Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal
Infect Genet Evol. 2021 Apr 15:104864. doi: 10.1016/j.meegid.2021.104864. Online ahead of print.NO ABSTRACTPMID:33866019 | DOI:10.1016/j.meegid.2021.104864 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 18, 2021 Category: Genetics & Stem Cells Authors: Amary Fall Farah Elawar Emma B Hodcroft Mamadou Malado Jallow Cheikh Talibouya Toure Mamadou A Barry Davy Evrard Kiori Sara Sy Yague Diaw D éborah Goudiaby Mbayame Ndiaye Niang Ndongo Dia Source Type: research

Insight into the drug resistance whole genome of Mycobacterium tuberculosis isolates from Khyber Pakhtunkhwa, Pakistan
Infect Genet Evol. 2021 Apr 13:104861. doi: 10.1016/j.meegid.2021.104861. Online ahead of print.ABSTRACTWhole genome sequencing (WGS) is one of the most reliable methods for detection of drug resistance, genetic diversity in other virulence factor and also evolutionary dynamics of Mycobacterium tuberculosis complex (MTBC). First-line anti-tuberculosis drugs are the major weapons against Mycobacterium tuberculosis (MTB). However, the emergence of drug resistance remained a major obstacle towards global tuberculosis (TB) control program 2030, especially in high burden countries including Pakistan. To overcome the resistance ...
Source: Infection, Genetics and Evolution - April 16, 2021 Category: Genetics & Stem Cells Authors: Muhammad Tahir Khan Sajid Ali Anwar Sheed Khan Arif Ali Abbas Khan Aman Chandra Kaushik Muhammad Irfan Sathishkumar Chinnasamy Shulin Zhang Yu-Juan Zhang Zhilei Cui Amie Jinghua Wei Yanjie Wang Mingzhu Zhao Kejia Liu Heng Wang Muhammad Tariq Zeb Dong Qing Source Type: research

Insight into the drug resistance whole genome of Mycobacterium tuberculosis isolates from Khyber Pakhtunkhwa, Pakistan
Infect Genet Evol. 2021 Apr 13:104861. doi: 10.1016/j.meegid.2021.104861. Online ahead of print.ABSTRACTWhole genome sequencing (WGS) is one of the most reliable methods for detection of drug resistance, genetic diversity in other virulence factor and also evolutionary dynamics of Mycobacterium tuberculosis complex (MTBC). First-line anti-tuberculosis drugs are the major weapons against Mycobacterium tuberculosis (MTB). However, the emergence of drug resistance remained a major obstacle towards global tuberculosis (TB) control program 2030, especially in high burden countries including Pakistan. To overcome the resistance ...
Source: Infection, Genetics and Evolution - April 16, 2021 Category: Genetics & Stem Cells Authors: Muhammad Tahir Khan Sajid Ali Anwar Sheed Khan Arif Ali Abbas Khan Aman Chandra Kaushik Muhammad Irfan Sathishkumar Chinnasamy Shulin Zhang Yu-Juan Zhang Zhilei Cui Amie Jinghua Wei Yanjie Wang Mingzhu Zhao Kejia Liu Heng Wang Muhammad Tariq Zeb Dong Qing Source Type: research

Unravelling the genetic diversity and relatedness of Echinococcus multilocularis isolates in Eurasia using the EmsB microsatellite nuclear marker
In this study, EmsB microsatellite genotyping of E. multilocularis was performed to describe the genetic diversity and relatedness of 785 E. multilocularis isolates from four western and nine eastern European countries, as well as from Armenia and the Asian parts of Russia and Turkey. The presence of the same E. multilocularis populations in the Benelux resulting from expansion from the historical Alpine focus can be deduced from the main profiles shared between these countries. All 33 EmsB profiles obtained from 528 samples from the nine eastern European countries belonged to the European clade, except one Asian profile f...
Source: Infection, Genetics and Evolution - April 15, 2021 Category: Genetics & Stem Cells Authors: G érald Umhang Vanessa Bastid Hamza Avcioglu Guna Bagrade Miljenko Bujani ć Oliveira Bjeli ć Čabrilo Adriano Casulli Pierre Dorny Joke van der Giessen Esin Guven Jiri Harna Jacek Karamon Vitaliy Kharchenko Jenny Knapp Libuse Kolarova Sergey Konyaev Le Source Type: research

