Last data update: Jun 11, 2024. (Total: 46992 publications since 2009)
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Query Trace: Naguib D [original query] |
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Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020.
Williams T , Jackson S , Barr I , Bi S , Bhiman J , Ellis J , von Gottberg A , Lindstrom S , Peret T , Rughooputh S , Viegas M , Hirve S , Zambon M , Zhang W , Dia N , Razanazatovo N , Al-Nabet Admh , Abubakar A , Tivane A , Barakat A , Naguib A , Aziz A , Vicari A , Moen A , Govindakarnavar A , Hall A , Darmaa B , Nathalie B , Herring B , Caetano BC , Whittaker B , Baumeister E , Nakouné E , Guthrie E , Inbanathan F , Nair H , Campbell H , Kadjo HA , Oumzil H , Heraud JM , Mott JA , Namulondo J , Leite J , Nahapetyan K , Al Ariqi L , Gazo MHI , Chadha M , Pisareva M , Venter M , Siqueira MM , Lumandas M , Niang M , Albuaini M , Salman M , Oberste S , Srikantiah P , Tang P , Couto P , Smith P , Coyle PV , Dussart P , Nguyen PN , Okada PA , Wijesinghe PR , Samuel R , Brown R , Pebody R , Fasce R , Jha R , Lindstrom S , Gerber S , Potdar V , Dong X , Deng YM . Influenza Other Respir Viruses 2023 17 (1) e13073 Background: External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019–2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019–2020 WHO RSV EQA. Methods: Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. Results: An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. Conclusions: The WHO RSV EQA 2019–2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets. © 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd. |
Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference.
Wang T , Guo Y , Roellig DM , Li N , Santín M , Lombard J , Kváč M , Naguib D , Zhang Z , Feng Y , Xiao L . Mol Biol Evol 2022 39 (7) Genetic recombination plays a critical role in the emergence of pathogens with phenotypes such as drug resistance, virulence, and host adaptation. Here, we tested the hypothesis that recombination between sympatric ancestral populations leads to the emergence of divergent variants of the zoonotic parasite Cryptosporidium parvum with modified host ranges. Comparative genomic analyses of 101 isolates have identified seven subpopulations isolated by distance. They appear to be descendants of two ancestral populations, IIa in northwestern Europe and IId from southwestern Asia. Sympatric recombination in areas with both ancestral subtypes and subsequent selective sweeps have led to the emergence of new subpopulations with mosaic genomes and modified host preference. Subtelomeric genes could be involved in the adaptive selection of subpopulations, while copy number variations of genes encoding invasion-associated proteins are potentially associated with modified host ranges. These observations reveal ancestral origins of zoonotic C. parvum and suggest that pathogen import through modern animal farming might promote the emergence of divergent subpopulations of C. parvum with modified host preference. |
Prevalence and genetic characterization of Enterocytozoon bieneusi in children in Northeast Egypt.
Naguib D , Roellig DM , Arafat N , Xiao L . Parasitol Res 2022 121 (7) 2087-2092 Enterocytozoon bieneusi is the most common microsporidia in humans worldwide, in addition to infecting a wide range of animals. However, there is limited information about this pathogen in children in Egypt. Here, we carried out a molecular epidemiological study of E. bieneusi in child care centers in three provinces in Egypt. Altogether, 585 fresh fecal samples were collected from children attending 18 child care centers in El-Dakahlia, El-Gharbia, and Damietta provinces in Northeast Egypt during March 2015 to April 2016. PCR and sequence analyses of the ribosomal internal transcribed spacer (ITS) were used to detect and genotype E. bieneusi. Twenty-seven fecal samples (4.6%, 27/585) were positive for E. bieneusi. Five genotypes were identified, including type IV (n = 13), Peru8 (n = 9), Peru6 (n = 2), Peru11 (n = 2), and D (n = 1). Phylogenetic analysis indicated that the five genotypes of E. bieneusi detected in this study were clustered into zoonotic group 1. These data provide important information on the prevalence and genetic diversity of E. bieneusi in children in this country. Further epidemiological studies should be conducted to elucidate the role of zoonotic transmission in human E. bieneusi infections. |
Genetic Characterization of Cryptosporidium cuniculus from Rabbits in Egypt.
