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1.
Viruses ; 13(1)2021 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-33430521

RESUMEN

We describe the complete capsid of a genotype C1-like Enterovirus A71 variant recovered from wastewater in a neighborhood in the greater Tempe, Arizona area (Southwest United States) in May 2020 using a pan-enterovirus amplicon-based high-throughput sequencing strategy. The variant seems to have been circulating for over two years, but its sequence has not been documented in that period. As the SARS-CoV-2 pandemic has resulted in changes in health-seeking behavior and overwhelmed pathogen diagnostics, our findings highlight the importance of wastewater-based epidemiology (WBE ) as an early warning system for virus surveillance.


Asunto(s)
Proteínas de la Cápside/genética , Enterovirus Humano A/genética , Enterovirus Humano A/aislamiento & purificación , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Aguas Residuales/virología , Monitoreo Epidemiológico Basado en Aguas Residuales , Arizona/epidemiología , Cápside/química , Infecciones por Enterovirus/epidemiología , Infecciones por Enterovirus/virología , Humanos , Epidemiología Molecular , Pandemias , Filogenia
2.
Arch Virol ; 166(2): 439-449, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33389105

RESUMEN

Chicken infectious anemia (CIA), caused by chicken anemia virus (CAV), is an important immunosuppressive disease that seriously threatens the global poultry industry. Here, we isolated and identified 30 new CAV strains from CAV-positive flocks. The VP1 genes of these strains were sequenced and analyzed at the nucleotide and amino acid levels and were found to have very similar nucleotide sequences (> 97% identity); however, they showed 93.9-100.0% sequence identity to the VP1 genes of 55 reference strains. Furthermore, alignment of the deduced amino acid sequences revealed some unique mutations. Phylogenetic analysis indicated the division of VP1 amino acid sequences into two groups (A and B) and four subgroups (A1, A2, A3 and A4). Interestingly, 22 of the newly isolated strains and some Asian reference strains belonged to the A1 group, whereas the remaining eight new isolates belonged to the A3 group. To evaluate the pathogenicity of the epidemic CAV strains from China, the representative strains CAV-JL16/8901 and CAV-HeN19/3001 and the reference strain Cux-1 were selected for animal experiments. Chickens infected with the isolates and reference strain all showed thymus atrophy and bone marrow yellowing. The mortality rates for CAV-JL16/8901, CAV-HeN19/3001, and the reference strain was 30%, 20%, and 0%, respectively, indicating that the epidemic strains pose a more serious threat to chickens. We not only analyzed the molecular evolution of the epidemic strains but also showed for the first time that the epidemic strains in China are more pathogenic than reference strain Cux-1. Effective measures should be established to prevent the spread of CIA in China.


Asunto(s)
Virus de la Anemia del Pollo/genética , Virus de la Anemia del Pollo/patogenicidad , Pollos/virología , Animales , China , Infecciones por Circoviridae/virología , ADN Viral/genética , Evolución Molecular , Genotipo , Epidemiología Molecular/métodos , Filogenia , Enfermedades de las Aves de Corral/virología , Análisis de Secuencia de ADN/métodos , Virulencia/genética
3.
Arch Virol ; 166(2): 451-460, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33392822

RESUMEN

To investigate the epidemic profile and genetic diversity of porcine bocavirus (PBoV), 281 clinical samples, including 236 intestinal tissue samples and 45 fecal samples were collected from diarrheic piglets on 37 different pig farms in central China, and two SYBR Green I-based quantitative PCR assays were developed to detect PBoV1/2 and PBoV3/4/5, respectively. One hundred forty-eight (52.67%) of the 281 clinical samples were positive for PBoV1/2, 117 (41.63%) were positive for PBoV3/4/5, 55 (19.57%) were positive for both PBoV1/2 and PBoV3/4/5, and 86.49% (32/37) of the pig farms were positive for PBoV. Overall, the prevalence of PBoV was 74.73% (210/281) in central China. Subsequently, nearly full-length genomic sequences of two PBoV strains (designated CH/HNZM and PBoV-TY) from two different farms were determined. Phylogenetic analysis demonstrated that the two PBoV strains obtained in this study belonged to the PBoV G2 group and had a close relationship to 10 other PBoV G2 strains but differed genetically from PBoV G1, PBoV G3, and seven other bocaviruses. CH/HNZM and PBoV-TY were closely related to the PBoV strain GD18 (KJ755666), which may be derived from the PBoV strains 0912/2012 (MH558677) and 57AT-HU (KF206160) through recombination. Compared with reference strain ZJD (HM053694)-China, more amino acid variation was found in the NS1 proteins of CH/HNZM and PBoV-TY. These data extend our understanding of the molecular epidemiology and evolution of PBoV.


