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Alasiri A, Soltane R, Hegazy A, Khalil AM, Mahmoud SH, Khalil AA, Martinez-Sobrido L, Mostafa A. Vaccination and Antiviral Treatment against Avian Influenza H5Nx Viruses: A Harbinger of Virus Control or Evolution. Vaccines (Basel) 2023; 11:1628. [PMID: 38005960 PMCID: PMC10675773 DOI: 10.3390/vaccines11111628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the panzootic nature of emergent highly pathogenic avian influenza H5Nx viruses in wild migratory birds and domestic poultry, only a limited number of human infections with H5Nx viruses have been identified since its emergence in 1996. Few countries with endemic avian influenza viruses (AIVs) have implemented vaccination as a control strategy, while most of the countries have adopted a culling strategy for the infected flocks. To date, China and Egypt are the two major sites where vaccination has been adopted to control avian influenza H5Nx infections, especially with the widespread circulation of clade 2.3.4.4b H5N1 viruses. This virus is currently circulating among birds and poultry, with occasional spillovers to mammals, including humans. Herein, we will discuss the history of AIVs in Egypt as one of the hotspots for infections and the improper implementation of prophylactic and therapeutic control strategies, leading to continuous flock outbreaks with remarkable virus evolution scenarios. Along with current pre-pandemic preparedness efforts, comprehensive surveillance of H5Nx viruses in wild birds, domestic poultry, and mammals, including humans, in endemic areas is critical to explore the public health risk of the newly emerging immune-evasive or drug-resistant H5Nx variants.
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Affiliation(s)
- Ahlam Alasiri
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (A.A.); (R.S.)
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (A.A.); (R.S.)
| | - Akram Hegazy
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, Giza 12613, Egypt;
| | - Ahmed Magdy Khalil
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Center, Giza 12622, Egypt;
| | - Ahmed A. Khalil
- Veterinary Sera and Vaccines Research Institute (VSVRI), Agriculture Research Center (ARC), Cairo 11435, Egypt;
| | | | - Ahmed Mostafa
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Center of Scientific Excellence for Influenza Viruses, National Research Center, Giza 12622, Egypt;
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Setta A, Yehia N, Shakak AO, Al-Quwaie DA, Al- Otaibi AM, El-Saadony MT, El-Tarabily KA, Salem H. Molecular detection of highly pathogenic avian influenza H5N8 in commercial broiler chicken farms from 2019 to 2022. Poult Sci 2023; 102:102639. [PMID: 37104901 PMCID: PMC10165147 DOI: 10.1016/j.psj.2023.102639] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/14/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) is a serious viral infection that causes massive economic losses in poultry. The current study investigated the HPAI virus prevalence in commercial broiler chicken flocks from 2019 to 2022. Organ samples, including trachea, cecal tonsils, spleen, brain, as well as tracheal and cloacal swabs, were harvested from 111 problematic broiler chicken flocks that suffered from variable mortalities accompanied with respiratory signs (103 H5-vaccinated and 8 nonvaccinated flocks) in Egypt during the observation duration. Molecular tools were used to analyze the samples, including real-time reverse transcription-polymerase chain reaction (rRT-PCR) and sequence analysis of some PCR positive strains. The results indicated that 24 flocks were positive for HPAI H5N8, representing 21.6%, with 22.3% (23/103) prevalence and 12.5% (1/8) detection in vaccinated and nonvaccinated flocks, respectively, and they were almost detected in the autumn and winter seasons. Phylogenetic evaluation of the hemagglutinin (HA) gene showed that the 6 Egyptian strains were clustered in clade 2.3.4.4b and allocated into 2 groups (I and II). The samples recovered in 2019 were clustered in new subgroup A, and samples recovered in 2020 to 2022 were clustered in new subgroup B with 10 nucleotide mutations (R72S, A83D, T140A). In conclusion, HPAI H5N8 is a serious threat even in vaccinated birds; to control such problems, periodic molecular monitoring with vaccine efficacy evaluation and the use of preventive strategies are recommended.
