboviruses in the city of Juazeiro do Norte, Ceará, Brazil. METHODS: In 2016, the Central Public Health Laboratory (LACEN) of Juazeiro do Norte received 182 plasma samples from patients who visited health facilities with symptoms compatible with arbovirus infection. The LACEN performed serological tests for detection of IgM/IgG to DENV and CHIKV. They then sent these samples to the Retrovirology Laboratory of the Federal University of São Paulo and Faculty of Medical of the ABC where molecular analyses to confirm the infection by DENV, ZIKV and CHIKV were performed. The prevalence of IgM/IgG antibodies and of infections confirmed by RT-qPCR were presented with 95% confidence interval. RESULTS: In serologic analysis, 125 samples were positive for antibodies against CHIKV and all were positive for antibodies against DENV. A higher prevalence of IgG against CHIKV (63.20% with 95% CI: 45.76-70.56) than against DENV (95.05% with 95% CI: 78.09-98.12) was observed. When the samples were submitted to analysis by RT-qPCR, we observed the following prevalence: mono-infection by ZIKV of 19.23% (95% CI: 14.29-34.82) patients, mono-infection by CHIKV of 3.84% (95% CI: 2.01-5.44) and co-infection with ZIKV and CHIKV of 1.09% (95% CI: 0.89-4.56). CONCLUSION: The serologic and molecular tests performed in this study were effective in analyzing the epidemiological profile of DENV, CHIKV and ZIKV in patients with suspected infection by these arboviruses in the city of Juazeiro do Norte, Ceará/Brazil.


Assuntos
Anticorpos Antivirais/sangue , Febre de Chikungunya/epidemiologia , Vírus Chikungunya/imunologia , Vírus da Dengue/imunologia , Dengue/epidemiologia , Infecção por Zika virus/epidemiologia , Zika virus/imunologia , Adulto , Brasil/epidemiologia , Febre de Chikungunya/terapia , Cidades/epidemiologia , Estudos Transversais , Dengue/terapia , Feminino , Humanos , Imunoglobulina G/sangue , Imunoglobulina M/sangue , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , Reação em Cadeia da Polimerase em Tempo Real , Medição de Risco , Testes Sorológicos , Infecção por Zika virus/terapia
17.
Medicine (Baltimore) ; 100(28): e26640, 2021 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-34260561

RESUMO

INTRODUCTION: In recent years, with the development of molecular epidemiology, molecular transmission networks based on evolutionary theory and sequence analysis have been widely used in research on human immunodeficiency virus (HIV)-1 transmission dynamics and precise intervention for high-risk populations. The HIV-1 molecular transmission network is a new method to study the population's access to the network, the characteristics of clustering, and the characteristics of interconnection in the network. Here, we analyzed the characteristics of the HIV-1 molecular transmission network of sexually transmitted people in Liaoning Province. METHODS: A study of HIV-infected persons who were sexually transmitted in Liaoning Province from 2003 to 2019. HIV-1 RNA was extracted, amplified and sequenced, and a phylogenetic tree was constructed to determine the subtype using the well matched pol gene region sequence. The gene distance between sequences was calculated, the threshold was determined, and the molecular transmission network was constructed. RESULTS: 109 samples of pol gene region were obtained. The main subtype of HIV-1 was CRF01_AE, followed by B, CRF07_BC, etc. 12.8% of them were resistant to HIV. At the threshold of 0.55 gene distance, 60.6% of them entered the HIV-1 molecular transmission network. Workers, sample source voluntary counseling and testing, other testing, subtype B and drug resistance are the factors influencing the access to HIV-1 molecular transmission network. The subtype of CRF01_AE formed 6 clusters in the molecular transmission network. In the network, the difference of connection degree between different subtypes was statistically significant. DISCUSSION: The three subtypes CRF01_AE, CRF07_BC and B that enter the molecular transmission network do not have interconnections, and they form clusters with each other. It shows that the risk of transmission among the three subtypes is less than the risk of transmission within each subtype. The factors affecting HIV-1 entry into the molecular transmission network were occupation, sample source, genotype and drug resistance. The L33F mutation at the HIV-1 resistance mutation site constitutes the interconnection in the largest transmission cluster in the network. The epidemiological characteristics of HIV-infected persons in each molecular transmission cluster show that 97% of the study subjects come from the same area and have a certain spatial aggregation. CONCLUSION: Constructing a molecular transmission network and conducting long-term monitoring, while taking targeted measures to block the spread of HIV can achieve precise prevention and control.


Assuntos
Infecções por HIV/epidemiologia , Infecções por HIV/genética , HIV-1/genética , Doenças Virais Sexualmente Transmissíveis/epidemiologia , Doenças Virais Sexualmente Transmissíveis/genética , Adulto , China/epidemiologia , Feminino , Genótipo , Infecções por HIV/etnologia , Infecções por HIV/transmissão , Comportamentos Relacionados com a Saúde , Humanos , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , RNA Viral , Análise de Sequência de DNA , Doenças Virais Sexualmente Transmissíveis/etnologia , Fatores Socioeconômicos
18.
Nat Commun ; 12(1): 4188, 2021 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-34234121

RESUMO

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.