Asunto(s)
Bocavirus/genética , Infecciones por Parvoviridae/virología , Enfermedades de los Porcinos/virología , Animales , China , Heces/virología , Variación Genética/genética , Epidemiología Molecular/métodos , Filogenia , Prevalencia , Porcinos
5.
Zhonghua Yu Fang Yi Xue Za Zhi ; 55(1): 78-83, 2021 Jan 06.
Artículo en Chino | MEDLINE | ID: mdl-33455136

RESUMEN

Objective: To analyze the etiological characteristics and molecular epidemiological correlation of five cases of typhoid fever during the same period in yantai city. Methods: Six S. Typhis strains were isolated from 5 typhoid patients and epidemiological samples in Yantai city in 2018. The onset time of the cases were from May 26, 2018 to July 24, 2018, distributed in Shuidao Town of Muping District, Dengzhou Street of Penglai District, Donglai Street of Longkou District, Wenhua Street of Muping District and Fulaishan Street of zhifu District. S. Typhis strains were analyzed by conventional bacterial isolation method and XbaⅠ/BlnⅠ double-enzyme digestion pulse-field gel electrophoresis (PFGE). Meanwhile, ViaB virulence gene detection and 27 common antibiotics sensitivity tests were conducted to study the etiology of S. Typhis. Results: Six strains of S. Typhi were isolated from 5 patients and the domestic egg of one patient, which were divided into 4 PFGE patterns by PFGE-XbaⅠ and PFGE-BlnⅠ and among which 3 strains had the same PFGE patterns.One multi-drug resistant strain (foreign patient), one single-drug resistant strain (patient with a history of provincial retention), and one completely sensitive strain were detected. The three strains of the same PFGE pattern exhibit the same drug-sensitive phenotype which were intermediate against aminoglycosides and quinolones and susceptibility against the other antibiotics.All of the strains carried the ViaB virulence factor except the strain from the foreign patient. Conclusion: Local S. Typhi is susceptibility or intermediate against antibiotics commonly used in clinic.Sporadic cases of typhoid fever and typhoid imported infections still need attention.


Asunto(s)
Fiebre Tifoidea , Antibacterianos/uso terapéutico , Electroforesis en Gel de Campo Pulsado , Humanos , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Salmonella typhi/genética , Fiebre Tifoidea/tratamiento farmacológico , Fiebre Tifoidea/epidemiología
6.
Curr Opin HIV AIDS ; 16(1): 11-24, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33186230

RESUMEN

PURPOSE OF REVIEW: The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics. RECENT FINDINGS: Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges. SUMMARY: Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.


Asunto(s)
/virología , Infecciones por VIH/virología , VIH/genética , /genética , /epidemiología , VIH/clasificación , VIH/aislamiento & purificación , Infecciones por VIH/epidemiología , Humanos , Epidemiología Molecular , Pandemias , /aislamiento & purificación
7.
Nat Microbiol ; 6(1): 112-122, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33349681

RESUMEN

Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.


Asunto(s)
/epidemiología , /genética , Adulto , Anciano , Europa (Continente)/epidemiología , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Filogenia , España/epidemiología , Viaje/estadística & datos numéricos
8.
APMIS ; 129(1): 23-31, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33015856

RESUMEN

Human adenoviruses (HAdVs) are responsible for various clinical diseases. Molecular epidemiological studies of respiratory HAdVs are limited in Turkey. To determine the main genotypes and epidemiological characteristics of HAdVs in patients with respiratory symptoms. HAdV PCR-positive extracts of nasal/nasopharyngeal specimens sent to the Turkish Public Health Institution from various cities of Turkey in 2015-2016 were investigated by seminested PCR. Partial sequence analysis of the hexon gene of HAdVs was performed. SPSSv.24.0 was used. A total of 23/68 (33.82%) HAdV-positive samples were amplified. Mastadenovirus B, C, D, and F were detected and mastadenovirus B (10/23; 43.5%) and C (10/23; 43.5%) were predominant strains. Interestingly, HAdV-F known to have gastrointestinal system tropism was detected in two patients with respiratory symptoms. HAdV-B3 was the most prevalent genotype (9/23; 39.1%). Also, HAdV-B7 is defined as a reemerging pathogen. It is noteworthy that there is a cluster of four HAdV-C strains showing a close paraphyletic relationship with HAdV-2/6 intertypic recombination. To our knowledge, this is the first study showing that HAdV-B7 reemerging pathogen circulating in patients with respiratory infections in our country. It is also necessary to emphasize that HAdV-2/6 recombinant strains were detected in this study for the first time in Turkey.