Naguib D , Roellig DM , Arafat N , Xiao L . Pathogens 2021 10 (6) Rabbits are increasingly farmed in Egypt for meat. They are, however, known reservoirs of infectious pathogens. Currently, no information is available on the genetic characteristics of Cryptosporidium spp. in rabbits in Egypt. To understand the prevalence and genetic identity of Cryptosporidium spp. in these animals, 235 fecal samples were collected from rabbits of different ages on nine farms in El-Dakahlia, El-Gharbia, and Damietta Provinces, Egypt during the period from July 2015 to April 2016. PCR-RFLP analysis of the small subunit rRNA gene was used to detect and genotype Cryptosporidium spp. The overall detection rate was 11.9% (28/235). All 28 samples were identified as Cryptosporidium cuniculus. The 16 samples successfully subtyped by the sequence analysis of the partial 60 kDa glycoprotein gene belonged to two subtypes, VbA19 (n = 1) and VbA33 (n = 15). As C. cuniculus is increasingly recognized as a cause of human cryptosporidiosis, Cryptosporidium spp. in rabbits from Egypt have zoonotic potential. |
Results from the WHO external quality assessment for the respiratory syncytial virus pilot, 2016-17
Jackson S , Peret TCT , Ziegler TT , Thornburg NJ , Besselaar T , Broor S , Barr I , Baumeister E , Chadha M , Chittaganpitch M , Darmaa B , Ellis J , Fasce R , Herring B , Herve K , Hirve S , Li Y , Pisareva M , Moen A , Naguib A , Palekar R , Potdar V , Siqueira M , Treurnicht F , Tivane A , Venter M , Wairagkar N , Zambon M , Zhang W . Influenza Other Respir Viruses 2020 14 (6) 671-677 BACKGROUND: External quality assessments (EQAs) for the molecular detection of respiratory syncytial virus (RSV) are necessary to ensure the provision of reliable and accurate results. One of the objectives of the pilot of the World Health Organization (WHO) Global RSV Surveillance, 2016-2017, was to evaluate and standardize RSV molecular tests used by participating countries. This paper describes the first WHO RSV EQA for the molecular detection of RSV. METHODS: The WHO implemented the pilot of Global RSV Surveillance based on the WHO Global Influenza Surveillance and Response System (GISRS) from 2016 to 2018 in 14 countries. To ensure standardization of tests, 13 participating laboratories were required to complete a 12 panel RSV EQA prepared and distributed by the Centers for Disease Control and Prevention (CDC), USA. The 14th laboratory joined the pilot late and participated in a separate EQA. Laboratories evaluated a RSV rRT-PCR assay developed by CDC and compared where applicable, other Laboratory Developed Tests (LDTs) or commercial assays already in use at their laboratories. RESULTS: Laboratories performed well using the CDC RSV rRT-PCR in comparison with LDTs and commercial assays. Using the CDC assay, 11 of 13 laboratories reported correct results. Two laboratories each reported one false-positive finding. Of the laboratories using LDTs or commercial assays, results as assessed by Ct values were 100% correct for 1/5 (20%). With corrective actions, all laboratories achieved satisfactory outputs. CONCLUSIONS: These findings indicate that reliable results can be expected from this pilot. Continued participation in EQAs for the molecular detection of RSV is recommended. |
Age patterns of Cryptosporidium species and Giardia duodenalis in dairy calves in Egypt
Naguib D , El-Gohary AH , Mohamed AA , Roellig DM , Arafat N , Xiao L . Parasitol Int 2018 67 (6) 736-741 Little is known of the occurrence and age patterns of species/genotypes and subtypes of Cryptosporidium spp. and Giardia duodenalis in calves in Egypt. In this study, 248 fecal specimens were collected from dairy calves aged 1day to 6months on eight farms in three provinces during March 2015 to April 2016. Cryptosporidium spp. were detected and genotyped by using PCR-RFLP analysis of the small subunit rRNA (SSU rRNA) gene, while G. duodenalis was detected and genotyped by using PCR and sequence analyses of the triose phosphate isomerase (tpi), glutamate dehydrogenase (gdh) and beta-giardin (bg) genes. The overall infection rates of Cryptosporidium spp. and G. duodenalis were 9.7 and 13.3%, respectively. The highest Cryptosporidium infection rate (26.7%) was in calves of age</=1month while the highest G. duodenalis infection rate (44.4%) was in calves of 2months. Three Cryptosporidium spp. were identified, including C. parvum (n=16), C. bovis (n=5) and C. ryanae (n=3), with the former being almost exclusively found in calves of </=3months of age and the latter two being only found in calves of over 3months. Subtyping of C. parvum by PCR-sequence analysis of the 60kDa glycoprotein gene identified subtypes IIaA15G1R1 (n=15) and IIaA15G2R1 (n=1). The G. duodenalis identified included both assemblages E (n=32) and A (n=1), with the latter belonging to the anthroponotic subtype A2. These data provide new insights into the genetic diversity and age patterns of Cryptosporidium spp. and G. duodenalis in calves in Egypt. |
Molecular characterization of Cryptosporidium spp. and Giardia duodenalis in children in Egypt.