Unravelling the genetic diversity and relatedness of Echinococcus multilocularis isolates in Eurasia using the EmsB microsatellite nuclear marker
In this study, EmsB microsatellite genotyping of E. multilocularis was performed to describe the genetic diversity and relatedness of 785 E. multilocularis isolates from four western and nine eastern European countries, as well as from Armenia and the Asian parts of Russia and Turkey. The presence of the same E. multilocularis populations in the Benelux resulting from expansion from the historical Alpine focus can be deduced from the main profiles shared between these countries. All 33 EmsB profiles obtained from 528 samples from the nine eastern European countries belonged to the European clade, except one Asian profile f...
Source: Infection, Genetics and Evolution - April 15, 2021 Category: Genetics & Stem Cells Authors: G érald Umhang Vanessa Bastid Hamza Avcioglu Guna Bagrade Miljenko Bujani ć Oliveira Bjeli ć Čabrilo Adriano Casulli Pierre Dorny Joke van der Giessen Esin Guven Jiri Harna Jacek Karamon Vitaliy Kharchenko Jenny Knapp Libuse Kolarova Sergey Konyaev Le Source Type: research

Systematizing the genomic order and relatedness in the open reading frames (ORFs) of the coronaviruses
Infect Genet Evol. 2021 Apr 10:104858. doi: 10.1016/j.meegid.2021.104858. Online ahead of print.ABSTRACTThe coronaviruses (CoVs), including SARS-CoV-2, the agent of the ongoing deadly CoVID-19 pandemic (Coronavirus disease-2019), represent a highly complex and diverse class of RNA viruses with large genomes, complex gene repertoire, and intricate transcriptional and translational mechanisms. The 3'-terminal one-third of the genome encodes four structural proteins, namely spike, envelope, membrane, and nucleocapsid, interspersed with genes for accessory proteins that are largely nonstructural and called 'open reading frame'...
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: Sailen Barik Source Type: research

Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype
Infect Genet Evol. 2021 Apr 10:104859. doi: 10.1016/j.meegid.2021.104859. Online ahead of print.ABSTRACTCryptosporidium is an important protozoan parasite and due to its resistance to chlorine is a major cause of swimming pool-associated gastroenteritis outbreaks. The present study combined contact tracing and molecular techniques to analyse cryptosporidiosis cases and outbreaks in Western Australia in 2019 and 2020. In the 2019 outbreak, subtyping at the 60 kDa glycoprotein (gp60) gene identified 89.0% (16/18) of samples were caused by the C. hominis IdA15G1 subtype. Amplicon next generation sequencing (NGS) at the gp60 l...
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: Kamil Braima Alireza Zahedi Siobhon Egan Jill Austen Lihua Xiao Yaoyu Feng Benjamin Witham Nevada Pingault Shalinie Perera Charlotte Oskam Simon Reid Una Ryan Source Type: research

Spleen and lung virome analysis of South American fur seals (Arctocephalus australis) collected on the southern Brazilian coast
Infect Genet Evol. 2021 Apr 10:104862. doi: 10.1016/j.meegid.2021.104862. Online ahead of print.ABSTRACTSouth American fur seals (Arctocephalus australis) are believed to reach the coast of Rio Grande do Sul (RS) through sea currents. They live in colonies and are frequently found resting on the beach. However, it is also common to find dead pinnipeds on beaches, sharing the environment with humans, domestic animals and other wild species on the coast and facilitating the transmission of pathogens. In the present study, a metagenomic approach was applied to evaluate the viral diversity in organs of fur seals found deceased...
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: R Canova R F Budaszewski M N Weber M S da Silva D E Puhl L O Battisti J F Soares P G Wagner A P M Varela F Q Mayer C W Canal Source Type: research

LncRNA ZFAS1 plays a role in regulating the inflammatory responses in sepsis-induced acute lung injury via mediating miR-193a-3p
CONCLUSION: Overexpression of ZFAS1, possibly via targeting the expression of miR-193a-3p, could inhibit the apoptosis and ameliorate the inflammatory responses of ALI in sepsis.PMID:33848686 | DOI:10.1016/j.meegid.2021.104860 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: Yan Jiang Wei Zhang Source Type: research

Systematizing the genomic order and relatedness in the open reading frames (ORFs) of the coronaviruses
Infect Genet Evol. 2021 Apr 10:104858. doi: 10.1016/j.meegid.2021.104858. Online ahead of print.ABSTRACTThe coronaviruses (CoVs), including SARS-CoV-2, the agent of the ongoing deadly CoVID-19 pandemic (Coronavirus disease-2019), represent a highly complex and diverse class of RNA viruses with large genomes, complex gene repertoire, and intricate transcriptional and translational mechanisms. The 3'-terminal one-third of the genome encodes four structural proteins, namely spike, envelope, membrane, and nucleocapsid, interspersed with genes for accessory proteins that are largely nonstructural and called 'open reading frame'...
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: Sailen Barik Source Type: research

Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype
Infect Genet Evol. 2021 Apr 10:104859. doi: 10.1016/j.meegid.2021.104859. Online ahead of print.ABSTRACTCryptosporidium is an important protozoan parasite and due to its resistance to chlorine is a major cause of swimming pool-associated gastroenteritis outbreaks. The present study combined contact tracing and molecular techniques to analyse cryptosporidiosis cases and outbreaks in Western Australia in 2019 and 2020. In the 2019 outbreak, subtyping at the 60 kDa glycoprotein (gp60) gene identified 89.0% (16/18) of samples were caused by the C. hominis IdA15G1 subtype. Amplicon next generation sequencing (NGS) at the gp60 l...
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: Kamil Braima Alireza Zahedi Siobhon Egan Jill Austen Lihua Xiao Yaoyu Feng Benjamin Witham Nevada Pingault Shalinie Perera Charlotte Oskam Simon Reid Una Ryan Source Type: research

Spleen and lung virome analysis of South American fur seals (Arctocephalus australis) collected on the southern Brazilian coast
Infect Genet Evol. 2021 Apr 10:104862. doi: 10.1016/j.meegid.2021.104862. Online ahead of print.ABSTRACTSouth American fur seals (Arctocephalus australis) are believed to reach the coast of Rio Grande do Sul (RS) through sea currents. They live in colonies and are frequently found resting on the beach. However, it is also common to find dead pinnipeds on beaches, sharing the environment with humans, domestic animals and other wild species on the coast and facilitating the transmission of pathogens. In the present study, a metagenomic approach was applied to evaluate the viral diversity in organs of fur seals found deceased...
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: R Canova R F Budaszewski M N Weber M S da Silva D E Puhl L O Battisti J F Soares P G Wagner A P M Varela F Q Mayer C W Canal Source Type: research

LncRNA ZFAS1 plays a role in regulating the inflammatory responses in sepsis-induced acute lung injury via mediating miR-193a-3p
CONCLUSION: Overexpression of ZFAS1, possibly via targeting the expression of miR-193a-3p, could inhibit the apoptosis and ameliorate the inflammatory responses of ALI in sepsis.PMID:33848686 | DOI:10.1016/j.meegid.2021.104860 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 13, 2021 Category: Genetics & Stem Cells Authors: Yan Jiang Wei Zhang Source Type: research

Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians
Infect Genet Evol. 2021 Apr 8:104855. doi: 10.1016/j.meegid.2021.104855. Online ahead of print.ABSTRACTINTRODUCTION: Non-classical class I human leukocyte antigens (HLA) molecules are known to modulate the function of cytotoxic cells (NK and T CD8+) during viral infection by interacting with inhibitory/activating receptors. However, little is known about the HLA-E/-F genetic variability on arbovirus infections.METHODS: We evaluated by massive parallel sequencing the full HLA-E/-F genetic diversity among patients infected during the arbovirus (ZIKV, DENV, and CHIKV) outbreak leading to a broad range of neurological complica...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Paulin Sonon Cristhianna V A Collares Maria L úcia Brito Ferreira Renata Santos Almeida Ibrahim Sadissou Marli Ten ório Cordeiro Maria de F átima Militão de Albuquerque Erick C Castelli Norma Lucena-Silva Eduardo A Donadi Source Type: research

Pharmacogenetic predictors of nevirapine pharmacokinetics in Ghanaian children living with HIV with or without TB coinfection
We examined the relationship between genetic variations in relevant drug disposition genes and NVP PK parameters in Ghanaian children living with HIV eligible to initiate NVP-based antiretroviral therapy. Participants received NVP plus zidovudine and lamivudine or abacavir and lamivudine twice daily, and those with tuberculosis (TB) coinfection received concurrent anti-TB therapy with NVP. Pharmacokinetic sampling was performed after at least 4 weeks of antiretroviral therapy. Nevirapine minimum concentration (Cmin), area under the concentration-time curve from time 0 to 12 h (AUC0-12h), and apparent clearance (CL/F) were ...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Taimour Langaee Mohammad H Al-Shaer Yan Gong Elizabeth Lima Sampson Antwi Anthony Enimil Albert Dompreh Hongmei Yang Wael A Alghamdi Lubbe Wiesner Charles A Peloquin Awewura Kwara Source Type: research

Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families
Infect Genet Evol. 2021 Apr 8:104853. doi: 10.1016/j.meegid.2021.104853. Online ahead of print.ABSTRACTMicrosatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Ci...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Ankit Jain Prakash C Sharma Source Type: research

Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil
Infect Genet Evol. 2021 Apr 8:104854. doi: 10.1016/j.meegid.2021.104854. Online ahead of print.ABSTRACTThe HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. HIV-1C proved to be the most frequent sub...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Hegger M Fritsch Amilcar Tanuri Aguinaldo R Pinto Tiago Gr äf Source Type: research

Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians
Infect Genet Evol. 2021 Apr 8:104855. doi: 10.1016/j.meegid.2021.104855. Online ahead of print.ABSTRACTINTRODUCTION: Non-classical class I human leukocyte antigens (HLA) molecules are known to modulate the function of cytotoxic cells (NK and T CD8+) during viral infection by interacting with inhibitory/activating receptors. However, little is known about the HLA-E/-F genetic variability on arbovirus infections.METHODS: We evaluated by massive parallel sequencing the full HLA-E/-F genetic diversity among patients infected during the arbovirus (ZIKV, DENV, and CHIKV) outbreak leading to a broad range of neurological complica...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Paulin Sonon Cristhianna V A Collares Maria L úcia Brito Ferreira Renata Santos Almeida Ibrahim Sadissou Marli Ten ório Cordeiro Maria de F átima Militão de Albuquerque Erick C Castelli Norma Lucena-Silva Eduardo A Donadi Source Type: research

Pharmacogenetic predictors of nevirapine pharmacokinetics in Ghanaian children living with HIV with or without TB coinfection
We examined the relationship between genetic variations in relevant drug disposition genes and NVP PK parameters in Ghanaian children living with HIV eligible to initiate NVP-based antiretroviral therapy. Participants received NVP plus zidovudine and lamivudine or abacavir and lamivudine twice daily, and those with tuberculosis (TB) coinfection received concurrent anti-TB therapy with NVP. Pharmacokinetic sampling was performed after at least 4 weeks of antiretroviral therapy. Nevirapine minimum concentration (Cmin), area under the concentration-time curve from time 0 to 12 h (AUC0-12h), and apparent clearance (CL/F) were ...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Taimour Langaee Mohammad H Al-Shaer Yan Gong Elizabeth Lima Sampson Antwi Anthony Enimil Albert Dompreh Hongmei Yang Wael A Alghamdi Lubbe Wiesner Charles A Peloquin Awewura Kwara Source Type: research

Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families
Infect Genet Evol. 2021 Apr 8:104853. doi: 10.1016/j.meegid.2021.104853. Online ahead of print.ABSTRACTMicrosatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Ci...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Ankit Jain Prakash C Sharma Source Type: research

Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil
Infect Genet Evol. 2021 Apr 8:104854. doi: 10.1016/j.meegid.2021.104854. Online ahead of print.ABSTRACTThe HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. HIV-1C proved to be the most frequent sub...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Hegger M Fritsch Amilcar Tanuri Aguinaldo R Pinto Tiago Gr äf Source Type: research

Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians
Infect Genet Evol. 2021 Apr 8:104855. doi: 10.1016/j.meegid.2021.104855. Online ahead of print.ABSTRACTINTRODUCTION: Non-classical class I human leukocyte antigens (HLA) molecules are known to modulate the function of cytotoxic cells (NK and T CD8+) during viral infection by interacting with inhibitory/activating receptors. However, little is known about the HLA-E/-F genetic variability on arbovirus infections.METHODS: We evaluated by massive parallel sequencing the full HLA-E/-F genetic diversity among patients infected during the arbovirus (ZIKV, DENV, and CHIKV) outbreak leading to a broad range of neurological complica...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Paulin Sonon Cristhianna V A Collares Maria L úcia Brito Ferreira Renata Santos Almeida Ibrahim Sadissou Marli Ten ório Cordeiro Maria de F átima Militão de Albuquerque Erick C Castelli Norma Lucena-Silva Eduardo A Donadi Source Type: research

Pharmacogenetic predictors of nevirapine pharmacokinetics in Ghanaian children living with HIV with or without TB coinfection
We examined the relationship between genetic variations in relevant drug disposition genes and NVP PK parameters in Ghanaian children living with HIV eligible to initiate NVP-based antiretroviral therapy. Participants received NVP plus zidovudine and lamivudine or abacavir and lamivudine twice daily, and those with tuberculosis (TB) coinfection received concurrent anti-TB therapy with NVP. Pharmacokinetic sampling was performed after at least 4 weeks of antiretroviral therapy. Nevirapine minimum concentration (Cmin), area under the concentration-time curve from time 0 to 12 h (AUC0-12h), and apparent clearance (CL/F) were ...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Taimour Langaee Mohammad H Al-Shaer Yan Gong Elizabeth Lima Sampson Antwi Anthony Enimil Albert Dompreh Hongmei Yang Wael A Alghamdi Lubbe Wiesner Charles A Peloquin Awewura Kwara Source Type: research

Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families
Infect Genet Evol. 2021 Apr 8:104853. doi: 10.1016/j.meegid.2021.104853. Online ahead of print.ABSTRACTMicrosatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Ci...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Ankit Jain Prakash C Sharma Source Type: research

Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil
Infect Genet Evol. 2021 Apr 8:104854. doi: 10.1016/j.meegid.2021.104854. Online ahead of print.ABSTRACTThe HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. HIV-1C proved to be the most frequent sub...
Source: Infection, Genetics and Evolution - April 11, 2021 Category: Genetics & Stem Cells Authors: Hegger M Fritsch Amilcar Tanuri Aguinaldo R Pinto Tiago Gr äf Source Type: research

EntroPhylo: An entropy-based tool to select phylogenetic informative regions and primer design
We present a novel entropy-based computational tool that selects phylogenetic informative genomic regions associated with degenerate primer design. This tool identifies proper phylogenetic markers and proposes suitable degenerate primers to amplify and sequence them. The algorithm calculates the entropy value per site, and the selected region is used for primer design. In order to evaluate the tool, sequences of bovine papillomavirus L1 gene were obtained. Once the molecular region was selected, the primers were designed by the software and used in a PCR reaction for viral detection. Three positive samples were tested with...
Source: Infection, Genetics and Evolution - April 10, 2021 Category: Genetics & Stem Cells Authors: Fernanda Lays Souza G óes Santos S érgio de Sá Leitão Paiva Júnior Antonio Carlos de Freitas Valdir de Queiroz Balbino Marcus Vinicius de Arag ão Batista Source Type: research

First report of N1575Y mutation in Anopheles gambiae in Sierra Leone
Infect Genet Evol. 2021 Apr 5:104852. doi: 10.1016/j.meegid.2021.104852. Online ahead of print.ABSTRACTThe resistance of mosquito vectors to insecticides is one of the biological obstacles in the fight against malaria. Understanding of the status and mechanisms underlying the insecticide resistance in Anopheles gambiae species is necessary for success of vector control efforts. The study aimed to determine the molecular forms of An. gambiae from four districts in Sierra Leone during May and June 2018, and the level of N1575Y mutation. The molecular form identification of adult female An. gambiae mosquitoes reared from larv...
Source: Infection, Genetics and Evolution - April 8, 2021 Category: Genetics & Stem Cells Authors: Jianhai Yin Frederick Yamba Canjun Zheng Samuel Juana Smith Lili Wang Hongmei Li Zhigui Xia Shuisen Zhou Ning Xiao Source Type: research

First report of N1575Y mutation in Anopheles gambiae in Sierra Leone
Infect Genet Evol. 2021 Apr 5:104852. doi: 10.1016/j.meegid.2021.104852. Online ahead of print.ABSTRACTThe resistance of mosquito vectors to insecticides is one of the biological obstacles in the fight against malaria. Understanding of the status and mechanisms underlying the insecticide resistance in Anopheles gambiae species is necessary for success of vector control efforts. The study aimed to determine the molecular forms of An. gambiae from four districts in Sierra Leone during May and June 2018, and the level of N1575Y mutation. The molecular form identification of adult female An. gambiae mosquitoes reared from larv...
Source: Infection, Genetics and Evolution - April 8, 2021 Category: Genetics & Stem Cells Authors: Jianhai Yin Frederick Yamba Canjun Zheng Samuel Juana Smith Lili Wang Hongmei Li Zhigui Xia Shuisen Zhou Ning Xiao Source Type: research

First report of N1575Y mutation in Anopheles gambiae in Sierra Leone
Infect Genet Evol. 2021 Apr 5:104852. doi: 10.1016/j.meegid.2021.104852. Online ahead of print.ABSTRACTThe resistance of mosquito vectors to insecticides is one of the biological obstacles in the fight against malaria. Understanding of the status and mechanisms underlying the insecticide resistance in Anopheles gambiae species is necessary for success of vector control efforts. The study aimed to determine the molecular forms of An. gambiae from four districts in Sierra Leone during May and June 2018, and the level of N1575Y mutation. The molecular form identification of adult female An. gambiae mosquitoes reared from larv...
Source: Infection, Genetics and Evolution - April 8, 2021 Category: Genetics & Stem Cells Authors: Jianhai Yin Frederick Yamba Canjun Zheng Samuel Juana Smith Lili Wang Hongmei Li Zhigui Xia Shuisen Zhou Ning Xiao Source Type: research

Conserved Plasmodium protein (PF3D7_0406000) of unknown function, in-silico analysis and cellular localization
Infect Genet Evol. 2021 Apr 3:104848. doi: 10.1016/j.meegid.2021.104848. Online ahead of print.ABSTRACTIn spite of a decrease in malaria cases, the threat of malaria due to Plasmodium falciparum still prevails. The sequencing of Plasmodium falciparum reveals that approximately 60% of the Plasmodium genes code for hypothetical/putative proteins. Here we report an in silico characterization and localization of one such protein. This was encoded by one of the hub genes, in a weighted gene co-expression based systems network, from in-vivo samples of patients suffering from uncomplicated malaria or complicated malaria disease l...
Source: Infection, Genetics and Evolution - April 6, 2021 Category: Genetics & Stem Cells Authors: Isha Pandey Afshana Quadiri Ishan Wadi C R Pillai Agam P Singh Ashis Das Source Type: research