Asunto(s)
Infecciones por Adenovirus Humanos/virología , Adenovirus Humanos/clasificación , Adenovirus Humanos/genética , Variación Genética , Infecciones del Sistema Respiratorio/virología , Infecciones por Adenovirus Humanos/epidemiología , Adenovirus Humanos/aislamiento & purificación , Adulto , Niño , Preescolar , Femenino , Genotipo , Humanos , Lactante , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Nasofaringe/virología , Filogenia , Reacción en Cadena de la Polimerasa , Infecciones del Sistema Respiratorio/epidemiología , Factores de Riesgo , Análisis de Secuencia de ADN , Turquia/epidemiología
9.
PLoS Negl Trop Dis ; 14(12): e0008979, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33370273

RESUMEN

BACKGROUND: Melioidosis is a neglected tropical disease with rising global public health and clinical importance. Melioidosis is endemic in Southeast Asia and Northern Australia and is of increasing concern in Malaysia. Despite a number of reported studies from Malaysia, these reports are limited to certain parts of the country and do not provide a cohesive link between epidemiology of melioidosis cases and the nation-wide distribution of the causative agent Burkholderia pseudomallei. METHODOLOGY/PRINCIPLE FINDINGS: Here we report on the distribution of B. pseudomallei sequence types (STs) in Malaysia and how the STs are related to STs globally. We obtained 84 culture-confirmed B. pseudomallei from confirmed septicaemic melioidosis patients from all over Malaysia. Prior to performing Multi Locus Sequence Typing, the isolates were subjected to antimicrobial susceptibility testing and detection of the YLF/BTFC genes and BimA allele. Up to 90.5% of the isolates were sensitive to all antimicrobials tested while resistance was observed for antimicrobials typically administered during the eradication stage of treatment. YLF gene cluster and bimABp allele variant were detected in all the isolates. The epidemiological distribution patterns of the Malaysian B. pseudomallei isolates were analysed in silico using phylogenetic tools and compared to Southeast Asian and world-wide isolates. Genotyping of the 84 Malaysian B. pseudomallei isolates revealed 29 different STs of which 6 (7.1%) were novel. ST50 was identified as the group founder followed by subgroup founders ST376, ST211 and ST84. A low-level diversity is noted for the B. pseudomallei isolates described in this study while phylogenetic analysis associated the Malaysian STs to Southeast Asian isolates especially isolates from Thailand. Further analysis also showed a strong association that implicates agriculture and domestication activities as high-risk routes of infection. CONCLUSIONS/SIGNIFICANCE: In conclusion, MLST analysis of B. pseudomallei clinical isolates from all states in Malaysia revealed low diversity and a close association to Southeast Asian isolates.


Asunto(s)
Burkholderia pseudomallei/genética , Burkholderia pseudomallei/aislamiento & purificación , Melioidosis/epidemiología , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Humanos , Malasia/epidemiología , Epidemiología Molecular , Tipificación de Secuencias Multilocus , Análisis de Secuencia de ADN
10.
Viruses ; 12(12)2020 12 14.
Artículo en Inglés | MEDLINE | ID: mdl-33327566

RESUMEN

Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with >1000 cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely sampled from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide "lockdown" (8 March-3 June). These were combined with 460 published SARS-CoV-2 sequences sampled across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy.


Asunto(s)
/epidemiología , Genoma Viral/genética , /genética , /prevención & control , /virología , Variación Genética , Humanos , Italia/epidemiología , Epidemiología Molecular , Filogenia , ARN Viral/genética , /aislamiento & purificación
11.
Biomedica ; 40(Supl. 2): 188-197, 2020 10 30.
Artículo en Inglés, Español | MEDLINE | ID: mdl-33152203