Naguib D , El-Gohary AH , Roellig D , Mohamed AA , Arafat N , Wang Y , Feng Y , Xiao L . Parasit Vectors 2018 11 (1) 403 BACKGROUND: The transmission of Cryptosporidium spp. and Giardia duodenalis into humans varies according to species/genotypes of the pathogens. Although infections with both parasites are recorded in Egypt, few data are available on the distribution of Cryptosporidium species and G. duodenalis genotypes. The present study assessed the occurrence and genetic diversity of Cryptosporidium spp. and G. duodenalis in Egyptian children. METHODS: In the present study, 585 fecal specimens were collected from children eight years old and younger in three provinces (El-Dakahlia, El-Gharbia and Damietta) during March 2015 to April 2016. PCR-RFLP analysis of the small subunit rRNA gene and sequence analysis of the 60 kDa glycoprotein gene were used to detect and subtype Cryptosporidium spp., respectively, whereas PCR and sequence analyses of the triose phosphate isomerase, glutamate dehydrogenase and beta-giardin genes were used to detect and genotype Giardia duodenalis. RESULTS: The overall infection rates of Cryptosporidium spp. and G. duodenalis were 1.4% and 11.3%, respectively. The Cryptosporidium species identified included C. hominis and C. parvum, each with three subtype families. The C. hominis subtypes were IbA6G3 (n = 2), IdA17 (n = 1), IdA24 (n = 1) and IfA14G1R5 (n = 1), while C. parvum subtypes were IIdA20G1 (n = 1), IIaA15G2R1 (n = 1), and IIcA5G3a (n = 1). The G. duodenalis identified included both assemblages A (n = 31) and B (n = 34). All G. duodenalis assemblage A belonged to the anthroponotic sub-assemblage AII, while a high genetic heterogeneity was seen within assemblage B. CONCLUSIONS: Data from this study are useful in our understanding of the genetic diversity of Cryptosporidium spp. and G. duodenalis in Egypt and the potential importance of anthroponotic transmission in the epidemiology of both pathogens. |
Microevolution of highly pathogenic avian influenza A(H5N1) viruses isolated from humans, Egypt, 2007-2011
Younan M , Poh MK , Elassal E , Davis T , Rivailler P , Balish AL , Simpson N , Jones J , Deyde V , Loughlin R , Perry I , Gubareva L , Elbadry MA , Truelove S , Gaynor AM , Mohareb E , Amin M , Cornelius C , Pimentel G , Earhart K , Naguib A , Abdelghani AS , Refaey S , Klimov AI , Donis RO , Kandeel A . Emerg Infect Dis 2013 19 (1) 43-50 We analyzed highly pathogenic avian influenza A(H5N1) viruses isolated from humans infected in Egypt during 2007-2011. All analyzed viruses evolved from the lineage of subtype H5N1 viruses introduced into Egypt in 2006; we found minimal evidence of reassortment and no exotic introductions. The hemagglutinin genes of the viruses from 2011 formed a monophyletic group within clade 2.2.1 that also included human viruses from 2009 and 2010 and contemporary viruses from poultry; this finding is consistent with zoonotic transmission. Although molecular markers suggestive of decreased susceptibility to antiviral drugs were detected sporadically in the neuraminidase and matrix 2 proteins, functional neuraminidase inhibition assays did not identify resistant viruses. No other mutations suggesting a change in the threat to public health were detected in the viral proteomes. However, a comparison of representative subtype H5N1 viruses from 2011 with older subtype H5N1 viruses from Egypt revealed substantial antigenic drift. |
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