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Hamzaoui Z, Ferjani S, Medini I, Charaa L, Landolsi I, Ben Ali R, Khaled W, Chammam S, Abid S, Kanzari L, Ferjani A, Fakhfakh A, Kebaier D, Bouslah Z, Ben Sassi M, Trabelsi S, Boutiba-Ben Boubaker I. Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing. IJID Reg 2024; 11:100356. [PMID: 38655560 PMCID: PMC11035039 DOI: 10.1016/j.ijregi.2024.100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Objectives This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs). Methods SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis. Results A comprehensive analysis of 10,783 viral genomic sequences from six North African countries revealed notable insights. SARS-CoV-2 sampling methods lack standardization, with a majority of countries lacking clear strategies. Over 59% of analyzed genomes lack essential clinical and demographic metadata, including patient age, sex, underlying health conditions, and clinical outcomes, which are essential for comprehensive genomic analysis and epidemiological studies, as submitted to the Global Initiative on Sharing All Influenza Data. Morocco reported the highest number of confirmed COVID-19 cases (1,272,490), whereas Tunisia leads in reported deaths (29,341), emphasizing regional variations in the pandemic's impact. The GRA clade emerged as predominant in North African countries. The lineage analysis showcased a diversity of 190 lineages in Egypt, 26 in Libya, 121 in Tunisia, 90 in Algeria, 146 in Morocco, and 10 in Mauritania. The temporal dynamics of SARS-CoV-2 variants revealed distinct waves driven by different variants. Conclusions This study contributes valuable insights into the genomic landscape of SARS-CoV-2 in North Africa, highlighting the importance of genomic surveillance in understanding viral dynamics and informing public health strategies.
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Affiliation(s)
- Zaineb Hamzaoui
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sana Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ines Medini
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Latifa Charaa
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ichrak Landolsi
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Roua Ben Ali
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Wissal Khaled
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sarra Chammam
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Salma Abid
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Lamia Kanzari
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Asma Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ahmed Fakhfakh
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Dhouha Kebaier
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Zoubeir Bouslah
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
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Reta MA, Said HM, Maningi NE, Wubetu GY, Agonafir M, Fourie PB. Genetic diversity of Mycobacterium tuberculosis strains isolated from spiritual holy water site attendees in Northwest Ethiopia. A cross-sectional study. New Microbes New Infect 2024; 59:101235. [PMID: 38590765 PMCID: PMC11000200 DOI: 10.1016/j.nmni.2024.101235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Background The genetic diversity of Mycobacterium tuberculosis complex (MTBC) strains was characterized among isolates from individuals with pulmonary tuberculosis (PTB) symptoms attended holy water sites (HWSs) in the Amhara region, Ethiopia. Methods A cross-sectional study was done from June 2019 to March 2020 to describe the genetic diversity and drug-resistance profiles of MTBC isolates. Sputum specimens were collected and cultured in the Löwenstein-Jensen culture medium. Line Probe Assay, MTBDRplus VER 2.0, and MTBDRsl VER 2.0 were used to detect first-and second-line anti-TB drug-resistance patterns. A spoligotyping technique was utilized to characterize the genetic diversity. Statistical analysis was performed using STATA 15. Results Of 560 PTB-symptomatic participants, 122 (21.8%) were culture-positive cases. Spoligotyping of 116 isolates revealed diverse MTBC sublineages, with four major lineages: Euro-American (EA) (Lineage 4), East-African-Indian (EAI) (Lineage 3), Ethiopian (ETH) (Lineage 7), East Asian (EA) (Lineage 2). The majority (96.6%) of the isolates were EA (lineage 4) and EAI, with proportions of 54.3% and 42.2%, respectively. A total of 31 spoligotype patterns were identified, 26 of which were documented in the SITVIT2 database. Of these, there were 15 unique spoligotypes, while eleven were grouped with 2-17 isolates. SIT149/T3-ETH (n = 17), SIT26/CAS1-DELHI (n = 16), SIT25/CAS1-DELHI (n = 12), and SIT52/T2 (n = 11) spoligotypes were predominant. A rare spoligotype pattern: SIT41/Turkey and SIT1/Beijing, has also been identified in North Shewa. The overall clustering rate of sub-lineages with known SIT was 76.4%.Of the 122 culture-positive isolates tested, 16.4% were resistant to rifampicin (RIF) and/or isoniazid (INH). Multidrug-resistant TB (MDR-TB) was detected in 12.3% of isolates, five of which were fluoroquinolones (FLQs) resistant. SIT149/T3-ETH and SIT21/CAS1-KILI sublineages showed a higher proportion of drug resistance. Conclusions Diverse MTBC spoligotypes were identified, with the T and CAS families and EA (lineage 4) predominating. A high prevalence of drug-resistant TB, with SIT149/T3-ETH and CAS1-KILI sublineages comprising a greater share, was observed. A study with large sample size and a sequencing method with stronger discriminatory power is warranted to understand better the genetic diversity of circulating MTBC in this cohort of study, which would help to adopt targeted interventions.
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Affiliation(s)
- Melese Abate Reta
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Department of Medical Laboratory Science, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - Halima M. Said
- National Institute for Communicable Diseases (NICD), Centre for Tuberculosis, Johannesburg, South Africa
| | - Nontuthuko Excellent Maningi
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwazulu Natal, Durban, South Africa
| | - Gizachew Yismaw Wubetu
- Amhara Public Health Institute (APHI), Bahir Dar, Ethiopia
- Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mulualem Agonafir
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - P. Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Remesar S, Castro-Scholten S, Morrondo P, Díaz P, Jiménez-Martín D, Muñoz-Fernández L, Fajardo T, Cano-Terriza D, García-Bocanegra I. Occurrence of Anaplasma spp. in wild lagomorphs from Southern Spain: Molecular detection of new Anaplasma bovis lineages. Res Vet Sci 2024; 166:105093. [PMID: 37980815 DOI: 10.1016/j.rvsc.2023.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Wild lagomorphs can act as reservoirs of several pathogens of public and animal health concern. However, the number of studies assessing the presence of Anaplasma spp. in these species is scarce. The aim of the present study was to molecularly identify Anaplasma spp. in wild rabbits (Oryctolagus cuniculus) and Iberian hares (Lepus granatensis) from Southern Spain and assess their epidemiological role in the maintenance of the bacterium. During 2017-2021, spleen samples of 394 wild rabbits and 145 Iberian hares were collected. Anaplasma DNA was detected using different PCR assays (16S rRNA and groEL) and phylogenetic analyses were carried out by Bayesian approach. The possible influence of lagomorph species, age and sex on the prevalence of Anaplasma spp. was evaluated by a multiple logistic regression model. The 9.4% of the rabbits were positive to Anaplasma bovis, but all the hares were negative. No significant differences were found in Anaplasma spp. prevalence regarding to age or sex. This is the first report of A. bovis in lagomorphs from Europe. The phylogenetic analysis of A. bovis confirms the existence of different clusters suggesting the existence of several lineages. In addition, a high divergence of nucleotide identity was observed within the lineage 4, which could result in the under-detection of some strains when using A. bovis-specific PCR, hindering its detection and characterization. Since this analysis is based on a limited number of nucleotide bases and sequences, more studies are needed for further characterize A. bovis, as well as its relationship with other Anaplasma spp.
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Affiliation(s)
- Susana Remesar
- Investigación en Sanidad Animal: Galicia (Grupo INVESAGA), Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Sabrina Castro-Scholten
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Patrocinio Morrondo
- Investigación en Sanidad Animal: Galicia (Grupo INVESAGA), Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Pablo Díaz
- Investigación en Sanidad Animal: Galicia (Grupo INVESAGA), Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Débora Jiménez-Martín
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Leonor Muñoz-Fernández
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Tomás Fajardo
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - David Cano-Terriza
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | - Ignacio García-Bocanegra
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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Afrin SZ, Sathi FA, Nooruzzaman M, Parvin R. Molecular insights into the SARS-CoV-2 Omicron variant from Bangladesh suggest diverse and continuous evolution. Virology 2023; 587:109882. [PMID: 37757731 DOI: 10.1016/j.virol.2023.109882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
The study analyzed the molecular dynamics of the circulating SARS-CoV-2 Omicron variant from its identification in November 2021 to January 2023. The SARS-CoV-2 sequences from Bangladesh revealed three distinct waves of the Omicron variant. More than 50 sub-lineages of Omicron variant were introduced into the country, with the majority belonging to the major lineages of BA.1-like (24.91%), BA.2-like (43.35%), BA.5-like (5.76%), XBB (10.47%), and "Others and Unassigned" (18.64%). Furthermore, the relative frequencies over time revealed that Omicron lineages existed for a short period of time before being replaced by other sub-lineages. Many potential mutations were found in the receptor binding domain of the Spike protein including G339D/H, S371 L/F, K417 N, T478K, E484A, Q493R, Q498R, and N501Y. In conclusion, the SARS-CoV-2 Omicron variant from Bangladesh showed diverse genetic features and continuous evolution. Therefore, the choice of vaccine and monitoring of hospitalized patients is important alongside genetic characterization of the circulating SARS-CoV-2.
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Affiliation(s)
| | - Fardousi Akter Sathi
- Department of Microbiology, Mymensingh Medical College, Mymensingh 2200, Bangladesh
| | - Mohammed Nooruzzaman
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Rokshana Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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Dlamini TC, Mkhize BT, Sydney C, Maningi NE, Malinga LA. Molecular investigations of Mycobacterium tuberculosis genotypes among baseline and follow-up strains circulating in four regions of Eswatini. BMC Infect Dis 2023; 23:566. [PMID: 37644382 PMCID: PMC10466871 DOI: 10.1186/s12879-023-08546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The tuberculosis (TB) epidemic remains a major global health problem and Eswatini is not excluded. Our study investigated the circulating genotypes in Eswatini and compared them at baseline (start of treatment) and follow-up during TB treatment. METHODS Three hundred and ninety (n = 390) participants were prospectively enrolled from referral clinics and patients who met the inclusion criteria, were included in the study. A total of 103 participants provided specimens at baseline and follow-up within six months. Mycobacterium tuberculosis (M.tb) strains were detected by GeneXpert® MTB/RIF assay (Cephied, USA) and Ziehl -Neelsen (ZN) microscopy respectively at baseline and follow-up time-points respectively. The 206 collected specimens were decontaminated and cultured on BACTEC™ MGIT™ 960 Mycobacteria Culture System (Becton Dickinson, USA). Drug sensitivity testing was performed at both baseline and follow-up time points. Spoligotyping was performed on both baseline and follow-up strains after DNA extraction. RESULTS Resistance to at least one first line drug was detected higher at baseline compared to follow-up specimens with most of them developing into multidrug-resistant (MDR)-TB. A total of four lineages and twenty genotypes were detected. The distribution of the lineages varied among the different regions in Eswatini. The Euro-American lineage was the most prevalent with 46.12% (95/206) followed by the East Asian with 24.27% (50/206); Indo-Oceanic at 9.71% (20/206) and Central Asian at 1.94% (4/206). Furthermore, a high proportion of the Beijing genotype at 24.27% (50/206) and S genotype at 16.50% (34/206) were detected. The Beijing genotype was predominant in follow-up specimens collected from the Manzini region with 48.9% (23/47) (p = 0.001). A significant proportion of follow-up specimens developed MDR-TB (p = 0.001) with Beijing being the major genotype in most follow-up specimens (p < 0.000). CONCLUSION Eswatini has a high M.tb genotypic diversity. A significant proportion of the TB infected participants had the Beijing genotype associated with MDR-TB in follow-up specimens and thus indicate community wide transmission.
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Affiliation(s)
- Talent C Dlamini
- Department of Medical Laboratory Sciences, Southern Africa Nazarene University, Manzini, Eswatini.