RESUMEN

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.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/epidemiología , Genoma Viral , Difusión de la Información , Epidemiología Molecular/tendencias , Pandemias , Neumonía Viral/epidemiología , Vigilancia de la Población , ARN Viral/genética , Análisis de Secuencia de ARN , Secuencia de Bases , Región del Caribe , Enfermedades Transmisibles Emergentes , Infecciones por Coronavirus/prevención & control , Infecciones por Coronavirus/virología , Planificación en Desastres , Brotes de Enfermedades , Humanos , América Latina/epidemiología , Epidemiología Molecular/métodos , Pandemias/prevención & control , Neumonía Viral/prevención & control , Neumonía Viral/virología , Utilización de Procedimientos y Técnicas , Salud Pública , RNA-Seq , Desarrollo Sostenible , Virosis/epidemiología
12.
Nat Commun ; 11(1): 5558, 2020 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-33144575

RESUMEN

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.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/transmisión , Genoma Viral/genética , Neumonía Viral/epidemiología , Neumonía Viral/transmisión , Infecciones por Coronavirus/prevención & control , Geografía , Humanos , Tamizaje Masivo/métodos , Epidemiología Molecular/métodos , Pandemias/prevención & control , Neumonía Viral/prevención & control , Dispositivos de Protección Respiratoria , Estados Unidos/epidemiología , Wisconsin/epidemiología
13.
BMC Infect Dis ; 20(1): 750, 2020 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-33050903

RESUMEN

BACKGROUND: Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. METHODS: MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. RESULTS: The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. CONCLUSION: The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.


Asunto(s)
Variación Genética , Mycobacterium bovis/genética , Mycobacterium tuberculosis/genética , Tuberculosis Pulmonar/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Alelos , Etiopía/epidemiología , Femenino , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Repeticiones de Minisatélite/genética , Epidemiología Molecular , Reacción en Cadena de la Polimerasa Multiplex , Mycobacterium bovis/aislamiento & purificación , Mycobacterium tuberculosis/aislamiento & purificación , Esputo/microbiología , Tuberculosis Pulmonar/microbiología , Adulto Joven
14.
BMC Res Notes ; 13(1): 497, 2020 Oct 27.
Artículo en Inglés | MEDLINE | ID: mdl-33109270

RESUMEN

OBJECTIVE: Nigeria bears 25% of global malaria burden despite concerted efforts towards its control and elimination. The emergence of drug resistance to first line drugs, artemisinin combination therapies (ACTs), indicates an urgent need for continuous molecular surveillance of drug resistance especially in high burden countries where drug interventions are heavily relied on. This study describes mutations in Plasmodium falciparum genes associated with drug resistance in malaria; Pfk13, Pfmdr1, PfATPase6 and Pfcrt in isolates obtained from 83 symptomatic malaria patients collected in August 2014, aged 1-61 years old from South-west Nigeria. RESULTS: Two Pfmdr1, N86 and Y184 variants were present at a prevalence of 56% and 13.25% of isolates respectively. There was one synonymous (S679S) and two non-synonymous (M699V, S769M) mutations in the PATPase6 gene, while Pfcrt genotype (CVIET), had a prevalence of 45%. The Pfk13 C580Y mutant allele was suspected by allelic discrimination in two samples with mixed genotypes although this could not be validated with independent isolation or additional methods. Our findings call for robust molecular surveillance of antimalarial drug resistance markers in west Africa especially with increased use of antimalarial drugs as prophylaxis for Covid-19.


Asunto(s)
Combinación Arteméter y Lumefantrina/uso terapéutico , ATPasas Transportadoras de Calcio/genética , Malaria Falciparum/tratamiento farmacológico , Proteínas de Transporte de Membrana/genética , Proteínas Asociadas a Resistencia a Múltiples Medicamentos/genética , Mutación , Plasmodium falciparum/efectos de los fármacos , Proteínas Protozoarias/genética , Adolescente , Adulto , Antimaláricos/uso terapéutico , Artemisininas/uso terapéutico , Niño , Preescolar , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/prevención & control , Resistencia a Medicamentos/genética , Femenino , Expresión Génica , Genotipo , Humanos , Lactante , Malaria Falciparum/epidemiología , Malaria Falciparum/parasitología , Persona de Mediana Edad , Epidemiología Molecular , Nigeria/epidemiología , Pandemias/prevención & control , Plasmodium falciparum/genética , Plasmodium falciparum/crecimiento & desarrollo , Neumonía Viral/epidemiología , Neumonía Viral/prevención & control
15.
BMC Infect Dis ; 20(1): 772, 2020 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-33076868