Assuntos
Proteínas de Bactérias/genética , Infecção Hospitalar/microbiologia , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Tipagem Molecular/métodos , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Conjuntos de Dados como Assunto , Farmacorresistência Bacteriana Múltipla/genética , Monitoramento Epidemiológico , Microbioma Gastrointestinal/genética , Genoma Bacteriano , Humanos , Lactente , Recém-Nascido , Infecções por Klebsiella/diagnóstico , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/patogenicidade , Metagenoma/genética , Epidemiologia Molecular/métodos , Mutação , Filogenia , Software , Virulência/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma , beta-Lactamases/genética
19.
West Afr J Med ; 38(6): 511-519, 2021 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-34174036

RESUMO

BACKGROUND: The Apolipoprotein 1 (APOL1) protein is a product of the human APOL1 gene located on chromosome 22q13.1 and performs functions including lipid transport and metabolism, programmed cell death, autophagy and innate immunity against intracellular pathogens. It is unique among its gene family in its possession of a signal peptide that confers on it the ability for export out of the cell and into the blood stream. The aim of this review is to explore the genetic epidemiology and biology of the APOL1 gene, describe its association with different renal and extra-renal disorders and highlight the timelines of the discoveries of the various associations. METHODS: A literature search was carried out using combination of terms including "apolipoproteins", "apolipoprotein L", "APOL1", "genetics of APOL1", "Chronic Kidney Disease (CKD) and APOL1"," APOL1 and associated diseases" covering the period January 1990 to April 2020. RESULTS: High frequency of the APOL1 gene arose as a result of natural selection in East and West Africa, regions endemic for Trypanosoma brucei infection. High frequencies are also reported among individuals of African ancestry in North America. APOL1 G1 and G2 variants protect against Trypanosoma brucei rhodesiense having overcome their virulence through the serum trypanolytic factor. Although protective against infection from trypanosomes, these alleles have also been shown to increase the risk of several disorders including various forms of chronic kidney diseases, schizophrenia, stroke, cancer, and pre - eclampsia. CONCLUSION: The elucidation of the APOL1 gene has deepened understanding of racial disparities in health and disease. Growing understanding of the genetics and functions of APOL1 has potential to enhance translational benefits for development of new biomarkers, preventive and therapeutic interventions in the context of precision medicine.


Assuntos
Apolipoproteína L1 , Lipoproteínas HDL , África Ocidental , Apolipoproteínas/genética , Humanos , Lipoproteínas HDL/genética , Epidemiologia Molecular
20.
Front Public Health ; 9: 669173, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34095072

RESUMO

Infection by carbapenem-resistant Klebsiella pneumoniae (CRKp) hampers the treatment of elderly patients with lower respiratory tract infection (LRTI); however, relevant data with respect to the characteristics of CRKp in elderly patients with LRTIs are limited. In the present study, K. pneumoniae isolated from elderly patients with LRTIs was collected and identified by VITEK-MS. VITEK 2 compact was used for drug sensitivity test to screen CRKps, and broth dilution method was used for drug sensitivity of tigecycline and colistin. The resistance genes, virulence genes, and serotypes of CRKps were detected via polymerase chain reaction. The homology of CRKps was analyzed via PFGE and MLST. Moreover, plasmid conjugation experiment was carried out to determine the transferability of carbapenem resistance. PCR-based replicon typing (PBRT) and S1 nuclease-PFGE were conducted for plasmid profiling. From January 2019 to August 2019, 258 elderly patients with LRTIs caused by K. pneumoniae were observed; of these, 31 (12.02%) infections were caused by CRKp strains. Majority of the patients were admitted to the intensive care unit and neurosurgery wards. Intracranial hemorrhage and pneumonia were the most common underlying diseases. Furthermore, 29 patients infected by CRKp had been exposed to various antimicrobial drugs before the positive culture. All isolates exhibited high resistance to ß-lactam antibiotics. The predominant carbapenem resistance gene was bla KPC-2, and CRKps carrying bla KPC-2 were all ST11 type. Two bla NDM-5 carrying isolates were assigned to ST307 and ST1562, respectively. Conjugative assays revealed that plasmids harboring bla NDM-5 gene were self-transmissible. Plasmid analysis suggested that two bla NDM-5 were located on a ~45 kb IncX3 type plasmid. The high incidence of CRKp in elderly patients with LRTIs indicates the urgent need for further surveillance and strict infection control measures.


Assuntos
Infecções por Klebsiella , Preparações Farmacêuticas , Infecções Respiratórias , Idoso , Proteínas de Bactérias/genética , Carbapenêmicos/farmacologia , Humanos , Infecções por Klebsiella/tratamento farmacológico , Klebsiella pneumoniae/genética , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Tipagem de Sequências Multilocus , Infecções Respiratórias/tratamento farmacológico , beta-Lactamases/genética
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