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa.
| | - Brenda T Mkhize
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa
| | - Clive Sydney
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa
| | | | - Lesibana A Malinga
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Dewi R, Yusoff NA, Abdul Razak SR, Abd Hamid Z. Analysis of self-renewing and differentiation-related microRNAs and transcription factors in multilineage mouse hematopoietic stem/progenitor cells induced by 1,4-benzoquinone. PeerJ 2023; 11:e15608. [PMID: 37456886 PMCID: PMC10340113 DOI: 10.7717/peerj.15608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Background HSPCs are targets for benzene-induced hematotoxicity and leukemogenesis. However, benzene toxicity targeting microRNAs (miRNAs) and transcription factors (TF) that are involve in regulating self-renewing and differentiation of HSPCs comprising of different hematopoietic lineages remains poorly understood. In this study, the effect of a benzene metabolite, 1,4-benzoquinone (1,4-BQ) exposure, in HSPCs focusing on the self-renewing (miRNAs: miR-196b and miR-29a; TF: HoxB4, Bmi-1) and differentiation (miRNAs: miR-181a, TF: GATA3) pathways were investigated. Methods Freshly isolated mouse BM cells were initially exposed to 1,4-BQ at 1.25 to 5 µM for 24 h, followed by miRNAs and TF studies in BM cells. Then, the miRNAs expression was further evaluated in HSPCs of different lineages comprised of myeloid, erythroid and pre-B lymphoid progenitors following 7-14 days of colony forming unit (CFU) assay. Results Exposure to 1,4-BQ in BM cells significantly (p < 0.05) reduced the miR-196b (2.5 and 5 µM), miR-181a (1.25, 2.5 and 5 µM) and miR-29a (1.25 µM) along with upregulation of miR-29a at 2.5 µM. Meanwhile, 1,4-BQ exposure in HSPCs significantly increased the miR-196b expression level (p < 0.05) only in myeloid and pre-B lymphoid progenitors at 2.5 and 5 µM. Significant (p < 0.05) reduction in expression of miR-181a in myeloid (1.25 µM), erythroid (5 µM) progenitors along with miR-29a in myeloid (1.25 µM) and pre-B lymphoid (5 µM) progenitors were noted following exposure to 1,4-BQ. Meanwhile, increased expression of miR-181a was observed in pre-B lymphoid progenitor upon exposure to 1,4-BQ, but only at 5 µM. As for TF studies, expression of HoxB4 protein was significantly increased (p < 0.05) at all 1,4-BQ concentrations as compared to Bmi-1 and GATA3, which were significantly (p < 0.05) elevated starting at 2.5 µM of 1,4-BQ. Conclusion 1,4-BQ induces aberration of miRNAs and transcription factors protein expression that are involved in regulating self-renewing and differentiation pathways of HSPCs. Moreover, epigenetic toxicity as evidenced from the miRNAs expression was found to be mediated by a lineage-driven mechanism. The role of cell lineage in governing the toxicity of 1,4-BQ in HSPCs lineages deserves further investigation.
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Affiliation(s)
- Ramya Dewi
- Biomedical Science Programme and Centre of Diagnostic, Therapeutic and Investigative Science, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
| | - Nur Afizah Yusoff
- Biomedical Science Programme and Centre of Diagnostic, Therapeutic and Investigative Science, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
| | - Siti Razila Abdul Razak
- Oncological and Radiological Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas, Pulau Pinang, Malaysia
| | - Zariyantey Abd Hamid
- Biomedical Science Programme and Centre of Diagnostic, Therapeutic and Investigative Science, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
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Haque R, Hossain ME, Miah M, Rahman M, Amin N, Rahman Z, Islam MS, Rahman MZ. Monitoring SARS-CoV-2 variants in wastewater of Dhaka City, Bangladesh: approach to complement public health surveillance systems. Hum Genomics 2023; 17:58. [PMID: 37420264 PMCID: PMC10326934 DOI: 10.1186/s40246-023-00505-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. RESULTS Out of 504 samples tested in RT-qPCR, 185 (36.7%) tested positive for SARS-CoV-2 viral RNA. The median log10 concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5.2, and the median log10 concentration of ORF1ab was 4.9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28.78 to 32.13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B.1, B.1.1, B.1.1.25, and B.1.617.2, with coverage ranging from 94.2 to 99.8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B.1.1.25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B.1.617.2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. CONCLUSION Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh.
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Affiliation(s)
- Rehnuma Haque
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185, Uppsala, Sweden.
| | - Mohammad Enayet Hossain
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mojnu Miah
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
- Institute for Sustainable Futures, The University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia
| | - Ziaur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Shariful Islam
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
- The School of Public Health, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammed Ziaur Rahman
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
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Otunuga OM, Yu A. Vaccine breakthrough and rebound infections modeling: Analysis for the United States and the ten U.S. HHS regions. Infect Dis Model 2023:S2468-0427(23)00043-X. [PMID: 37361410 PMCID: PMC10234841 DOI: 10.1016/j.idm.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
A vaccine breakthrough infection and a rebound infection cases of COVID-19 are studied and analyzed for the ten U.S. Department of Health and Human Services (HHS) regions and the United States as a nation in this work. An innovative multi-strain susceptible-vaccinated-exposed-asymptomatic-symptomatic-recovered (SVEAIR) epidemic model is developed for this purpose for a population assumed to be susceptible to n-different variants of the disease, and those who are vaccinated and recovered from a specific strain k(k ≤ n) of the disease are immune to present strain and its predecessors j = 1, 2, …, k, but can still be infected by newer emerging strains j = k + 1, k + 2, …, n. The model is used to estimate epidemiological parameters, namely, the latent and infectious periods, the transmission rates, vaccination rates, recovery rates for each of the Delta B.1.617.2, Omicron B.1.1.529, and lineages BA.2, BA.2.12.1, BA.4, BA.5, BA.1.1, BA.4.6, and BA.5.2.6 for the United States and for each of the ten HHS regions. The transmission rate is estimated for both the asymptomatic and symptomatic cases. The effect of vaccines on each strain is analyzed. Condition that guarantees existence of an endemic with certain number of strains is derived and used to describe the endemic state of the population.
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Affiliation(s)
| | - Alexandra Yu
- Department of Mathematics, Augusta University, 1120 15th Str, GE 2018, Augusta, GA, 30912, USA
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9
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Menezes KMF, Dábilla N, Souza M, Damasceno AD, Torres BBJ. Identification of a new polymorphism on the wild-type canine distemper virus genome: could this contribute to vaccine failures? Braz J Microbiol 2023; 54:665-678. [PMID: 37140816 PMCID: PMC10235312 DOI: 10.1007/s42770-023-00971-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/07/2023] [Indexed: 05/05/2023] Open
Abstract
The canine distemper virus (CDV) is responsible for a multisystem infectious disease with high prevalence in dogs and wild carnivores and has vaccination as the main control measure. However, recent studies show an increase in cases including vaccinated dogs in different parts of the world. There are several reasons for vaccine failures, including differences between vaccine strains and wild-type strains. In this study, a phylogenetic analysis of CDV strains from samples of naturally infected, vaccinated, and symptomatic dogs in Goiânia, Goiás, Brazil was performed with partial sequencing of the hemagglutinin (H) gene of CDV. Different sites of amino acid substitutions were found, and one strain had the Y549H mutation, typically present in samples from wild animals. Substitutions in epitopes (residues 367, 376, 379, 381, 386, and 388) that may interfere with the vaccine's ability to provide adequate protection against infection for CDV were observed. The identified strains were grouped in the South America 1/Europe lineage, with a significant difference from other lineages and vaccine strains. Twelve subgenotypes were characterized, considering a nucleotide identity of at least 98% among the strains. These findings highlight the relevance of canine distemper infection and support the need better monitoring of the circulating strains that contribute to elucidate if there is a need for vaccine update.
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Affiliation(s)
| | - Nathânia Dábilla
- Instituto de Patologia Tropical E Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Menira Souza
- Instituto de Patologia Tropical E Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Adilson Donizeti Damasceno
- Escola de Veterinária E Zootecnia, Universidade Federal de Goiás - UFG, Campus II CEP 74690900, Goiânia, GO, Brazil
| | - Bruno Benetti Junta Torres
- Escola de Veterinária E Zootecnia, Universidade Federal de Goiás - UFG, Campus II CEP 74690900, Goiânia, GO, Brazil
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Noorizhab MNF, Zainal Abidin N, Teh LK, Tang TH, Onyejepu N, Kunle-Ope C, Tochukwu NE, Sheshi MA, Nwafor T, Akinwale OP, Ismail AI, Nor NM, Salleh MZ. Exploration of the diversity of multi-drug resistant Mycobacterium tuberculosis complex in Lagos, Nigeria using WGS: Distribution of lineages, drug resistance patterns and genetic mutations. Tuberculosis (Edinb) 2023; 140:102343. [PMID: 37080082 DOI: 10.1016/j.tube.2023.102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/19/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023]
Abstract
Multidrug-resistant (MDR) or extensively drug-resistant (XDR) Tuberculosis (TB) is a major challenge to global TB control. Therefore, accurate tracing of in-country MDR-TB transmission are crucial for the development of optimal TB management strategies. This study aimed to investigate the diversity of MTBC in Nigeria. The lineage and drug-resistance patterns of the clinical MTBC isolates of TB patients in Southwestern region of Nigeria were determined using the WGS approach. The phenotypic DST of the isolates was determined for nine anti-TB drugs. The sequencing achieved average genome coverage of 65.99X. The most represented lineages were L4 (n = 52, 83%), L1 (n = 8, 12%), L2 (n = 2, 3%) and L5 (n = 1, 2%), suggesting a diversified MTB population. In term of detection of M/XDR-TB, while mutations in katG and rpoB genes are the strong predictors for the presence of M/XDR-TB, the current study also found the lack of good genetic markers for drug resistance amongst the MTBC in Nigeria which may pose greater problems on local tuberculosis management efforts. This high-resolution molecular epidemiological data provides valuable insights into the mechanistic for M/XDR TB in Lagos, Nigeria.
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Affiliation(s)
- Mohd Nur Fakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Norzuliana Zainal Abidin
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Thean Hock Tang
- Advance Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Nneka Onyejepu
- Microbiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Chioma Kunle-Ope
- Microbiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Nwanneka E Tochukwu
- Microbiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | | | - Timothy Nwafor
- Public Health and Epidemiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Olaoluwa P Akinwale
- Public Health and Epidemiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria.
| | | | - Norazmi Mohd Nor
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia.
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Kandimalla P, Omoto JJ, Hong EJ, Hartenstein V. Lineages to circuits: the developmental and evolutionary architecture of information channels into the central complex. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2023:10.1007/s00359-023-01616-y. [PMID: 36932234 DOI: 10.1007/s00359-023-01616-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 03/19/2023]
Abstract
The representation and integration of internal and external cues is crucial for any organism to execute appropriate behaviors. In insects, a highly conserved region of the brain, the central complex (CX), functions in the representation of spatial information and behavioral states, as well as the transformation of this information into desired navigational commands. How does this relatively invariant structure enable the incorporation of information from the diversity of anatomical, behavioral, and ecological niches occupied by insects? Here, we examine the input channels to the CX in the context of their development and evolution. Insect brains develop from ~ 100 neuroblasts per hemisphere that divide systematically to form "lineages" of sister neurons, that project to their target neuropils along anatomically characteristic tracts. Overlaying this developmental tract information onto the recently generated Drosophila "hemibrain" connectome and integrating this information with the anatomical and physiological recording of neurons in other species, we observe neuropil and lineage-specific innervation, connectivity, and activity profiles in CX input channels. We posit that the proliferative potential of neuroblasts and the lineage-based architecture of information channels enable the modification of neural networks across existing, novel, and deprecated modalities in a species-specific manner, thus forming the substrate for the evolution and diversification of insect navigational circuits.
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Affiliation(s)
- Pratyush Kandimalla
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. .,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
| | - Jaison Jiro Omoto
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Elizabeth J Hong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
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12
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Becker AS, Silva Júnior JVJ, Weiblen R, Flores EF. An appraisal of gene targets for phylogenetic classification of canine distemper virus: Is the hemagglutinin the best candidate? Virus Res 2023; 325:199043. [PMID: 36634899 DOI: 10.1016/j.virusres.2023.199043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
Sequence analysis of the canine distemper virus (CDV) hemagglutinin (H) gene may provide important insights on virus-host interactions and has also been frequently used for CDV phylogenetic classification. Herein, we performed an in silico analysis of CDV complete genomes (CGs) available in GenBank in order to investigate the suitability of H for CDV classification into lineages/genotypes. In addition, we analyzed the other viral genes for their potential use in CDV classification. Initially, we collected 116 CDV CGs from GenBank and compared their phylogenetic classification with that of their respective H nucleotide (nt) and amino acid (aa) sequences. Subsequently, we calculated the geodesic distance between the CG and H phylogenetic trees. These analyses were later performed with other CDV genes. All CDV CGs were also evaluated for possible recombination events. Nucleotide and aa analyses of H misclassified some Vaccine/America 1/Asia 3 lineage sequences compared to CG analysis, finding supported by both Maximum Likelihood (ML) and Bayesian Markov Chain Monte Carlo (B-MCMC) methods. Moreover, aa-based H analysis showed additional disagreements with the classification obtained by CG. The geodesic distance between the H and CG trees was 0.0680. Strong recombination signals were identified in the H gene, including Vaccine/America 1/Asia 3 lineage sequences. In contrast, C and P were the only genes that fully reproduced the CG classification (by ML and/or B-MCMC) and that did not show strong recombination signals. Furthermore, the P phylogenetic tree showed the lowest geodesic distance from the CG tree (0.0369). These findings suggest C and P as potential targets for CDV phylogenetic classification, especially when full genome sequencing is not possible. Finally, since our results were obtained considering the CDV CGs available to date, future analyses performed as more CDV sequences become available will be useful to assess probable issues of H-based phylogeny and to consolidate the suitability of the C and P genes for CDV classification.