RESUMEN

BACKGROUND: CRF_BC recombinants, including CRF07_BC and CRF08_BC, were considered the predominant subtypes in China. Since the discovery of HIV-1 circulating recombinant form CRF 85_BC in Southwest China in 2016, this BC recombinant forms had been reported in different regions of China. However, the history and magnitude of CRF85_BC transmission were still to be investigated. METHOD: We conducted the most recent molecular epidemiology of HIV-1 among newly reported HIV-1 infected patients in Sichuan in 2019 by sequencing and phylogenetic analysis of 1291 pol sequences. Then, we used maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of pol sequences to reconstruct the phylogeographic and demographic dynamics of the CRF85_BC. RESULTS: HIV-1 CRF85_BC (68/1291, 5.27%) became the fourth most prevalent strain revealing a significant increase in local population. CRF85_BC were only found in heterosexually infected individuals and the majority of CRF85_BC (95.45%) were circulating among the people living with HIV aged 50 years and over (PLHIV50+), suggesting a unique prevalent pattern. The founder lineages of CRF85_BC were likely to have first emerged in Yunnan, a province of Southwest China bordering Sichuan, in the early 2000s. It then spread exponentially to various places (including Guangxi, Sichuan, et al) and became endemic around 2008.6 (2006.7-2010.2) in Sichuan. CONCLUSION: Taken together, our findings on HIV-1 subtype CRF85_BC infections provided new insights into the spread of this virus and extended the understanding of the HIV epidemic in China.


Asunto(s)
Infecciones por VIH/transmisión , Infecciones por VIH/virología , VIH-1/clasificación , Adulto , Teorema de Bayes , China/epidemiología , Epidemias , Femenino , Genotipo , Infecciones por VIH/epidemiología , VIH-1/genética , VIH-1/aislamiento & purificación , Heterosexualidad , Humanos , Funciones de Verosimilitud , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Filogenia , Filogeografía
16.
Zhonghua Yu Fang Yi Xue Za Zhi ; 54(10): 1115-1120, 2020 Oct 06.
Artículo en Chino | MEDLINE | ID: mdl-33115198

RESUMEN

Objective: To understand the detection of group A rotavirus (RVA) in domestic sewage and its molecular epidemiological characteristics, and further explore the feasibility and necessity of RVA environmental surveillance. Methods: From 2016 to 2018, we collected domestic sewage samples monthly in Jinan city, and concentrated them via anion membrane adsorption-elution method. Then RNA extraction and RVA VP7 and VP4 coding region RT-PCR amplification were performed. After purification, TA cloning and sequencing, homology analysis and phylogenetic analysis were conducted on the obtained sequences. Results: RVA G gene was detected in 31 of the 36 sewage samples (86.1% detection rate); RVA P genotype was detected in 33 samples (91.7% detection rate). A total of 536 RVA sequences were obtained, of which 225 G-type sequences belonged to 6 genotypes, and the G9 accounted for 92.4% (208/225); 311 P-type sequences were obtained, which belonged to 4 genotypes. The dominant P[8] accounted for 50.1% (156/311), followed by P[4] with 41.8% (130/311). Phylogenetic analysis shows that there were multiple transmission chains circulating in the dominant genotypes G9 and P[8]. Conclusion: The genotype, homology, and phylogenetic characteristics of sequences obtained from domestic sewage in Jinan area were described, which further confirmeing that RVA environmental surveillance is not feasible but also necessary.


Asunto(s)
Infecciones por Rotavirus , Rotavirus , Antígenos Virales , Proteínas de la Cápside/genética , Heces , Genotipo , Humanos , Epidemiología Molecular , Filogenia , Rotavirus/genética , Infecciones por Rotavirus/epidemiología , Aguas del Alcantarillado
17.
Viruses ; 12(10)2020 10 14.
Artículo en Inglés | MEDLINE | ID: mdl-33066701

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/virología , Neumonía Viral/virología , Betacoronavirus/aislamiento & purificación , Técnicas de Laboratorio Clínico , Infecciones por Coronavirus/diagnóstico , ADN Complementario/análisis , ADN Complementario/genética , ADN Viral/análisis , ADN Viral/genética , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Epidemiología Molecular , Reacción en Cadena de la Polimerasa Multiplex , Pandemias , Neumonía Viral/diagnóstico , ARN Viral/análisis , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Análisis de Secuencia
18.
Sci Rep ; 10(1): 16602, 2020 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-33024144