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Rehman S, Prasetya RR, Rahardjo K, Effendi MH, Rantam FA, Rahmahani J, Witaningrum AM, Nastri AM, Dewantari JR, Mori Y, Shimizu K. Whole-genome sequence and genesis of an avian influenza virus H5N1 isolated from a healthy chicken in a live bird market in Indonesia: accumulation of mammalian adaptation markers in avian hosts. PeerJ 2023; 11:e14917. [PMID: 36846456 PMCID: PMC9951803 DOI: 10.7717/peerj.14917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/26/2023] [Indexed: 02/25/2023] Open
Abstract
Background Influenza A viruses are a major pathogen that causes significant clinical and economic harm to many animals. In Indonesia, the highly pathogenic avian influenza (HPAI) H5N1 virus has been endemic in poultry since 2003 and has caused sporadic deadly infections in humans. The genetic bases that determine host range have not yet been fully elucidated. We analyzed the whole-genome sequence of a recent H5 isolate to reveal the evolution toward its mammalian adaptation. Methods We determined the whole-genome sequence of A/chicken/East Java/Av1955/2022 (hereafter, "Av1955") from a healthy chicken in April 2022 and conducted phylogenetic and mutational analysis. Results Phylogenetic analysis revealed that Av1955 belonged to the H5N1 clade 2.3.2.1c (Eurasian lineage). The six gene segments (PB1, PB2, HA, NP, NA, and NS) out of the eight segments derived from viruses of H5N1 Eurasian lineage, one (PB2) from the H3N6 subtype and the remaining one (M) from the H5N1 clade 2.1.3.2b (Indonesian lineage). The donor of the PB2 segment was a reassortant among three viruses of H5N1 Eurasian and Indonesian lineages and the H3N6 subtype. The HA amino acid sequence contained multiple basic amino acids at the cleavage site. Mutation analysis revealed that Av1955 possessed the maximal number of mammalian adaptation marker mutations. Conclusions Av1955 was a virus of H5N1 Eurasian lineage. The HA protein contains an HPAI H5N1-type cleavage site sequence, while the virus was isolated from a healthy chicken suggesting its low pathogenicity nature. The virus has increased mammalian adaptation markers by mutation and intra- and inter-subtype reassortment, gathering gene segments possessing the most abundant maker mutations among previously circulating viruses. The increasing mammalian adaptation mutation in avian hosts suggests that they might be adaptive to infection in mammalian and avian hosts. It highlights the importance of genomic surveillance and adequate control measures for H5N1 infection in live poultry markets.
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Affiliation(s)
- Saifur Rehman
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, Indonesia
| | - Rima Ratnanggana Prasetya
- Indonesia-Japan Collaborative Research Center, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, Indonesia
| | - Krisnoadi Rahardjo
- Indonesia-Japan Collaborative Research Center, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, Indonesia
| | - Mustofa Helmi Effendi
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, Indonesia
| | - Fedik Abdul Rantam
- Laboratory of Virology and Immunology, Division of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, Indonesia
| | - Jola Rahmahani
- Laboratory of Virology and Immunology, Division of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, Indonesia
| | - Adiana Mutamsari Witaningrum
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, Indonesia
| | - Aldise Mareta Nastri
- Indonesia-Japan Collaborative Research Center, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, Indonesia
| | - Jezzy Renova Dewantari
- Indonesia-Japan Collaborative Research Center, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, Indonesia
| | - Yasuko Mori
- Center for Infectious Diseases, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Kazufumi Shimizu
- Indonesia-Japan Collaborative Research Center, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, Indonesia,Center for Infectious Diseases, Graduate School of Medicine, Kobe University, Kobe, Japan
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Genetic Evolution of Avian Influenza A (H9N2) Viruses Isolated from Domestic Poultry in Uganda Reveals Evidence of Mammalian Host Adaptation, Increased Virulence and Reduced Sensitivity to Baloxavir. Viruses 2022; 14:v14092074. [PMID: 36146881 PMCID: PMC9505320 DOI: 10.3390/v14092074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/23/2022] Open
Abstract
A (H9N2) avian influenza A viruses were first detected in Uganda in 2017 and have since established themselves in live bird markets. The aim of this study was to establish the subsequent genetic evolution of H9N2 viruses in Uganda. Cloacal samples collected from live bird market stalls in Kampala from 2017 to 2019 were screened by RT-PCR for influenza A virus and H9N2 viruses were isolated in embryonated eggs. One hundred and fifty H9N2 isolates were subjected to whole genome sequencing on the Illumina MiSeq platform. The sequence data analysis and comparison with contemporary isolates revealed that the virus was first introduced into Uganda in 2014 from ancestors in the Middle East. There has since been an increase in nucleotide substitutions and reassortments among the viruses within and between live bird markets, leading to variations in phylogeny of the different segments, although overall diversity remained low. The isolates had several mutations such as HA-Q226L and NS-I106M that enable mammalian host adaptation, NP-M105V, PB1-D3V, and M1-T215A known for increased virulence/pathogenicity and replication, and PA-E199D, NS-P42S, and M2-S31N that promote drug resistance. The PA-E199D substitution in particular confers resistance to the endonuclease inhibitor Baloxavir acid, which is one of the new anti-influenza drugs. Higher EC50 was observed in isolates with a double F105L+E199D substitution that may suggest a possible synergistic effect. These H9N2 viruses have established an endemic situation in live bird markets in Uganda because of poor biosecurity practices and therefore pose a zoonotic threat. Regular surveillance is necessary to further generate the needed evidence for effective control strategies and to minimize the threats.