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Affiliation(s)
- Alice Silveira Becker
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - José Valter Joaquim Silva Júnior
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Setor de Virologia, Instituto Keizo Asami, Universidade Federal de Pernambuco, Pernambuco, Brazil; Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
| | - Rudi Weiblen
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Eduardo Furtado Flores
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
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Morey-León G, Andrade-Molina D, Fernández-Cadena JC, Berná L. Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador. BMC Genomics 2022; 23:844. [PMID: 36544084 PMCID: PMC9769008 DOI: 10.1186/s12864-022-09042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. RESULTS Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. CONCLUSION This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.
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Affiliation(s)
- Gabriel Morey-León
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.442157.10000 0001 1183 0630Universidad de Guayaquil, Guayaquil, Ecuador ,grid.442156.00000 0000 9557 7590Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Derly Andrade-Molina
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Juan Carlos Fernández-Cadena
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Luisa Berná
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.11630.350000000121657640Facultad de Ciencias, Unidad de Genómica Evolutiva, Universidad de La República, Montevideo, Uruguay
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Rodríguez-Aguilar ED, Martínez-Barnetche J, Rodríguez MH. Three highly variable genome regions of the four dengue virus serotypes can accurately recapitulate the CDS phylogeny. MethodsX 2022; 9:101859. [PMID: 36187156 PMCID: PMC9516459 DOI: 10.1016/j.mex.2022.101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/10/2022] [Indexed: 11/18/2022] Open
Abstract
The circulation of the four-dengue virus (DENV) serotypes has significantly increased in recent years, accompanied by an increase in viral genetic diversity. In order to conduct disease surveillance and understand DENV evolution and its effects on virus transmission and disease, efficient and accurate methods for phylogenetic classification are required. Phylogenetic analysis of different viral genes sequences is the most used method, the envelope gene (E) being the most frequently selected target. We explored the genetic variability of the four DENV serotypes throughout their complete coding sequence (CDS) of sequences available in GenBank and used genomic regions of different variability rate to recapitulate the phylogeny obtained with the DENV CDS. Our results indicate that the use of high or low variable regions accurately recapitulate the phylogeny obtained with CDS of sequences from different DENV genotypes. However, when analyzing the phylogeny of a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny. The use of three concatenated highly variable regions was not statistically different in distance branch length and support to that obtained in CDS phylogeny.•This study demonstrated the ability of highly variable regions of the DENV genome to recapitulate the phylogeny obtained with the full coding sequence (CDS).•The use of genomic regions of high or low variability did not affect the performance in recapitulating the phylogeny obtained with CDS from different genotypes. However, when phylogeny was analyzed for sequences from a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny.•The use of concatenated highly variable genome regions represent a useful option for recapitulating genome-wide phylogenies in analyses of sequences belonging to the same DENV genotype.
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Kolk M, Skirbekk V. Fading family lines- women and men without children, grandchildren and great-grandchildren in 19th, 20th and 21st Century Northern Sweden. Adv Life Course Res 2022; 53:100481. [PMID: 36652207 DOI: 10.1016/j.alcr.2022.100481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 04/14/2022] [Accepted: 05/21/2022] [Indexed: 06/17/2023]
Abstract
We studied to what extent family lines die out over the course of 122 years based on Swedish population-level data. Our data included demographic and socioeconomic information for four generations in the Skellefteå region of northern Sweden from 1885 to 2007. The first generation in our sample consisted of men and women born between 1885 and 1899 (N = 5850), and we observed their children, grandchildren, and great-grandchildren. We found that 48% of the first generation did not have any living descendants (great-grandchildren) by 2007. The risk of a family line dying out within the four-generational framework was highest among those who had relatively low fertility in the first generation. Mortality during reproductive years was also a leading reason why individuals in the first generation ended up with a greater risk of not leaving descendants. We identified socioeconomic differences: both the highest-status and the lowest-status occupational groups saw an increased risk of not leaving any descendants. Almost all lineages that made it to the third generation also made it to the fourth generation.
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Affiliation(s)
- Martin Kolk
- Dept.of Sociology, Demography Unit, Stockholm University, Stockholm, Sweden; Center for the Study of Cultural Evolution, Stockholm University, Stockholm, Sweden; Institute for Future Studies, Stockholm, Sweden; Åbo Akademi, Vasa, Finland.
| | - Vegard Skirbekk
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Columbia aging Center, Mailman School of Public Health, Columbia University, NY, USA
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Mutayoba BK, Michael Hoelscher, Heinrich N, Joloba ML, Lyamuya E, Kilale AM, Range NS, Ngowi BJ, Ntinginya NE, Mfaume SM, Wilfred A, Doulla B, Lyimo J, Kisonga R, Kingalu A, Kabahita JM, Guido O, Kabugo J, Adam I, Luutu M, Namaganda MM, Namutebi J, Kasule GW, Nakato H, Byabajungu H, Lutaaya P, Musisi K, Oola D, Mboowa G, Pletschette M. Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania. BMC Genomics 2022; 23:561. [PMID: 35931954 PMCID: PMC9356438 DOI: 10.1186/s12864-022-08791-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome sequencing (WGS) has emerged as a new diagnostic tool to reliably inform the occurrence of phylogenetic lineages of Mycobacterium tuberculosis and examine their relationship with patient demographic characteristics and multidrug-resistance development. METHODS 191 Mycobacterium tuberculosis isolates obtained from a 2017/2018 Tanzanian drug resistance survey were sequenced on the Illumina Miseq platform at Supranational Tuberculosis Reference Laboratory in Uganda. Obtained fast-q files were imported into tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5). Additionally for phylogenetic tree construction, RaxML-NG v1.0.3(25) was used to generate a maximum likelihood phylogeny with 800 bootstrap replicates. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4 RESULTS: Most [172(90.0%)] of the isolates were from newly treated Pulmonary TB patients. Coinfection with HIV was observed in 33(17.3%) TB patients. Of the 191 isolates, 22(11.5%) were resistant to one or more commonly used first line anti-TB drugs (FLD), 9(4.7%) isolates were MDR-TB while 3(1.6%) were resistant to all the drugs. Of the 24 isolates with any resistance conferring mutations, 13(54.2%) and 10(41.6%) had mutations in genes associated with resistance to INH and RIF respectively. The findings also show four major lineages i.e. Lineage 3[81 (42.4%)], followed by Lineage 4 [74 (38.7%)], the Lineage 1 [23 (12.0%)] and Lineages 2 [13 (6.8%)] circulaing in Tanzania. CONCLUSION The findings in this study show that Lineage 3 is the most prevalent lineage in Tanzania whereas drug resistant mutations were more frequent among isolates that belonged to Lineage 4.
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Affiliation(s)
- Beatrice Kemilembe Mutayoba
- Department of Preventive Services, Ministry of Health, Dodoma, Tanzania.
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany.
| | - Michael Hoelscher
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany
| | - Norbert Heinrich
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany
| | - Moses L Joloba
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eligius Lyamuya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Andrew Martin Kilale
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Nyagosya Segere Range
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Bernard James Ngowi
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- University of Dar Es Salaam, Mbeya College of Health and Allied Sciences, Mbeya, Tanzania
| | | | - Saidi Mwinjuma Mfaume
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Amani Wilfred
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Basra Doulla
- Central Tuberculosis Reference Laboratory, Ministry of Health, National TB and Leprosy Programme, Dar es Salaam, Tanzania
| | - Johnson Lyimo
- Department of Preventive Services, Ministry of Health, National Tuberculosis and Leprosy Programme, Dodoma, Tanzania
| | - Riziki Kisonga
- Department of Preventive Services, Ministry of Health, National Tuberculosis and Leprosy Programme, Dodoma, Tanzania
| | - Amri Kingalu
- Central Tuberculosis Reference Laboratory, Ministry of Health, National TB and Leprosy Programme, Dar es Salaam, Tanzania
| | - Jupiter Marina Kabahita
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Ocung Guido
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Joel Kabugo
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Isa Adam
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Moses Luutu
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Maria Magdalene Namaganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Joanitah Namutebi
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - George William Kasule
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Hasfah Nakato
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Henry Byabajungu
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Pius Lutaaya
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Kenneth Musisi
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Denis Oola
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention, African Union Commission, Addis Ababa, Ethiopia
| | - Michel Pletschette
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany
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González AD, Lotta-Arevalo I, Fuentes-Rodríguez GA, Macías-Zacipa J, Acevedo-Cendales LD, Matta NE. Is Haemoproteus gabaldoni a valid species? An approach from morphology and molecular tools applied to parasites of Anseriformes. Acta Trop 2022; 233:106540. [PMID: 35623401 DOI: 10.1016/j.actatropica.2022.106540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022]
Abstract
Currently, there are three recognized species of haemoproteids infecting Anseriformes: Haemoproteus nettionis, H. macrovacuolatus, and H. greineri. Unfortunately, genetic information associated with a morphotype is available only for H. macrovacuolatus. We recently found a parasite morphologically compatible with Haemoproteus gabaldoni, a species Bennet (1993) described in a Cairina moschata (Muscovy duck) from Venezuela. This species was synonymized to H. nettionis by Valkiūnas (2005), arguing not enough morphological differentiation between them; it was said that H. greineri could be as well a synonym of H. nettionis. In this study, we aimed to provide evidence to determine if Haemoproteus gabaldoni is a different species of H. nettionis and help to clarify other species status. We first performed morphological and morphometrical analyses and compared this information against the parahapantotypes of H. greineri, H. gabaldoni and material diagnosed as H. nettionis provided by the International Reference center for Avian Haematozoa (IRCAH), and H. macrovacuolatus from the Host-Parasite Relationship Study Group (GERPH, in Spanish Grupo de Estudio Relación Parásito Hospedero) biological collection. We used Principal Component Analysis (PCA) of dimensionless standard morphometrical variables from gametocytes. Furthermore, we amplified a small fragment of cytochrome b (cyt b) to compare the sequence with information in GenBank and Malavi through phylogenetic analyses and haplotype networks. PCA analyses revealed the presence of three distinct groups in the samples studied, supported in the morphological traits of each parasite species analyzed; phylogenetic analyses grouped parasite lineages separately according to the host and continent of provenance. Such results indicate that, H. gabaldoni, is a different species from H. nettionis. One more time, it is demonstrated the importance of linking barcode surveys to morphological studies. Finally, it is highlighted the importance of biological collections as repositories of worldwide biodiversity.
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Affiliation(s)
- Angie D González
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia.
| | - Ingrid Lotta-Arevalo
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia
| | - Gustavo A Fuentes-Rodríguez
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia; Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Sede, Bogotá, Colombia
| | - Jhon Macías-Zacipa
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia; Programa Bacteriología y Laboratorio Clínico, Facultad de Ciencias de la Salud, Universidad Colegio Mayor de Cundinamarca, Bogotá, Colombia
| | | | - Nubia E Matta
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia
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Tejashree A, Mahesh PA, Krishna Karthik M, Azeem A, Reddy RHR, Ravichandra C, Nagaraja SB. Era of TB elimination: Growing need to understand diversities of Mycobacterium tuberculosis lineages! Indian J Tuberc 2022; 69:79-84. [PMID: 35074155 DOI: 10.1016/j.ijtb.2021.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 06/14/2023]
Abstract
INTRODUCTION The mycobacterium tuberculosis complex (MTBC) has highly clonal population structure which made the organism spread globally mirroring human migration out of Africa and resulted in the formation of seven lineages. We conducted this study to determine the proportion of spoligotype lineages and drug susceptibility profile of Mycobacterium tuberculosis isolates among smear positive TB patients attending a tertiary care hospital in Mysore, Karnataka, India. METHODS It is a descriptive study conducted at JSS Hospital a tertiary care centre at Mysore, India during 2018-19. The sputum smear positive samples were subjected to solid culture and drug susceptibility testing and spoligotyping for identification of lineages. RESULTS Of the 100 samples which were culture positive, 94 isolates were clustered into five spoligotype international types with SIT-126 (EAI-5) being the largest cluster of 46 (46%) isolates, followed by SIT-62 (H1) with 24 (24%), SIT -26 (CAS 1-DELHI) with 20 (20%), SIT-53 (T1) with 03 (3%) and SIT-482 (BOV-1) with 01 (1%). Among the remaining six isolates, two had unique Cameroon spoligotypes and four were orphans CONCLUSION: The study finding reveals that a diverse pattern of genotypes is circulating in the region of which EAI-5, Harleem (H1) and CAS-DELHI pattern forms the majority (88%). It is evident that there is a wide range of MTB genetic lineages in circulation and further research is needed to understand the diversity across the country.