Genomic sequences and pathogenic characteristics of two variant duck reoviruses associated with spleen necrosis
This study will help us to formulate effective prevention and control strategies against NDRV and enrich our understanding of the intra- and inter-species relationships of orthoreoviruses.PMID:33823307 | DOI:10.1016/j.meegid.2021.104847 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 6, 2021 Category: Genetics & Stem Cells Authors: Dan Luo Rui Liu Lixue Weng Kai Li Xiaole Qi Yulong Gao Changjun Liu Yanping Zhang Hongyu Cui Qing Pan Li Gao Xiaomei Wang Source Type: research

Conserved Plasmodium protein (PF3D7_0406000) of unknown function, in-silico analysis and cellular localization
Infect Genet Evol. 2021 Apr 3:104848. doi: 10.1016/j.meegid.2021.104848. Online ahead of print.ABSTRACTIn spite of a decrease in malaria cases, the threat of malaria due to Plasmodium falciparum still prevails. The sequencing of Plasmodium falciparum reveals that approximately 60% of the Plasmodium genes code for hypothetical/putative proteins. Here we report an in silico characterization and localization of one such protein. This was encoded by one of the hub genes, in a weighted gene co-expression based systems network, from in-vivo samples of patients suffering from uncomplicated malaria or complicated malaria disease l...
Source: Infection, Genetics and Evolution - April 6, 2021 Category: Genetics & Stem Cells Authors: Isha Pandey Afshana Quadiri Ishan Wadi C R Pillai Agam P Singh Ashis Das Source Type: research

Genomic sequences and pathogenic characteristics of two variant duck reoviruses associated with spleen necrosis
This study will help us to formulate effective prevention and control strategies against NDRV and enrich our understanding of the intra- and inter-species relationships of orthoreoviruses.PMID:33823307 | DOI:10.1016/j.meegid.2021.104847 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 6, 2021 Category: Genetics & Stem Cells Authors: Dan Luo Rui Liu Lixue Weng Kai Li Xiaole Qi Yulong Gao Changjun Liu Yanping Zhang Hongyu Cui Qing Pan Li Gao Xiaomei Wang Source Type: research

Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes
Infect Genet Evol. 2021 Apr 2;92:104823. doi: 10.1016/j.meegid.2021.104823. Online ahead of print.ABSTRACTThe surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in ...
Source: Infection, Genetics and Evolution - April 5, 2021 Category: Genetics & Stem Cells Authors: Nimisha Ghosh Nikhil Sharma Indrajit Saha Source Type: research

Genetic characterization of Neospora caninum from aborted bovine fetuses in Hokkaido, Japan
This study describes, for the first time, the genetic characterization of isolates of N. caninum implicated in cattle abortions in Japan. Brains from five aborted fetuses were successfully genotyped based on multilocus microsatellite markers. Assigned genotypes showed high frequencies of mixed alleles in the sequenced markers MS7 and MS10, raising concerns about the subpopulation structures of N. caninum infecting animals in Japan. Clustering analysis of the genotypes, together with those from a previous dataset, showed that five of the six genotypes were distinct from other clusters. Meanwhile, the remaining genotype, tog...
Source: Infection, Genetics and Evolution - April 5, 2021 Category: Genetics & Stem Cells Authors: El-Sayed El-Alfy Yuma Ohari Naomi Shimoda Yoshifumi Nishikawa Source Type: research

Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes
Infect Genet Evol. 2021 Apr 2:104823. doi: 10.1016/j.meegid.2021.104823. Online ahead of print.ABSTRACTThe surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in thi...
Source: Infection, Genetics and Evolution - April 5, 2021 Category: Genetics & Stem Cells Authors: Nimisha Ghosh Nikhil Sharma Indrajit Saha Source Type: research

Genetic characterization of Neospora caninum from aborted bovine fetuses in Hokkaido, Japan
This study describes, for the first time, the genetic characterization of isolates of N. caninum implicated in cattle abortions in Japan. Brains from five aborted fetuses were successfully genotyped based on multilocus microsatellite markers. Assigned genotypes showed high frequencies of mixed alleles in the sequenced markers MS7 and MS10, raising concerns about the subpopulation structures of N. caninum infecting animals in Japan. Clustering analysis of the genotypes, together with those from a previous dataset, showed that five of the six genotypes were distinct from other clusters. Meanwhile, the remaining genotype, tog...
Source: Infection, Genetics and Evolution - April 5, 2021 Category: Genetics & Stem Cells Authors: El-Sayed El-Alfy Yuma Ohari Naomi Shimoda Yoshifumi Nishikawa Source Type: research