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Mercan Y, Atim G, Kayed AE, Azbazdar ME, Kandeil A, Ali MA, Rubrum A, McKenzie P, Webby RJ, Erima B, Wabwire-Mangen F, Ukuli QA, Tugume T, Byarugaba DK, Kayali G, Ducatez MF, Koçer ZA. Molecular Characterization of Closely Related H6N2 Avian Influenza Viruses Isolated from Turkey, Egypt, and Uganda. Viruses 2021; 13:v13040607. [PMID: 33918166 PMCID: PMC8065897 DOI: 10.3390/v13040607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 01/22/2023] Open
Abstract
Genetic analysis of circulating avian influenza viruses (AIVs) in wild birds at different geographical regions during the same period could improve our knowledge about virus transmission dynamics in natural hosts, virus evolution as well as zoonotic potential. Here, we report the genetic and molecular characterization of H6N2 influenza viruses isolated from migratory birds in Turkey, Egypt, and Uganda during 2017–2018. The Egyptian and Turkish isolates were genetically closer to each other than they were to the virus isolated from Uganda. Our results also suggest that multiple reassortment events were involved in the genesis of the isolated viruses. All viruses contained molecular markers previously associated with increased replication and/or pathogenicity in mammals. The results of this study indicate that H6N2 viruses carried by migratory birds on the West Asian/East African and Mediterranean/Black Sea flyways have the potential to transmit to mammals including humans. Additionally, adaptation markers in these viruses indicate the potential risk for poultry, which also increases the possibility of human exposure to these viruses.
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Affiliation(s)
- Yavuz Mercan
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey; (Y.M.); (M.E.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Gladys Atim
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Ahmed E. Kayed
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12311, Egypt; (A.E.K.); (A.K.); (M.A.A.)
| | - M. Ekin Azbazdar
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey; (Y.M.); (M.E.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12311, Egypt; (A.E.K.); (A.K.); (M.A.A.)
| | - Mohamed A. Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12311, Egypt; (A.E.K.); (A.K.); (M.A.A.)
| | - Adam Rubrum
- St Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (P.M.); (R.J.W.)
| | - Pamela McKenzie
- St Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (P.M.); (R.J.W.)
| | - Richard J. Webby
- St Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (P.M.); (R.J.W.)
| | - Bernard Erima
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
- School of Public Health, Makerere University, P.O. Box 7062 Kampala, Uganda
| | - Qouilazoni A. Ukuli
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Titus Tugume
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
| | - Denis K. Byarugaba
- Makerere University Walter Reed Project, P.O. Box 7062 Kampala, Uganda; (G.A.); (B.E.); (F.W.-M.); (Q.A.U.); (T.T.); (D.K.B.)