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Affiliation(s)
- A Tejashree
- Department of Microbiology, JSS Medical College and Hospital, JSSAHER, Mysore, India.
| | - P A Mahesh
- Department of Pulmonology, JSS Medical College and Hospital, JSSAHER, Mysore, India
| | - M Krishna Karthik
- Department of Microbiology, JSS Medical College and Hospital, JSSAHER, Mysore, India
| | - Abdul Azeem
- State TB Demonstration Centre, Intermediate Reference Laboratory, Bengaluru, India
| | - Raveendra H R Reddy
- Department of Community Medicine, Vydehi Institute of Medical Sciences, Bengaluru, India
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19
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Muñoz M, Patiño LH, Ballesteros N, Castañeda S, Luna N, Delgado L, Hernandez-Pereira C, Shaban MV, Muñoz SA, Paniz-Mondolfi A, Ramírez JD. Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources. One Health 2021; 14:100363. [PMID: 34931174 PMCID: PMC8673956 DOI: 10.1016/j.onehlt.2021.100363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/18/2022] Open
Abstract
Due to the necessity to control human-to-human spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the overwhelming majority of the generated data on this virus was solely related to the genomic characteristics of strains infecting humans; conversely, this work aimed to recover and analyze the diversity of viral genomes from non-human sources. From a set of 3595 publicly available SARS-CoV-2 genome sequences, 128 lineages were identified in non-human hosts, the majority represented by the variants of concern Delta (n = 1105, 30.7%) and Alpha (n = 466, 12.9%), followed by B.1.1.298 lineage (n = 458, 12.7%). Environment, Neovison vison, Odocoileus virginianus and Felis catus were the non-human sources with the highest number of lineages (14, 12 and 10, respectively). Phylogenomic analyses showed viral clusters from environmental sources, N. vison, O. virginianus, Panthera tigris, and Panthera leo. These clusters were collectively related to human viruses as well as all other non-human sources that were heterogeneously distributed in the phylogenetic tree. Further, the genetic details of viral genomes from bats and pangolins were independently investigated owing to their high divergence, revealing five distinct clusters. Cluster 4 exclusively included bat-sourced genomes and the SARS-CoV-2 reference strain Wuhan-01. In summary, this study identified new genetic landmarks of SARS-CoV-2 evolution. We propose potential interspecies transmission routes of SARS-CoV-2 between animals and humans, which should be considered in order to establish better pathogen surveillance and containment strategies.
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Affiliation(s)
- Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolás Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lourdes Delgado
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Carlos Hernandez-Pereira
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Maryia V Shaban
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Shirly Alexandra Muñoz
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia.,Unidad de Salud de Ibagué (USI) E.S.E., Ibagué, Colombia
| | - Alberto Paniz-Mondolfi
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela.,Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
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20
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Gupta D, Sharma P, Singh M, Kumar M, Ethayathulla AS, Kaur P. Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants. Cell Mol Life Sci 2021; 78:7967-7989. [PMID: 34731254 PMCID: PMC11073194 DOI: 10.1007/s00018-021-04008-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023]
Abstract
Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India.
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21
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Fatihi S, Rathore S, Pathak AK, Gahlot D, Mukerji M, Jatana N, Thukral L. A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Curr Res Struct Biol 2021; 3:290-300. [PMID: 34806033 PMCID: PMC8590475 DOI: 10.1016/j.crstbi.2021.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
The recent release of SARS-CoV-2 genomic data from several countries has provided clues into the potential antigenic drift of the coronavirus population. In particular, the genomic instability observed in the spike protein necessitates immediate action and further exploration in the context of viral-host interactions. By temporally tracking 527,988 SARS-CoV-2 genomes, we identified invariant and hypervariable regions within the spike protein. We evaluated combination of mutations from SARS-CoV-2 lineages and found that maximum number of lineage-defining mutations were present in the N-terminal domain (NTD). Based on mutant 3D-structural models of known Variants of Concern (VOCs), we found that structural properties such as accessibility, secondary structural type, and intra-protein interactions at local mutation sites are greatly altered. Further, we observed significant differences between intra-protein networks of wild-type and Delta mutant, with the latter showing dense intra-protein contacts. Extensive molecular dynamics simulations of D614G mutant spike structure with hACE2 further revealed dynamic features with 47.7% of mutations mapping on flexible regions of spike protein. Thus, we propose that significant changes within spike protein structure have occurred that may impact SARS-CoV-2 pathogenesis, and repositioning of vaccine candidates is required to contain the spread of COVID-19 pathogen.
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Affiliation(s)
- Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Surabhi Rathore
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Ankit K. Pathak
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
| | - Deepanshi Gahlot
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Nidhi Jatana
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
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22
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Mohamad Noordin N, Tan JL, Chong CK, Chem YK, Tajudin N, Abu Bakar RS, Sengol S, Phoon HYP, Che Azid NAM, W Mohd Arifin WNA, Aziz ZA, Hussin H, Ibrahim NS, Omar A, Ravi U, Kamarul Zaman KH, Yamin MA, Ngeow YF. Genomic diversity of SARS-CoV-2 in Malaysia. PeerJ 2021; 9:e12449. [PMID: 34760404 PMCID: PMC8571957 DOI: 10.7717/peerj.12449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Background More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. Methods We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. Results We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10-4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. Conclusion The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health.
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Affiliation(s)
- Noorliza Mohamad Noordin
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Joon Liang Tan
- Faculty of Information Science and Technology, Multimedia University, Melaka, Melaka, Malaysia
| | | | - Yu Kie Chem
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Norazimah Tajudin
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Rehan Shuhada Abu Bakar
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Selvanesan Sengol
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Hannah Yik Phing Phoon
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | | | | | - Zirwatul Adilah Aziz
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Hani Hussin
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Nurul Syahida Ibrahim
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Aziyati Omar
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Ushananthiny Ravi
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | | | - Mohd Asri Yamin
- National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, Malaysia
| | - Yun Fong Ngeow
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Selangor, Malaysia.,Center for Research on Communincable Diseases, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Selangor, Malaysia
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23
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González-Candelas F, Shaw MA, Phan T, Kulkarni-Kale U, Paraskevis D, Luciani F, Kimura H, Sironi M. One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages. Infect Genet Evol 2021; 92:104869. [PMID: 33915216 PMCID: PMC8074502 DOI: 10.1016/j.meegid.2021.104869] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/17/2021] [Accepted: 04/21/2021] [Indexed: 12/19/2022]
Abstract
The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.
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Affiliation(s)
- Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio) and CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Tung Phan
- Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Fabio Luciani
- University of New South Wales, Sydney 2052, New South Wales, Australia
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School, Takasaki, Gunma 370-0006, Japan
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS E. MEDEA, Bosisio Parini (LC), Italy.
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Guevara Andino JE, Pitman NCA, Ter Steege H, Peralvo M, Cerón C, Fine PVA. The contribution of environmental and dispersal filters on phylogenetic and taxonomic beta diversity patterns in Amazonian tree communities. Oecologia 2021; 196:1119-37. [PMID: 34324078 DOI: 10.1007/s00442-021-04981-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 06/28/2021] [Indexed: 10/28/2022]
Abstract
Environmental and dispersal filters are key determinants of species distributions of Amazonian tree communities. However, a comprehensive analysis of the role of environmental and dispersal filters is needed to understand the ecological and evolutionary processes that drive phylogenetic and taxonomic turnover of Amazonian tree communities. We compare measures of taxonomic and phylogenetic beta diversity in 41 one-hectare plots to test the relative importance of climate, soils, geology, geomorphology, pure spatial variables and the spatial variation of environmental drivers of phylogenetic and taxonomic turnover in Ecuadorian Amazon tree communities. We found low phylogenetic and high taxonomic turnover with respect to environmental and dispersal filters. In addition, our results suggest that climate is a significantly better predictor of phylogenetic turnover and taxonomic turnover than geomorphology and soils at all spatial scales. The influence of climate as a predictor of phylogenetic turnover was stronger at broader spatial scales (50 km2) whereas geomorphology and soils appear to be better predictors of taxonomic turnover at mid (5 km2) and fine spatial scales (0.5 km2) but a weak predictor of phylogenetic turnover at broad spatial scales. We also found that the combined effect of geomorphology and soils was significantly higher for taxonomic turnover at all spatial scales but not for phylogenetic turnover at large spatial scales. Geographic distances as proxy of dispersal limitation was a better predictor of phylogenetic turnover at distances of 50 < 500 km. Our findings suggest that climatic variation at regional scales can better predict phylogenetic and taxonomic turnover than geomorphology and soils.
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25
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Patiño LH, Ballesteros N, Muñoz M, Castañeda S, Hernández C, Gomez S, Florez C, Rico A, Pardo L, Hernandez-Pereira CE, Delgado-Noguera L, Grillet ME, Hernandez MM, Khan Z, van de Guchte A, Dutta J, Gonzalez-Reiche AS, Simon V, van Bakel H, Sordillo EM, Ramírez JD, Paniz-Mondolfi AE. SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia. Int J Infect Dis 2021; 110:410-416. [PMID: 34333122 PMCID: PMC10130730 DOI: 10.1016/j.ijid.2021.07.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/30/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To evaluate the genomic epidemiology of SARS-CoV-2 from Venezuelan migrants living in Colombia. METHODS This study sequenced SARS-CoV-2 from 30 clinical specimens collected from Venezuelan migrants. Genomes were compared with the Wuhan reference genome to identify polymorphisms, reconstruct phylogenetic relationships and perform comparative genomic analyses. Geographic, sociodemographic and clinical data were also studied across genotypes. RESULTS This study demonstrated the presence of six distinct SARS-CoV-2 lineages circulating among Venezuelan migrants, as well as a close relationship between SARS-CoV-2 genomic sequences obtained from individuals living in the Venezuelan-Colombian border regions of La Guajira (Colombia) and Zulia (Venezuela). Three clusters (C-1, C-2 and C-3) were well supported by phylogenomic inference, supporting the hypothesis of three potential transmission routes across the Colombian-Venezuelan border. These genomes included point mutations previously associated with increased infectivity. A mutation (L18F) in the N-terminal domain of the spike protein that has been associated with compromised binding of neutralizing antibodies was found in 2 of 30 (6.6%) genomes. A statistically significant association was identified with symptomatology for cluster C2. CONCLUSION The close phylogenetic relationships between SARS-CoV-2 genomes from Venezuelan migrants and from people living at the Venezuela-Colombian border support the importance of human movements for the spread of COVID-19 and for emerging virus variants.
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Affiliation(s)
- Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Hernández
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | | | | | | | | | - Carlos E Hernandez-Pereira
- Instituto de Investigaciones Biomédicas IDB/Emerging Pathogens Network-Incubadora Venezolana de la Ciencia, Cabudare, Venezuela
| | - Lourdes Delgado-Noguera
- Instituto de Investigaciones Biomédicas IDB/Emerging Pathogens Network-Incubadora Venezolana de la Ciencia, Cabudare, Venezuela
| | - Maria E Grillet
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; St. Luke's-Roosevelt Institute for Health Sciences, Mount Sinai Health System, New York, NY, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
| | - Alberto E Paniz-Mondolfi
- Instituto de Investigaciones Biomédicas IDB/Emerging Pathogens Network-Incubadora Venezolana de la Ciencia, Cabudare, Venezuela; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Cella E, Benedetti F, Fabris S, Borsetti A, Pezzuto A, Ciotti M, Pascarella S, Ceccarelli G, Zella D, Ciccozzi M, Giovanetti M. SARS-CoV-2 Lineages and Sub-Lineages Circulating Worldwide: A Dynamic Overview. Chemotherapy 2021; 66:3-7. [PMID: 33735881 PMCID: PMC8089399 DOI: 10.1159/000515340] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/28/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China, in early December 2019 has rapidly widespread worldwide, becoming one of the major global public health issues of the last centuries. Key Messages: Over the course of the pandemic, due to the advanced whole-genome sequencing technologies, an unprecedented amount of genomes have been generated, providing invaluable insights into the ongoing evolution and epidemiology of the virus during the pandemic. Therefore, this large amount of data played an important role in the SARS-CoV-2 mitigation and control strategies. Key Messages: The active monitoring and characterization of the SARS-CoV-2 lineages circulating worldwide is useful for a more specific diagnosis, better care, and timely treatment. In this review, a concise characterization of all the lineages and sub-lineages circulating and co-circulating across the world has been presented in order to determine the magnitude of the SARS-CoV-2 threat and to better understand the virus genetic diversity and its dispersion dynamics.