RESUMEN

The coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global concern. Several SARS-CoV-2 gene mutations have been reported. In the current study associations between SARS-CoV-2 gene variation and exposure history during the first wave of the outbreak in Thailand between January and May 2020 were investigated. Forty samples were collected at different time points during the outbreak, and parts of the SARS-CoV-2 genome sequence were used to assess genomic variation patterns. The phylogenetics of the 40 samples were clustered into L, GH, GR, O and T types. T types were predominant in Bangkok during the first local outbreak centered at a boxing stadium and entertainment venues in March 2020. Imported cases were infected with various types, including L, GH, GR and O. In southern Thailand introductions of different genotypes were identified at different times. No clinical parameters were significantly associated with differences in genotype. The results indicated local transmission (type T, Spike protein (A829T)) and imported cases (types L, GH, GR and O) during the first wave in Thailand. Genetic and epidemiological data may contribute to national policy formulation, transmission tracking and the implementation of measures to control viral spread.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/transmisión , Genoma Viral/genética , Neumonía Viral/epidemiología , Neumonía Viral/transmisión , Secuencia de Bases , Infecciones por Coronavirus/virología , Genotipo , Humanos , Epidemiología Molecular , Mutación , Pandemias , Filogenia , Neumonía Viral/virología , Reacción en Cadena de la Polimerasa/métodos , Polimorfismo de Nucleótido Simple , Tailandia/epidemiología
19.
J Cosmet Sci ; 71(3): 133-148, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33022209

RESUMEN

Many outbreaks of Burkholderia cepacia complex (Bcc) infections are associated with contaminations in personal care products (PCPs). This study aimed to analyze a collection of Bcc isolates in PCPs and assess the susceptibility of preservatives, including dimethoxy dimethyl hydantoin (DMDMH), methylisothiazolinone-chloromethylisothiazolinone (MIT/cMIT), and methyl 4-hydroxybenzoate (MH). The Bcc isolates collected during the 3-year (2015-2017) study period were further examined by biochemical identification system, phylogenetic analysis based on recA nucleotide sequences, and multilocus sequence typing analysis. Preservatives susceptibility testing of Bcc bacteria were evaluated by minimum inhibitory concentration and minimum bactericidal concentration. A total of seven distinct sequence types (STs) were identified, which belonged to four different Bcc species: Burkholderia cenocepacia (ST621, ST258, and novel ST), Burkholderia lata (ST339 and ST336), Burkholderia contaminans (ST482), Burkholderia cepacia (ST922). For DMDMH and MH, the maximum permitted concentrations according to the safety specification of cosmetics (0.6% and 0.4%) were able to inhibit or kill all Bcc strains, but 40% of Bcc isolates could survive at higher than maximum permitted concentrations of MIT/cMIT (of a mixture in the ratio 3:1 of 5-chloro-2-methyl-4-isothiazolin-3-one and 2-methyl-4-isothiazolin-3-one). The PCPs contamination of Bcc strains should be given more attention by manufacturers because of its diversity in molecular epidemiology and its low susceptibility to preservatives such as MIT/cMIT.


Asunto(s)
Complejo Burkholderia cepacia , Cosméticos , Técnicas de Tipificación Bacteriana , Burkholderia , Complejo Burkholderia cepacia/genética , Cosméticos/efectos adversos , Epidemiología Molecular , Filogenia
20.
Curr Biol ; 30(19): R1124-R1130, 2020 10 05.
Artículo en Inglés | MEDLINE | ID: mdl-33022254

RESUMEN

Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these 'microbe hunters' have learned to combine epidemiological information with knowledge of the infectious agent(s). In this essay, I reflect on the evolution of microbe hunting, beginning with the history of pre-germ theory epidemiological studies, through the microbiological and molecular eras. Now in the genomic age, modern-day microbe hunters are combining pathogen whole-genome sequencing with epidemiological data to enhance epidemiological investigations, advance our understanding of the natural history of pathogens and drivers of disease, and ultimately reshape our plans and priorities for global disease control and eradication. Indeed, as we have seen during the ongoing Covid-19 pandemic, the role of microbe hunters is now more important than ever. Despite the advances already made by microbial genomic epidemiology, the field is still maturing, with many more exciting developments on the horizon.


Asunto(s)
Bacterias/genética , Infecciones Bacterianas/diagnóstico , Infecciones Bacterianas/epidemiología , Epidemiología Molecular/métodos , Prevención Primaria/métodos , Bacterias/patogenicidad , Betacoronavirus/genética , Betacoronavirus/patogenicidad , Infecciones por Coronavirus/epidemiología , Genoma Bacteriano/genética , Genoma Viral/genética , Historia del Siglo XIX , Historia del Siglo XX , Humanos , Microbiota/genética , Pandemias , Neumonía Viral/epidemiología
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