In silico analysis of molecular interactions between HIV-1 glycoprotein gp120 and TNF receptors
In conclusion, gp120 may stimulate pro-inflammatory and apoptotic signaling transduction pathways mediated by TNFR2 and may act as an attachment factor retaining HIV-1 viral particles on the host cell surface.PMID:33813078 | DOI:10.1016/j.meegid.2021.104837 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 4, 2021 Category: Genetics & Stem Cells Authors: Neyla Maria Pereira Alves Ronald Rodrigues de Moura Lucas Co êlho Bernardo Almerinda Agrelli Ana Sofia Lima Estev ão de Oliveira Nat ália Pereira da Silva Sergio Crovella Lucas Andr é Cavalcanti Brandão Source Type: research

In silico analysis of molecular interactions between HIV-1 glycoprotein gp120 and TNF receptors
In conclusion, gp120 may stimulate pro-inflammatory and apoptotic signaling transduction pathways mediated by TNFR2 and may act as an attachment factor retaining HIV-1 viral particles on the host cell surface.PMID:33813078 | DOI:10.1016/j.meegid.2021.104837 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 4, 2021 Category: Genetics & Stem Cells Authors: Neyla Maria Pereira Alves Ronald Rodrigues de Moura Lucas Co êlho Bernardo Almerinda Agrelli Ana Sofia Lima Estev ão de Oliveira Nat ália Pereira da Silva Sergio Crovella Lucas Andr é Cavalcanti Brandão Source Type: research

The role of microRNAs in modulating SARS-CoV-2 infection in human cells: a systematic review
In conclusion, despite the limited number of studies identified, based on the search terms and eligibility criteria applied, this systematic review provides evidence on the impact of miRNAs on SARS-CoV-2 infection and COVID-19. Although most of the reported viral/host miRNAs interactions were based on in silico prediction analysis, they demonstrate the relevance of the viral/host miRNA interaction for viral activity and host responses. In addition, the identified studies highlight the potential use of miRNAs as therapeutic targets against COVID-19, and other viral human diseases (This review was registered at the Internati...
Source: Infection, Genetics and Evolution - April 3, 2021 Category: Genetics & Stem Cells Authors: Rafael Marchi Bruna Sugita Ariana Centa Aline S Fonseca Stefanne Bortoletto Karine Fiorentin Solange Ferreira Luciane R Cavalli Source Type: research

Predictive analysis of COVID-19 eradication with vaccination in India, Brazil, and U.S.A
Infect Genet Evol. 2021 Mar 30:104834. doi: 10.1016/j.meegid.2021.104834. Online ahead of print.ABSTRACTThe most important question and concern in these circumstances of COVID-19 epidemic outspread is when will the pandemic end? Vaccination is the only solution to restore life to normalcy in the fastest and safest possible manner. Therefore, we have carried out a predictive analysis for realistic time scale estimates for overcoming the epidemic considering vaccination rate effect on the dynamics of COVID-19 control. In particular we discuss the worst affected large countries like India, Brazil and USA for estimating effect...
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Deepa Chaturvedi U Chakravarty Source Type: research

Virulent African horse sickness virus serotype 4 interferes with the innate immune response in horse peripheral blood mononuclear cells in vitro
Infect Genet Evol. 2021 Mar 30:104836. doi: 10.1016/j.meegid.2021.104836. Online ahead of print.ABSTRACTAfrican horse sickness (AHS) is caused by African horse sickness virus (AHSV), a double stranded RNA (dsRNA) virus of the genus Orbivirus, family Reoviridae. For the development of new generation AHS vaccines or antiviral treatments, it is crucial to understand the host immune response against the virus and the immune evasion strategies the virus employs. To achieve this, the current study used transcriptome analysis of RNA sequences to characterize and compare the innate immune responses activated during the attenuated ...
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Erika Faber Selaelo Ivy Tshilwane Mirinda Van Kleef Alri Pretorius Source Type: research

Genotyping of Entamoeba nuttalli strains from the wild rhesus macaques of Myanmar and comparison with those from the wild rhesus macaques of Nepal and China
In this study, the prevalence of Entamoeba infections was examined in wild rhesus macaques by examining 73 and 90 fecal samples collected from two sites, Popa Taung Kalat (PTK) and Pho Win Taung (PWT), in Myanmar. The positive rates of E. nuttalli detected using PCR were 49% and 31% in PTK and PWT, respectively, but no infections of E. histolytica and E. moshkovskii were found. Entamoeba dispar was detected in 6% of samples only from PWT. Positive rates of E. chattoni and E. coli were both 70% in PWT and 67% and 79% in PTK, respectively. Six E. nuttalli strains from PTK and eight from PWT were obtained in the culture with ...
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Hla Myat Mon Meng Feng Urassaya Pattanwong Rattiporn Kosuwin Tetsuo Yanagi Seiki Kobayashi Chaturong Putaporntip Somchai Jongwutiwes Xunjia Cheng Hiroshi Tachibana Source Type: research

Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes
In this study, we comprehensively analyzed genetic variations in SARS-CoV-2, gaining insights into amino acid variations in ORF1ab and COVID-19 outcomes.PMID:33798758 | DOI:10.1016/j.meegid.2021.104831 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Canhui Cao Liang He Yuan Tian Yu Qin Haiyin Sun Wencheng Ding Lingli Gui Peng Wu Source Type: research

Seroprevalence investigation and genetic analysis of pseudorabies virus within pig populations in Henan province of China during 2018-2019
This study suggests that three PRV isolates may belong to PRV variants, and the development of a novel vaccine against PRV variants is particularly urgent.PMID:33798759 | DOI:10.1016/j.meegid.2021.104835 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Hui-Hua Zheng Yue Jin Cheng-Yao Hou Xin-Sheng Li Li Zhao Zhen-Ya Wang Hong-Ying Chen Source Type: research

Predictive analysis of COVID-19 eradication with vaccination in India, Brazil, and U.S.A
Infect Genet Evol. 2021 Mar 30:104834. doi: 10.1016/j.meegid.2021.104834. Online ahead of print.ABSTRACTThe most important question and concern in these circumstances of COVID-19 epidemic outspread is when will the pandemic end? Vaccination is the only solution to restore life to normalcy in the fastest and safest possible manner. Therefore, we have carried out a predictive analysis for realistic time scale estimates for overcoming the epidemic considering vaccination rate effect on the dynamics of COVID-19 control. In particular we discuss the worst affected large countries like India, Brazil and USA for estimating effect...
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Deepa Chaturvedi U Chakravarty Source Type: research

Virulent African horse sickness virus serotype 4 interferes with the innate immune response in horse peripheral blood mononuclear cells in vitro
Infect Genet Evol. 2021 Mar 30:104836. doi: 10.1016/j.meegid.2021.104836. Online ahead of print.ABSTRACTAfrican horse sickness (AHS) is caused by African horse sickness virus (AHSV), a double stranded RNA (dsRNA) virus of the genus Orbivirus, family Reoviridae. For the development of new generation AHS vaccines or antiviral treatments, it is crucial to understand the host immune response against the virus and the immune evasion strategies the virus employs. To achieve this, the current study used transcriptome analysis of RNA sequences to characterize and compare the innate immune responses activated during the attenuated ...
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Erika Faber Selaelo Ivy Tshilwane Mirinda Van Kleef Alri Pretorius Source Type: research

Genotyping of Entamoeba nuttalli strains from the wild rhesus macaques of Myanmar and comparison with those from the wild rhesus macaques of Nepal and China
In this study, the prevalence of Entamoeba infections was examined in wild rhesus macaques by examining 73 and 90 fecal samples collected from two sites, Popa Taung Kalat (PTK) and Pho Win Taung (PWT), in Myanmar. The positive rates of E. nuttalli detected using PCR were 49% and 31% in PTK and PWT, respectively, but no infections of E. histolytica and E. moshkovskii were found. Entamoeba dispar was detected in 6% of samples only from PWT. Positive rates of E. chattoni and E. coli were both 70% in PWT and 67% and 79% in PTK, respectively. Six E. nuttalli strains from PTK and eight from PWT were obtained in the culture with ...
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Hla Myat Mon Meng Feng Urassaya Pattanwong Rattiporn Kosuwin Tetsuo Yanagi Seiki Kobayashi Chaturong Putaporntip Somchai Jongwutiwes Xunjia Cheng Hiroshi Tachibana Source Type: research

Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes
In this study, we comprehensively analyzed genetic variations in SARS-CoV-2, gaining insights into amino acid variations in ORF1ab and COVID-19 outcomes.PMID:33798758 | DOI:10.1016/j.meegid.2021.104831 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Canhui Cao Liang He Yuan Tian Yu Qin Haiyin Sun Wencheng Ding Lingli Gui Peng Wu Source Type: research

Seroprevalence investigation and genetic analysis of pseudorabies virus within pig populations in Henan province of China during 2018-2019
This study suggests that three PRV isolates may belong to PRV variants, and the development of a novel vaccine against PRV variants is particularly urgent.PMID:33798759 | DOI:10.1016/j.meegid.2021.104835 (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 2, 2021 Category: Genetics & Stem Cells Authors: Hui-Hua Zheng Yue Jin Cheng-Yao Hou Xin-Sheng Li Li Zhao Zhen-Ya Wang Hong-Ying Chen Source Type: research