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Affiliation(s)
- Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Silvia Fabris
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | | | - Aldo Pezzuto
- Cardiovascular-Respiratory Sciences Department, Sant' Andrea Hospital-Sapienza Università, Rome, Italy
| | - Marco Ciotti
- Dipartimento di Scienze Biochimiche e Centro di Biologia Molecolare del Consiglio Nazionale delle Ricerche, Università La Sapienza, Roma, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli,” University of Rome “La Sapienza,”, Rome, Italy
| | - Giancarlo Ceccarelli
- Dipartimento di Salute Pubblica e Malattie Infettive, Policlinico Umberto I Università “Sapienza,”, Rome, Italy
| | - Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Moe Sann WW, Namwat W, Faksri K, Swe TL, Swe KK, Thwin T, Sangka A. Genetic diversity of Mycobacterium tuberculosis using 24-locus MIRU-VNTR typing and Spoligotyping in Upper Myanmar. J Infect Dev Ctries 2020; 14:1296-1305. [PMID: 33296343 DOI: 10.3855/jidc.12998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/30/2020] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION MIRU-VNTR typing and Spoligotyping are the useful molecular tools for TB epidemiology study. Information regarding genetic diversity and tuberculosis (TB) transmission in Upper Myanmar only is scares. METHODOLOGY We determined the genetic diversity of Mycobacterium tuberculosis (Mtb) and TB transmission from Upper Myanmar TB Reference Laboratory, Mandalay Region, including Mandalay (72), Shan (22), Magway (15), Sagaing (13), Nay Pyi Taw (8), Kachin (7), Chin (2) and Kayah (1). One hundred and forty Mtb isolates were genotyped using 24-locus MIRU-VNTR typing and spoligotyping. Lineage classification and TB transmission analysis were performed. RESULTS 24-locus MIRU-VNTR typing identified 135 unique profiles and two clusters compared to 35 spoligotyping profiles which contained 12 clusters and 23 unique isolates, Beijing (n=100, 71.4%) was found to be prominent lineage by combine two methods. The expected proportion attributable to recent transmission based on clustering rate was 2.1%. One cluster case was more likely to be in MDR patient. CONCLUSIONS Our findings showed Beijing genotypes were dominant in Upper Myanmar. The usage and analysis of 24-locus MIRU-VNTR typing might prove useful for our broader understanding of TB outbreaks and epidemiology than spoligotyping. The genotypic pattern of this combined method suggests that the lower transmission rate may be due to a higher possibility of reactivation cases in Upper Myanmar.
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Affiliation(s)
- Waing Waing Moe Sann
- Medical Technology Program, Faculty of Associated medical Sciences, Khon Kaen University, Khon Kaen,Thailand.
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
| | | | - Kyi Kyi Swe
- National TB Control Program, Upper Myanmar TB Reference Laboratory, Mandalay Region, Myanmar.
| | - Thandar Thwin
- National TB Control Program, Upper Myanmar TB Reference Laboratory, Mandalay Region, Myanmar.
| | - Arunnee Sangka
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
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Weiss LD, van den Driessche P, Lowengrub JS, Wodarz D, Komarova NL. Effect of feedback regulation on stem cell fractions in tissues and tumors: Understanding chemoresistance in cancer. J Theor Biol 2020; 509:110499. [PMID: 33130064 DOI: 10.1016/j.jtbi.2020.110499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/16/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022]
Abstract
While resistance mutations are often implicated in the failure of cancer therapy, lack of response also occurs without such mutants. In bladder cancer mouse xenografts, repeated chemotherapy cycles have resulted in cancer stem cell (CSC) enrichment, and consequent loss of therapy response due to the reduced susceptibility of CSCs to drugs. A particular feedback loop present in the xenografts has been shown to promote CSC enrichment in this system. Yet, many other regulatory loops might also be operational and might promote CSC enrichment. Their identification is central to improving therapy response. Here, we perform a comprehensive mathematical analysis to define what types of regulatory feedback loops can and cannot contribute to CSC enrichment, providing guidance to the experimental identification of feedback molecules. We derive a formula that reveals whether or not the cell population experiences CSC enrichment over time, based on the properties of the feedback. We find that negative feedback on the CSC division rate or positive feedback on differentiated cell death rate can lead to CSC enrichment. Further, the feedback mediators that achieve CSC enrichment can be secreted by either CSCs or by more differentiated cells. The extent of enrichment is determined by the CSC death rate, the CSC self-renewal probability, and by feedback strength. Defining these general characteristics of feedback loops can guide the experimental screening for and identification of feedback mediators that can promote CSC enrichment in bladder cancer and potentially other tumors. This can help understand and overcome the phenomenon of CSC-based therapy resistance.
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Affiliation(s)
- Lora D Weiss
- Department of Mathematics, University of California Irvine, Irvine, CA 92697, United States
| | - P van den Driessche
- Department of Mathematics and Statistics, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - John S Lowengrub
- Department of Mathematics, University of California Irvine, Irvine, CA 92697, United States
| | - Dominik Wodarz
- Department of Mathematics, University of California Irvine, Irvine, CA 92697, United States; Department of Population Health and Disease Prevention, Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, United States
| | - Natalia L Komarova
- Department of Mathematics, University of California Irvine, Irvine, CA 92697, United States.
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Rosas-Valdez R, Morrone JJ, Pinacho-Pinacho CD, Domínguez-Domínguez O, García-Varela M. Genetic diversification of acanthocephalans of the genus Floridosentis Ward 1953 (Acanthocephala: Neoechinorhynchidae), parasites of mullets from the Americas. Infect Genet Evol 2020; 85:104535. [PMID: 32920194 DOI: 10.1016/j.meegid.2020.104535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 01/05/2023]
Abstract
Adult worms of the genus Floridosentis are endoparasites of marine fishes of the genus Mugil and are broadly distributed in the Americas. Currently, Floridosentis includes two species, F. mugilis, distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, restricted to the Pacific Ocean coast. The aim of this study was to explore the species limit of both species of the genus Floridosentis, collected in 37 localities in eight countries: Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, Ecuador and Venezuela. We sequenced 253 specimens to build a comprehensive dataset for three genes: the cytochrome c oxidase subunit I (cox 1) from mitochondrial DNA, the internal transcribed spacers ITS1 and ITS2 including the 5.8S gene (ITS region), and the D2 + D3 domains of the large subunit (LSU) of nuclear DNA. Maximum likelihood and Bayesian analyses with the cox 1 and concatenated (cox 1 + ITS+LSU) datasets were conducted. Two species delimitation methods were implemented, the Automatic Barcode Gap Discovery (ABGD), and Bayesian species delimitation (BPP), plus a haplotype network inferred with 253 specimens, allowing us to validate two nominal species of Floridosentis., F. mugilis, plus one linage distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, plus two additional lineages distributed along the Pacific Ocean coast. All these lineages are shared by both species of mullet (Mugil curema and M. cephalus). The currents in the Atlantic Ocean, Pacific Ocean and Gulf of Mexico, in combination with the biology of the definitive hosts, have played a key role in the distribution of the two nominal species and of the three lineages of Floridosentis across the Americas.
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Affiliation(s)
- Rogelio Rosas-Valdez
- Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Av. Preparatoria s/n. Col. Agronómica, 98066 Zacatecas, Mexico
| | - Juan José Morrone
- Museo de Zoología "Alfonso L. Herrera", Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado postal 70-399, 04510 Mexico City, Mexico
| | - Carlos Daniel Pinacho-Pinacho
- Cátedras CONACyT, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Carretera antigua a Coatepec 351, El Haya, Xalapa, 91070 Veracruz, Mexico
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Martín García-Varela
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Circuito exterior s/n, Ciudad Universitaria, 04510 Mexico City, Mexico.
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Babcock G. Asexual organisms, identity and vertical gene transfer. Stud Hist Philos Biol Biomed Sci 2020; 81:101265. [PMID: 32044223 DOI: 10.1016/j.shpsc.2020.101265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a phylogenetic tree will split differently than if the identity of an organism does not survive the fission process.
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Affiliation(s)
- Gunnar Babcock
- Philosophy Dept, University at Albany, 1400 Washington Ave, Albany, NY, 12067, USA.
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31
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Moopanar K, Mvubu NE. Lineage-specific differences in lipid metabolism and its impact on clinical strains of Mycobacterium tuberculosis. Microb Pathog 2020; 146:104250. [PMID: 32407863 DOI: 10.1016/j.micpath.2020.104250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
Mycobacterium tuberculosis (M. tb) is the causative agent of TB and its incidences has been on the rise since 1993. Lipid metabolism is an imperative metabolic process, which grants M. tb the ability to utilize host-derived lipids as a secondary source of nutrition during infection. In addition to degrading host lipids, M. tb is proficient at using lipids, such as cholesterol, to facilitate its entry into macrophages. Mycolic acids, constituents of the mycobacterial cell wall, offer protection and aid in persistence of the bacterium. These are effectively synthesized using a complex fatty acid synthase system. Many pathogenesis studies have reported differences in lipid-metabolism of clinical strains of M. tb that belongs to diverse lineages of the Mycobacterium tuberculosis complex (MTBC). East-Asian and Euro-American lineages possess "unique" cell wall-associated lipids compared to the less transmissible Ethiopian lineage, which may offer these lineages a competitive advantage. Therefore, it is crucial to comprehend the complexities among the MTBC lineages with lipid metabolism and their impact on virulence, transmissibility and pathogenesis. Thus, this review provides an insight into lipid metabolism in various lineages of the MTBC and their impact on virulence and persistence during infection, as this may provide critical insight into developing novel therapeutics to combat TB.
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Affiliation(s)
- K Moopanar
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
| | - N E Mvubu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
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32
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Farabaugh SM, Litzenburger BC, Elangovan A, Pecar G, Walheim L, Atkinson JM, Lee AV. IGF1R constitutive activation expands luminal progenitors and influences lineage differentiation during breast tumorigenesis. Dev Biol 2020; 463:77-87. [PMID: 32376245 DOI: 10.1016/j.ydbio.2020.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/11/2020] [Accepted: 04/15/2020] [Indexed: 12/16/2022]
Abstract
Breast tumors display tremendous heterogeneity in part due to varying molecular alterations, divergent cells of origin, and differentiation. Understanding where and how this heterogeneity develops is likely important for effective breast cancer eradication. Insulin-like growth factor (IGF) signaling is critical for normal mammary gland development and function, and has an established role in tumor development and resistance to therapy. Here we demonstrate that constitutive activation of the IGF1 receptor (IGF1R) influences lineage differentiation during mammary tumorigenesis. Transgenic IGF1R constitutive activation promotes tumors with mixed histologies, multiple cell lineages and an expanded bi-progenitor population. In these tumors, IGF1R expands the luminal-progenitor population while influencing myoepithelial differentiation. Mammary gland transplantation with IGF1R-infected mammary epithelial cells (MECs) resulted in hyperplastic, highly differentiated outgrowths and attenuated reconstitution. Restricting IGF1R constitutive activation to luminal versus myoepithelial lineage-sorted MECs resulted in ductal reconstitutions co-expressing high IGF1R levels in the opposite lineage of origin. Using in vitro models, IGF1R constitutively activated MCF10A cells showed increased mammosphere formation and CD44+/CD24-population, which was dependent upon Snail and NFκB signaling. These results suggest that IGF1R expands luminal progenitor populations while also stimulating myoepithelial cell differentiation. This ability to influence lineage differentiation may promote heterogeneous mammary tumors, and have implications for clinical treatment.
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Affiliation(s)
- Susan M Farabaugh
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, USA
| | - Beate C Litzenburger
- Lester and Sue Smith Breast Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ashuvinee Elangovan
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, USA
| | - Geoffrey Pecar
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, USA
| | - Lauren Walheim
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, USA
| | - Jennifer M Atkinson
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, USA
| | - Adrian V Lee
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, USA.
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Machado CM, de Souza ACMF, Romano CM, Dos Santos Freire W, Costa ÂA, Figueiredo WM, Pannuti CS, Luna EJA. Influenza A and B in a cohort of outpatient children and adolescent with influenza like-illness during two consecutive influenza seasons. Braz J Infect Dis 2020; 24:73-80. [PMID: 31951818 PMCID: PMC7110568 DOI: 10.1016/j.bjid.2019.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/10/2019] [Accepted: 12/15/2019] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Influenza is an important cause of morbimortality worldwide. Although people at the extremes of age have a greater risk of complications, influenza has been more frequently investigated in the elderly than in children, and inpatients than outpatients. Yearly vaccination with trivalent or quadrivalent vaccines is the main strategy to control influenza. OBJECTIVES Determine the clinical and molecular characteristics of influenza A and B infections in children and adolescents with influenza-like illness (ILI). METHODS A cohort of outpatient children and adolescents with ILI was followed for 20 months. Influenza was diagnosed with commercial multiplex PCR platforms. RESULTS 179 patients had 277 episodes of ILI, being 79 episodes of influenza A and 20 episodes of influenza B. Influenza A and B cases were mild and had similar presentation. Phylogenetic tree of influenza B viruses showed that 91.6% belonged to the B/Yamagata lineage, which is not included in trivalent vaccines. CONCLUSIONS Influenza A and B are often detected in children and adolescents with ILI episodes, with similar and mild presentation in outpatients. The mismatch between the circulating influenza viruses and the trivalent vaccine offered in Brazil may have contributed to the high frequency of influenza A and B in this population.
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Affiliation(s)
- Clarisse M Machado
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Virologia, São Paulo, SP, Brazil; Universidade de São Paulo, Faculdade de Medicina, Hospital das Clinicas HCFMUSP (LIM52), São Paulo, SP, Brazil.
| | | | - Camila Malta Romano
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Virologia, São Paulo, SP, Brazil; Universidade de São Paulo, Faculdade de Medicina, Hospital das Clinicas HCFMUSP (LIM52), São Paulo, SP, Brazil
| | - Wilton Dos Santos Freire
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Virologia, São Paulo, SP, Brazil
| | - Ângela Aparecida Costa
- Faculdade de Saúde Pública da USP, Serviço Especial de Saúde de Araraquara- SESA, São Paulo, SP, Brazil
| | - Walter Manso Figueiredo
- Faculdade de Saúde Pública da USP, Serviço Especial de Saúde de Araraquara- SESA, São Paulo, SP, Brazil
| | - Cláudio S Pannuti
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Virologia, São Paulo, SP, Brazil
| | - Expedito J A Luna
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Medicina Preventiva, São Paulo, SP, Brazil
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Ye C, Huang Q, Chen T, Jiang J, Hou F, Xu D, Peng Y, Fang R, Chen J. First detection and genotypic analysis of goat enzootic nasal tumor virus 2 in Chongqing, China. Arch Virol 2019; 164:1647-1650. [PMID: 30877451 DOI: 10.1007/s00705-019-04211-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 01/04/2023]
Abstract
Enzootic nasal adenocarcinoma (ENA) of goats, characterized by transformation of epithelial cells of the ethmoid turbinates, is caused by enzootic nasal tumor virus 2 (ENTV-2). ENTV-2 belongs to the genus Betaretrovirus and has extended its distribution globally with a high prevalence; however, the genetic diversity and genotypic distribution for ENTV-2 have not been analyzed systematically due to the limited availability of sequence data. In this study, an infection by ENTV-2 was detected by RT-PCR in Chongqing in July 2018, and the complete sequence of one strain (CQ1) was determined. Phylogenetic analysis indicated a high degree of genetic heterogeneity among ENTV-2 sequences, with the existence of two main lineages. Lineage 1 and 2 were composed of ENTV-2 from China and the UK, respectively. Although CQ1 was closely related to recent ENTV-2 strains collected in the neighboring provinces of Chongqing (Shaanxi and Sichuan), it formed a separate sublineage of lineage 1 (sublineage 1.3). This report will enhance our understanding of the epidemiology of ENTV-2 in China.
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Affiliation(s)
- Chao Ye
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Qingyuan Huang
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Tingting Chen
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Jiali Jiang
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Fengqing Hou
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Dongyi Xu
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Yuanyi Peng
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Rendong Fang
- College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400715, China.
| | - Jing Chen
- Chongqing Academy of Animal Sciences, No. 238 Renmin Road, Yuzhong district, Chongqing, 402460, China.
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da Silva Medeiros TN, Lorenzetti E, Alfieri AF, Alfieri AA. G and P genotype profiles of rotavirus A field strains circulating in beef and dairy cattle herds in Brazil, 2006-2015. Comp Immunol Microbiol Infect Dis 2019; 64:90-98. [PMID: 31174706 DOI: 10.1016/j.cimid.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/04/2019] [Indexed: 11/25/2022]
Abstract
The aim of this retrospective study was to use RT-PCR and nucleotide sequencing analysis to determine the G (VP7 gene) and P (VP4 gene) genotypes of 155 Brazilian bovine rotavirus A (RVA) wild-type strains detected in diarrheic calves from all Brazilian geographical regions from 2006 to 2015. The RVA strains evaluated belonged to the G6, G10, P[5], and P[11] genotypes. The G6P[5] genotype was prevalent (65.5%; P < 0.05) in beef, and the G10P[11] (38.4%) and G6P[11] (30.8%) genotypes were more prevalent in dairy cattle herds. The Midwest was the region with the highest number of genotyped RVA strains, where the genotypes G6, P[5], and P[11] were identified. Genotype combination G6-IV/P[5]-IX, prevalent in beef herds, and G6-III/P[11]-III or G10-IV/P[11]-III, prevalent in dairy herds, were detected. In addition, for the first time in Brazil, we detected the P[5] and P[11] genotype RVA strains that belong to lineage II and VII, respectively.
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Affiliation(s)
- Thais Neris da Silva Medeiros
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil.
| | - Elis Lorenzetti
- Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil; National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil.
| | - Alice Fernandes Alfieri
- Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil; National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil.
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil; Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil; National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina (UEL), Celso Garcia Cid Road, PR455 Km 380, P.O. Box 10011, CEP 86057-970, Londrina, Paraná, Brazil.
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Utzeri VJ, Schiavo G, Ribani A, Bertolini F, Bovo S, Fontanesi L. A next generation sequencing approach for targeted Varroa destructor (Acari: Varroidae) mitochondrial DNA analysis based on honey derived environmental DNA. J Invertebr Pathol 2019; 161:47-53. [PMID: 30707918 DOI: 10.1016/j.jip.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 11/19/2022]
Abstract
Honey contains DNA from many different organisms that are part of hive micro-environmental niches and honey bee pathospheres. In this study, we recovered and sequenced mite mitochondrial DNA (mtDNA) from honey from different locations around the world (Europe, Asia, Africa, North and South America). DNA extracted from 17 honey samples was amplified with eight primer pairs targeting three mite mtDNA genes, obtaining 88 amplicons that were sequenced with an Ion Torrent sequencing platform. A bioinformatic pipeline compared produced reads with Varroa spp. mtDNA sequence entries available in GenBank and assigned them to different mitotypes. In all honey samples, the highest percentage of reads was attributed to the K1 lineage, including a few variants derived from it, in addition to J1 reads observed in the two South American samples and C1-1 reads obtained from the Chinese honey. This study opens new possibilities to analyse mite lineages and variants and monitor their geographical and temporal distribution, simplifying surveillance against this damaging honey bee parasite.
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Affiliation(s)
- Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.
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Ahamed SF, Rosario V, Britto C, Dias M, Nayak K, Chandele A, Kaja MK, Shet A. Emergence of new genotypes and lineages of dengue viruses during the 2012-15 epidemics in southern India. Int J Infect Dis 2019; 84S:S34-S43. [PMID: 30639622 DOI: 10.1016/j.ijid.2019.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012-13/2014-15 outbreaks in southern India. METHODS Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n=612), a representative selection of DENV isolates (n=99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. RESULTS In 2012-13 (n=113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014-15 (n=499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012-13 and 2014-15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012-13, ceding to GI predominance (80.8%) in 2014-15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, 'GIVc'. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. CONCLUSIONS New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.
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Affiliation(s)
- Syed Fazil Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore, 560064, Karnataka, India.
| | - Vivek Rosario
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Carl Britto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK.
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; Department of Microbiology, St. John's Medical College Hospital, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Murali-Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Pediatrics, Emory University, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
| | - Anita Shet
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, 415 N Washington St, Baltimore 21231, USA.
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Jornist I, Muhsen K, Ram D, Lustig Y, Levy V, Orzitser S, Azar R, Weil M, Indenbaum V, Sofer D, Mendelson E, Mandelboim M, Hindiyeh M. Characterization of human parainfluenza virus-3 circulating in Israel, 2012-2015. J Clin Virol 2018; 107:19-24. [PMID: 30114677 DOI: 10.1016/j.jcv.2018.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/03/2018] [Accepted: 08/09/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Human parainfluenza virus 3 (hPIV-3) causes respiratory tract infection. OBJECTIVES The objective of this study was to describe the epidemiology of hPIV-3 infection among hospitalized patients and characterize the circulating strains. STUDY DESIGN A cross-sectional study was conducted using respiratory samples of 15,946 hospitalized patients with respiratory symptoms in 2012-2015 in Israel. All samples were subjected to q-PCR and q-RT-PCR to determine the presence of hPIV-3 and other respiratory viruses. Samples positive for hPIV-3 were subjected to molecular typing and phylogenetic analysis. RESULTS Overall, 547 samples 3.4% (95% CI 3.2-3.7) were positive for hPIV-3. Of these 87 (15.9%) were mixed infections; 41.4% with adenovirus, 40.2% with RSV (40.2%) and 19.5% influenza A viruses. The prevalence of hPIV-3 was highest (5.1%) in children aged 0-4 years. Hospitalization in oncology department was associated with increased likelihood of hPIV-3 infection: adjusted odds ratio [aOR] 2.29 (95% confidence intervals [CI] 1.78-2.96), as well as hospitalization in organ transplantation department: aOR 3.65 (95% CI 2.80-4.76). The predominant lineages were C3c (62.3%) and C1b (24.6%), followed by sub-lineages C5 (8.7%) and C3b (2.9%). A new sub-lineage emerged in our analysis, named C1d, which was 17 (1.5%) nucleotide different from C1a, 25 (2.2%) nucleotide different from C1b and 24 (2.1%) nucleotide different from C1c. DISCUSSION Young children and immunocompromised patients are likely the risk groups for severe respiratory infections with hPIV-3. Strains belonging to lineages C3c and C1b, which are present worldwide, should be targeted in vaccine development. The emergence of new lineage might have public health implications and on vaccine development.
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Affiliation(s)
- Irina Jornist
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Microbiology and Immunology, Tel-Aviv University, Tel-Aviv, Israel
| | - Khitam Muhsen
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Daniela Ram
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Virginia Levy
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Sara Orzitser
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Merav Weil
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Viki Indenbaum
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Musa Hindiyeh
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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Anis E, Newell TK, Dyer N, Wilkes RP. Phylogenetic analysis of the wild-type strains of canine distemper virus circulating in the United States. Virol J 2018; 15:118. [PMID: 30068352 PMCID: PMC6090796 DOI: 10.1186/s12985-018-1027-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022] Open
Abstract
Background Canine distemper (CD) is a highly contagious, systemic, viral disease of dogs seen worldwide. Despite intensive vaccination in developed countries, recent reports suggest both the re-emergence and increased activity of Canine distemper virus (CDV) worldwide, including the United States. CDV is an RNA virus of the genus Morbillivirus within the family Paramyxoviridae. Viral genomic RNA encodes six structural proteins. Of the six structural proteins, the hemagglutinin (H) gene has the greatest genetic variation and is therefore a suitable target for molecular epidemiological studies. The majority of neutralizing epitopes are found on the H protein, making this gene also important for evaluation of changes over time that may result in antigenic differences among strains. The aim of this study was to determine the phylogenetic relationship of CDV strains circulating in the US. Methods Fifty-nine positive canine distemper virus samples collected from dogs from different regions and states from 2014 to 2017 were sequenced with a targeted next-generation sequencing (NGS) method. The sequences of the H, F, and P genes and the matrix-fusion (M-F) intergenic region of the amplified CDVs were analyzed individually. Results Sequence analysis of the H gene revealed that there are at least 3 different lineages of CDV currently circulating in the US. These lineages include America-3 (Edomex), America-4, and a clade that was previously reported in association with an outbreak in Wyoming, which was linked to a domestic dog-breeding facility in Kansas in 2010. These lineages differ from the historically identified lineages in the US, including America-1, which contains the majority of the vaccine strains. Genetic differences may result in significant changes to the neutralizing epitopes that consequently may lead to vaccine failure. Phylogenetic analyses of the nucleotide sequences obtained in this study of the F and P genes and the M-F intergenic region with sequences from the GenBank database produced similar findings to the H gene analysis. Conclusions The CDV lineages currently circulating in the US differ from the historically identified lineages America-1. Continuous surveillance is required for monitoring circulating CDV strains in the US, to prevent potential vaccine breakthrough events. Electronic supplementary material The online version of this article (10.1186/s12985-018-1027-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eman Anis
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, PO Box 1389, 43 Brighton Rd, Tifton, GA, 31793, USA.,The Department of Virology, Faculty of Veterinary Medicine, University of Sadat, Sadat City, Egypt
| | - Teresa K Newell
- Veterinary Diagnostic Services Department, North Dakota State University, Dept. 7691, P.O. Box 6050, Fargo, North, Dakota, 58105, USA
| | - Neil Dyer
- Veterinary Diagnostic Services Department, North Dakota State University, Dept. 7691, P.O. Box 6050, Fargo, North, Dakota, 58105, USA
| | - Rebecca P Wilkes
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, PO Box 1389, 43 Brighton Rd, Tifton, GA, 31793, USA.
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Vergara A, Marangi M, Caradonna T, Pennisi L, Paludi D, Papini R, Ianieri A, Giangaspero A, Normanno G. Toxoplasma gondii Lineages Circulating in Slaughtered Industrial Pigs and Potential Risk for Consumers. J Food Prot 2018; 81:1373-1378. [PMID: 30019961 DOI: 10.4315/0362-028x.jfp-17-496] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Toxoplasma gondii is a cosmopolitan zoonotic protozoan parasite, and the consumption of raw or undercooked pig meat is one of the most important sources of T. gondii infection. Three predominant lineages, types I, II, and III, are widespread in Europe. Although still poorly understood, a relationship between each type and the severity of illness represents a public health issue. To gain further knowledge of the genotypes in circulation and of the potential risk for consumers, one heart sample and one diaphragm sample (206 total) were taken from each of 103 pig carcasses at an abattoir in Italy. Then, we used 529-bp repetitive element PCR and a B1 real-time PCR high-resolution melting assay coupled with sequencing to detect and genotype T. gondii isolates. T. gondii DNA was detected in 14 pigs (13.6%, 95% confidence interval = 7 to 20.2%), and types I (3.9%), II (5.8%), and III (3.9%) were identified. We found that heart tissue had a significantly higher PCR positivity rate for T. gondii than did diaphragm tissue. This is Europe's largest study on genotyping of T. gondii from pigs, and it demonstrates that all three main lineages are present in carcasses of industrially reared pigs in Italy. There is a potential risk to consumers of infection with any or all of the three lineages, and the related clinical consequences should be taken into account. This study suggests that monitoring of T. gondii types in meat is essential, especially in meat that is traditionally eaten raw or that is minimally processed.
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Affiliation(s)
- Alberto Vergara
- 1 Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Marianna Marangi
- 2 Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy
| | - Tiziana Caradonna
- 2 Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy
| | - Luca Pennisi
- 1 Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Domenico Paludi
- 1 Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Roberto Papini
- 3 Department of Veterinary Science, University of Pisa, 56126 Pisa, Italy; and
| | - Adriana Ianieri
- 4 Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Annunziata Giangaspero
- 2 Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy
| | - Giovanni Normanno
- 2 Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy
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Cavalcante FS, Pinheiro MV, Ferreira DDC, Alvarenga CVDCG, Guimarães ACF, Nouér SA, Dos Santos KRN. Characteristics of methicillin-resistant Staphylococcus aureus in patients on admission to a teaching hospital in Rio de Janeiro, Brazil. Am J Infect Control 2017; 45:1190-1193. [PMID: 28751036 DOI: 10.1016/j.ajic.2017.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/03/2017] [Accepted: 06/05/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are associated with greater mortality and morbidity; however, risk factors for community-acquired infections caused by MRSA have not been established. Therefore, community patients who are admitted to hospitals without the necessary contact precautions and are infected with community-acquired lineages eventually cause these lineages to spread to these settings. The aim of this study was to detect community-acquired lineages of MRSA in patients on admission to a Brazilian teaching hospital. METHODS The antimicrobial susceptibility of the MRSA isolates from nasal swabs was evaluated as was the molecular characteristics of the staphylococcal cassette chromosome mec (SCCmec). The clonality was determined using pulsed-field gel electrophoresis and multilocus sequence type analysis. RESULTS A total of 702 patients were evaluated between March 2012 and March 2013; 180 (25%) of them were colonized by S aureus, and 21 (3%) were MRSA. The SCCmec IV/USA1100/sequence type (ST) 30 was the predominant MRSA lineage (42.8%), followed by SCCmec IV/USA800/ST5 (23.8%). CONCLUSIONS The occurrence of MRSA colonization was very low, and only 1 patient from cardiac surgery developed an infection, which was caused by an SCCmec II/USA100/ST5 isolate. Screening for MRSA colonization on admission does not seem to be productive; however, for populations submitted to specific surgeries, active surveillance should be implemented.
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Affiliation(s)
| | | | - Dennis de Carvalho Ferreira
- School of Dentistry, Veiga de Almeida University, Rio de Janeiro, Brazil; School of Dentistry, Estácio de Sá University, Rio de Janeiro, Brazil
| | | | | | - Simone Aranha Nouér
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Tkachev SE, Chicherina GS, Golovljova I, Belokopytova PS, Tikunov AY, Zadora OV, Glupov VV, Tikunova NV. New genetic lineage within the Siberian subtype of tick-borne encephalitis virus found in Western Siberia, Russia. Infect Genet Evol 2017; 56:36-43. [PMID: 29069610 DOI: 10.1016/j.meegid.2017.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/06/2017] [Accepted: 10/21/2017] [Indexed: 11/20/2022]
Abstract
Tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is a causative agent of a severe neurological disease. There are three main TBEV subtypes: the European (TBEV-Eu), Far Eastern (TBEV-FE), and Siberian (TBEV-Sib). Currently, three lineages within TBEV-Sib have been recorded. In this study, the genetic and biological characteristics of a new original strain, TBEV-2871, isolated in the Novosibirsk province of Western Siberia, Russia were investigated. The strain has low neuroinvasiveness in mice. Phylogenetic analysis demonstrated that TBEV-2871 belongs to TBEV-Sib, but does not cluster with any of the TBEV-Sib lineages. The TBEV-2871 strain has 88-89% nucleotide sequence identity with the other TBEV-Sib strains, 84-86% nucleotide sequence identity with the TBEV-FE and TBEV-Eu subtypes and is genetically close to the subtype division border. The TBEV-2871 polyprotein sequence includes 43 unique amino acid substitutions, 30 of which are recorded at positions that are conserved among all TBEV subtypes. Strain TBEV-2871 and two similar but not identical isolates found in Kemerovo province, Western Siberia are separated into a new lineage tentatively named Obskaya after the name of Ob riber, in the vicinity of which the TBEV-2871 was first found. A molecular evolution investigation demonstrated that within TBEV-Sib, the Obskaya lineage likely separated 1535years ago, which is even earlier than the Baltic lineage.
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Papini R, di Ciccio P, Marangi M, Ghidini S, Zanardi E, Vergara A, Giangaspero A, Nardoni S, Rocchigiani G, Mancianti F, Ianieri A. Occurrence of Toxoplasma gondii in Carcasses of Pigs Reared in Intensive Systems in Northern Italy. J Food Prot 2017; 80:515-522. [PMID: 28207292 DOI: 10.4315/0362-028x.jfp-16-314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To evaluate the occurrence of Toxoplasma gondii and to genetically characterize its isolates in carcasses of industrial fattening pigs, blood, diaphragm, and heart samples were collected from 375 carcasses of pigs slaughtered to be processed for Parma ham production. Pigs had been bred on approved farms (n = 75) located in the so-called Food Valley in Italy. Sera were examined for immunoglobulin G antibodies to T. gondii by modified agglutination test (MAT). Both heart and diaphragm samples from seropositive carcasses were processed for the presence of T. gondii DNA (B1 locus) by real-time PCR and high resolution melting (HRM) assay. Anti-Toxoplasma antibodies were detected in 2.1% of pig carcasses, with titers from 1:10 to 1:320. T. gondii DNA was detected in all (eight) seropositive carcasses and in 11 (5 heart and 6 diaphragm samples) of 16 samples; that is, it was detected in heart tissue in two subjects, in diaphragm tissue in three subjects, and in both muscle tissues in three subjects. Toxoplasma genotypes were determined in seven of eight carcasses: type III was identified in four carcasses, type II in two, and both III and II in one carcass. The serological findings and the molecular detection of T. gondii strains suggest that cured meat products obtained from industrially bred pigs may be potential sources of toxoplasmosis for humans. Our results provide novel, important information regarding the seroprevalence and molecular prevalence of T. gondii in intensively reared pigs within this specific region of Italy, particularly because Parma ham from this region is known and consumed worldwide. On-farm preventive measures combined with slaughterhouse monitoring of carcasses of pigs bred for cured meat production should never be overlooked to prevent the introduction of T. gondii into the food chain and to ensure safety for consumers of these products.
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Affiliation(s)
- Roberto Papini
- 1 Dipartimento di Scienze Veterinarie, Università degli Studi di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Pierluigi di Ciccio
- 2 Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Marianna Marangi
- 3 Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università degli Studi di Foggia, Via Napoli 25, 71121 Foggia, Italy
| | - Sergio Ghidini
- 2 Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Emanuela Zanardi
- 2 Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Alberto Vergara
- 4 Facoltà di Medicina Veterinaria, Università degli Studi di Teramo, SP 18, 64100 Teramo, Italy
| | - Annunziata Giangaspero
- 3 Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università degli Studi di Foggia, Via Napoli 25, 71121 Foggia, Italy
| | - Simona Nardoni
- 1 Dipartimento di Scienze Veterinarie, Università degli Studi di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Guido Rocchigiani
- 1 Dipartimento di Scienze Veterinarie, Università degli Studi di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Francesca Mancianti
- 1 Dipartimento di Scienze Veterinarie, Università degli Studi di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Adriana Ianieri
- 2 Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Via del Taglio 10, 43126 Parma, Italy
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de Bruycker-Nogueira F, Mir D, Dos Santos FB, Bello G. Evolutionary history and spatiotemporal dynamics of DENV-1 genotype V in the Americas. Infect Genet Evol 2016; 45:454-460. [PMID: 27713055 DOI: 10.1016/j.meegid.2016.09.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/20/2016] [Accepted: 09/30/2016] [Indexed: 01/05/2023]
Abstract
The genotype V has been the most prevalent dengue virus type 1 (DENV-1) clade circulating in the Americas over the last 40years. In this study, we investigate the spatiotemporal pattern of emergence and dissemination of DENV-1 lineages in the continent. We applied phylogenetic and phylogeographic approaches to a comprehensive data set of 836 DENV-1 E gene sequences of the genotype V isolated from 46 different countries around the world over a period of 50years (1962 to 2014). Our study reveals that genetic diversity of DENV-1 genotype V in the Americas resulted from two independent introductions of this genotype from India. The first genotype V strain was most probably introduced into the Lesser Antilles at around the early 1970s and this Caribbean region becomes the source population of several DENV-1 lineages that spread in the Americas during the 1970s and 1980s. Most of those lineages appear to become extinct during the 1990s, except one that persisted in Venezuela and later spread to other American countries, dominating the DENV-1 epidemics in the region from the early 2000s onwards. The second genotype V strain of Indian origin was also most probably introduced into the Lesser Antilles at around the early 1980s. This lineage remained almost undetected for nearly 15years, until it was introduced in Northern Brazil around the middle 1990s and later spread to other country regions. These results demonstrate that different geographic regions have played a role in maintaining and spreading the DENV-1 genotype V in the Americas over time. DENV-1 genotype V lineages have originated, spread and died out in the Americas with very different dynamics and the phenomenon of lineage replacement across successive DENV-1 epidemic outbreaks was a common characteristic in most American countries.
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Affiliation(s)
- Fernanda de Bruycker-Nogueira
- Laboratory of Viral Immunology, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
| | - Daiana Mir
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
| | - Flavia Barreto Dos Santos
- Laboratory of Viral Immunology, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil.
| | - Gonzalo Bello
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
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45
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Simonin Y, Loustalot F, Desmetz C, Foulongne V, Constant O, Fournier-Wirth C, Leon F, Molès JP, Goubaud A, Lemaitre JM, Maquart M, Leparc-Goffart I, Briant L, Nagot N, Van de Perre P, Salinas S. Zika Virus Strains Potentially Display Different Infectious Profiles in Human Neural Cells. EBioMedicine 2016; 12:161-169. [PMID: 27688094 PMCID: PMC5078617 DOI: 10.1016/j.ebiom.2016.09.020] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/15/2016] [Accepted: 09/19/2016] [Indexed: 01/28/2023] Open
Abstract
The recent Zika virus (ZIKV) epidemic has highlighted the poor knowledge on its physiopathology. Recent studies showed that ZIKV of the Asian lineage, responsible for this international outbreak, causes neuropathology in vitro and in vivo. However, two African lineages exist and the virus is currently found circulating in Africa. The original African strain was also suggested to be neurovirulent but its laboratory usage has been criticized due to its multiple passages. In this study, we compared the French Polynesian (Asian) ZIKV strain to an African strain isolated in Central African Republic and show a difference in infectivity and cellular response between both strains in human neural stem cells and astrocytes. Consistently, this African strain led to a higher infection rate and viral production, as well as stronger cell death and anti-viral response. Our results highlight the need to better characterize the physiopathology and predict neurological impairment associated with African ZIKV.
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Affiliation(s)
- Yannick Simonin
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France; Université de Montpellier, Montpellier, France.
| | - Fabien Loustalot
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France
| | | | - Vincent Foulongne
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France; Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Orianne Constant
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France
| | - Chantal Fournier-Wirth
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France; Etablissement Français du Sang, Montpellier, France
| | - Fanny Leon
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France; Etablissement Français du Sang, Montpellier, France
| | - Jean-Pierre Molès
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France
| | - Aurélien Goubaud
- Institut de Médecine Régénératrice et Biothérapies, INSERM, U1183, Université de Montpellier, CHU Montpellier, Montpellier, France; Plateforme CHU SAFE-IPS, Infrastructure Nationale INGESTEM, Montpellier, France
| | - Jean-Marc Lemaitre
- Institut de Médecine Régénératrice et Biothérapies, INSERM, U1183, Université de Montpellier, CHU Montpellier, Montpellier, France; Plateforme CHU SAFE-IPS, Infrastructure Nationale INGESTEM, Montpellier, France
| | - Marianne Maquart
- Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Isabelle Leparc-Goffart
- Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Laurence Briant
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, FRE3689, CNRS-Université de Montpellier, Montpellier, France
| | - Nicolas Nagot
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France; Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Philippe Van de Perre
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France; Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Sara Salinas
- UMR 1058, INSERM, Université de Montpellier, Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Inserm, Montpellier, France.
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Rawool DB, Doijad SP, Poharkar KV, Negi M, Kale SB, Malik SVS, Kurkure NV, Chakraborty T, Barbuddhe SB. A multiplex PCR for detection of Listeria monocytogenes and its lineages. J Microbiol Methods 2016; 130:144-147. [PMID: 27671346 DOI: 10.1016/j.mimet.2016.09.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/22/2016] [Accepted: 09/22/2016] [Indexed: 10/21/2022]
Abstract
A novel multiplex PCR assay was developed to identify genus Listeria, and discriminate Listeria monocytogenes and its major lineages (LI, LII, LIII). This assay is a rapid and inexpensive subtyping method for screening and characterization of L. monocytogenes.
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Affiliation(s)
- Deepak B Rawool
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar 243 122, India
| | - Swapnil P Doijad
- Department of Pathology, Nagpur Veterinary College, Seminary Hills, Nagpur 440006, India
| | - Krupali V Poharkar
- Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
| | - Mamta Negi
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar 243 122, India
| | - Satyajit B Kale
- Department of Pathology, Nagpur Veterinary College, Seminary Hills, Nagpur 440006, India
| | - S V S Malik
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar 243 122, India
| | - Nitin V Kurkure
- Department of Pathology, Nagpur Veterinary College, Seminary Hills, Nagpur 440006, India
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
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47
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Vázquez A, Herrero L, Negredo A, Hernández L, Sánchez-Seco MP, Tenorio A. Real time PCR assay for detection of all known lineages of West Nile virus. J Virol Methods 2016; 236:266-270. [PMID: 27481597 DOI: 10.1016/j.jviromet.2016.07.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 07/29/2016] [Accepted: 07/29/2016] [Indexed: 11/17/2022]
Abstract
West Nile virus (WNV) is one of the most widespread arbovirus and a large variety of WNV strains and lineages have been described. The molecular methods for the diagnosis of WNV target mainly lineages 1 and 2, which have caused outbreaks in humans, equines and birds. But the last few years new and putative WNV lineages of unknown pathogenicity have been described. Here we describe a new sensitive and specific real-time PCR assay for the detection and quantification of all the WNV lineages described until now. Primers and probe were designed in the 3'-untranslated region (3'-UTR) of the WNV genome and were designed to match all sequenced WNV strains perfectly. The sensitivity of the assay ranged from 1,5 to 15 copies per reaction depending on the WNV lineage tested. The method was validated for WNV diagnosis using different viral strains, human samples (cerebrospinal fluid, biopsies, serum and plasma) and mosquito pools. The assay did not amplify any other phylogenetically or symptomatically related viruses. All of the above make it a very suitable tool for the diagnosis of WNV and for surveillance studies.
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Affiliation(s)
- Ana Vázquez
- Laboratory of Arboviruses and Imported Viral Diseases, National Centre for Microbiology, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, km. 2, 28220 Majadahonda, Madrid, Spain.
| | - Laura Herrero
- Laboratory of Arboviruses and Imported Viral Diseases, National Centre for Microbiology, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, km. 2, 28220 Majadahonda, Madrid, Spain
| | - Anabel Negredo
- Laboratory of Arboviruses and Imported Viral Diseases, National Centre for Microbiology, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, km. 2, 28220 Majadahonda, Madrid, Spain
| | - Lourdes Hernández
- Laboratory of Arboviruses and Imported Viral Diseases, National Centre for Microbiology, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, km. 2, 28220 Majadahonda, Madrid, Spain
| | - María Paz Sánchez-Seco
- Laboratory of Arboviruses and Imported Viral Diseases, National Centre for Microbiology, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, km. 2, 28220 Majadahonda, Madrid, Spain
| | - Antonio Tenorio
- Laboratory of Arboviruses and Imported Viral Diseases, National Centre for Microbiology, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, km. 2, 28220 Majadahonda, Madrid, Spain
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48
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Krumbholz A, Egerer R, Braun H, Schmidtke M, Rimek D, Kroh C, Hennig B, Groth M, Sauerbrei A, Zell R. Analysis of an echovirus 18 outbreak in Thuringia, Germany: insights into the molecular epidemiology and evolution of several enterovirus species B members. Med Microbiol Immunol 2016; 205:471-83. [PMID: 27369854 DOI: 10.1007/s00430-016-0464-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022]
Abstract
In October and November 2010, six children and one woman were presented with symptoms of aseptic meningitis in Jena, Thuringia, Germany. Enterovirus RNA was detected in the cerebrospinal fluid of all patients by RT-PCR, and preliminary molecular typing revealed echovirus 18 (E-18) as causative agent. Virus isolates were obtained from stool samples of three patients and several contact persons. Again, most isolates were typed as E-18. In addition, coxsackievirus B5 (CV-B5) and echovirus 25 (E-25) were found to co-circulate. As only few complete E-18 sequences are available in GenBank, the entire genomes of these isolates were determined using direct RNA-sequencing technology. We did not find evidence for recombination between E-18, E-25 or CV-B5 during the outbreak. Viral protein 1 gene sequences and the cognate 3D polymerase gene sequences of each isolate and GenBank sequences were analysed in order to define type-specific recombination groups (recogroups).
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Affiliation(s)
- Andi Krumbholz
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany. .,Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany. .,Institute of Medical Microbiology, Jena University Hospital, Jena, Germany. .,Medical Laboratory Dr. Krause and colleagues MVZ GmbH, Steenbeker Weg 23, 24106, Kiel, Germany.
| | - Renate Egerer
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany.,Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Heike Braun
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
| | - Michaela Schmidtke
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
| | - Dagmar Rimek
- Thuringian State Authority for Consumer Protection (TLV), Bad Langensalza, Germany
| | - Claudia Kroh
- Public Health Authority, City Council of Jena, Jena, Germany
| | - Bert Hennig
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Andreas Sauerbrei
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
| | - Roland Zell
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
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Cunha MDP, Guimarães VN, Souza M, de Paula Cardoso DDD, de Almeida TNV, de Oliveira TS, Fiaccadori FS. Phylodynamics of DENV-1 reveals the spatiotemporal co-circulation of two distinct lineages in 2013 and multiple introductions of dengue virus in Goiás, Brazil. Infect Genet Evol 2016; 43:130-4. [PMID: 27223633 DOI: 10.1016/j.meegid.2016.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/02/2023]
Abstract
Dengue virus type 1 (DENV-1) was the first serotype introduced in Brazil, during in the 1980s. Since then, this virus has spread in the Brazilian territory, causing several outbreaks. In 2013 the highest number of dengue cases was notified, when compared to the previous years in Brazil, and the state of Goiás reported over 160 thousand cases. In this study, we aimed to present the Phylodynamics of DENV-1 isolates from the state of Goiás, Brazil, during 2013 outbreak, based on the envelope gene (E) sequences. Phylogenetic analysis revealed that Brazilian DENV-1 isolates are grouped together with viruses from genotype V in two distinct lineages (lineage I and lineage II) reflecting co-circulation. Phylogeographic analyses showed that these lineages were introduced in different moments in Goiás, Brazil, using distinct routes, likely originated from the Caribbean. Lineage I was first introduced coming from Rio de Janeiro (2007-2012), followed by the introduction from Argentina (2010-2013). Lineage II was introduced in a single moment from Rio de Janeiro and this clade has existed since 2007-2010. The different viral introduction events demonstrate the viral dispersion process with neighboring regions, which is essential for the maintenance of outbreaks and introduction of new emerging viruses. In conclusion, obtained data reveals the importance of continuous molecular surveillance of this virus in different regions, providing a better understanding of DENV-1 circulation, considering the evolutionary and virus spread patterns.
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Affiliation(s)
| | | | - Menira Souza
- Federal University of Goiás, Goiânia, Goiás, Brazil
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50
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Hertz FB, Nielsen JB, Schønning K, Littauer P, Knudsen JD, Løbner-Olesen A, Frimodt-Møller N. "Population structure of drug-susceptible,-resistant and ESBL-producing Escherichia coli from community-acquired urinary tract". BMC Microbiol 2016; 16:63. [PMID: 27067536 PMCID: PMC4827192 DOI: 10.1186/s12866-016-0681-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/29/2016] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli is the most common cause of urinary tract infection (UTI). The pathogenic isolates are becoming increasingly resistant to antibiotics; with a worldwide dissemination of resistant sequence types (ST). We characterized three different uropathogenic E. coli populations, from non-hospitalized patients to describe the genetic kinship between resistant and susceptible isolates. We studied the populations by use of multi-locus sequence typing (MLST) and abbreviated-multi locus variable number of tandem repeat analysis (a-MLVA). Urine samples submitted for testing, by general practitioners, were identified at Dept. of Clinical Microbiology at Hvidovre Hospital, Denmark, from Oct. 2011 to July 2012. We included 94 fully susceptible, 94 resistant (non-ESBL) and 98 Extended Spectrum Beta-lactamases- (ESBL)-producing E. coli isolates. Results The ESBL population was dominated vastly by ST131 (51 %), ST38 (9 %) and ST69 (6 %). In the resistant group ST69 (18 %), ST73 (11 %) and ST131 (15 %) were the largest clusters. In the susceptible population more STs and a-MLVA codes were identified compared to the other groups and ST73 and ST95 were found as the only clusters with 16 % and 6 %, respectively. Ninety-eight per cent of the ESBL-producing E. coli isolates were CTX-M-producers. Conclusion ST131 dominated the population of community-associated uropathogenic ESBL-producing E. coli, but was less frequent among non-ESBL-producing E. coli. The fully susceptible E. coli population was a much more diverse group than the resistant and ESBL-producing E. coli populations. Overall, these findings suggest that dominant ESBL-producing lineages are derived from UPEC lineages already established in the general UPEC population. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0681-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederik Boëtius Hertz
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark. .,Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Boye Nielsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Pia Littauer
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Jenny Dahl Knudsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
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