- College of Veterinary Medicine, Makerere University, P.O. Box 7062 Kampala, Uganda
| | - Ghazi Kayali
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas, Houston, TX 77030, USA;
- Human Link, Dubai, United Arab Emirates
| | | | - Zeynep A. Koçer
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey; (Y.M.); (M.E.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
- Correspondence: ; Tel.: +90-232-299-4165
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Yudhawati R, Prasetya RR, Dewantari JR, Nastri AM, Rahardjo K, Novianti AN, Amin M, Rantam FA, Poetranto ED, Wulandari L, Lusida MI, Soetjipto, Soegiarto G, Shimizu YK, Mori Y, Shimizu K. Comparison of Virulence and Lethality in Mice for Avian Influenza Viruses of Two A/H5N1 and One A/H3N6 Isolated from Poultry during Year 2013-2014 in Indonesia. Jpn J Infect Dis 2020; 73:336-342. [PMID: 32350224 DOI: 10.7883/yoken.jjid.2020.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Indonesia, the highly pathogenic avian influenza A/H5N1 virus has become endemic and has been linked with direct transmission to humans. From 2013 to 2014, we isolated avian influenza A/H5N1 and A/H3N6 viruses from poultry in Indonesia. This study aimed to reveal their pathogenicity in mammals using a mouse model. Three of the isolates, Av154 of A/H5N1 clade 2.3.2.1c, Av240 of A/H5N1 clade 2.1.3.2b, and Av39 of A/H3N6, were inoculated into BALB/c mice. To assess morbidity and mortality, we measured body weight daily and monitored survival for 20 d. Av154- and Av240-infected mice lost 25% of their starting body weight by day 7, while Av39-infected mice did not. Most of the Av154-infected mice died on day 8, while the majority of the Av240-infected mice survived until day 20. A 50% mouse lethal dose was calculated to be 2.0 × 101 50% egg infectious doses for Av154, 1.1 × 105 for Av240 and > 3.2 × 106 for Av39. The Av154 virus was highly virulent and lethal in mice without prior adaptation, suggesting its high pathogenic potential in mammals. The Av240 virus was highly virulent but modestly lethal, whereas the Av39 virus was neither virulent nor lethal. Several mammalian adaptive markers of amino acid residues were associated with the highly virulent and lethal phenotypes of the Av154 virus.
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Affiliation(s)
- Resti Yudhawati
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Indnesia.,Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Rima R Prasetya
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Jezzy R Dewantari
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Aldise M Nastri
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Krisnoadi Rahardjo
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Arindita N Novianti
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Muhammad Amin
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Indnesia
| | - Fedik A Rantam
- Department of Virology and Immunology, Faculty of Veterinary Medicine / Stem Cell Research and Development Center, Airlangga University, Indonesia
| | - Emmanuel D Poetranto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Laksmi Wulandari
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Indnesia.,Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Maria I Lusida
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Soetjipto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Gatot Soegiarto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia
| | - Yohko K Shimizu
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Japan
| | - Yasuko Mori
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Japan
| | - Kazufumi Shimizu
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Indonesia.,Center for Infectious Diseases, Kobe University Graduate School of Medicine, Japan
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Genetic variability of avian influenza virus subtype H5N8 in Egypt in 2017 and 2018. Arch Virol 2020; 165:1357-1366. [PMID: 32285202 DOI: 10.1007/s00705-020-04621-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/24/2020] [Indexed: 01/07/2023]
Abstract
Since the incursion of avian influenza virus subtype H5N8 in Egypt in late 2016, it has spread rapidly, causing severe losses in poultry production. Multiple introductions of different reassorted strains were observed in 2017. In this study, a genetic characterization of the HA gene was carried out with 31 isolates selected from different governorates and sectors. Fifteen isolates were selected for NA gene sequence analysis. The HA and NA genes were divided into two subgroups (I and II) with positive selection pressure identified at positions 174 and 29, respectively. The HA gene contained two novel mutations in the antigenic sites, A and E. The HA nucleotide sequence identity ranged from 77 to 90% with different vaccine seeds. Full-genome sequence analysis was carried out for eight viruses, representing different governorates and sectors, to identify the predominant reassorted strain in Egypt. All viruses were similar to a reassorted strain of clade 2.3.4.4b that has been identified in Germany, among other countries. Analysis of these viruses revealed mutations specific to Egyptian strains and not the original virus characterized in 2017 (A/duck/Egypt/F446/2017), with a novel antiviral resistance marker, V27A, indicating resistance to amantadine in the M2 protein of two strains. The results indicate increased variability of circulating H5N8 viruses compared to earlier viruses sequenced in 2016 and 2017. The predominant reassorted virus circulating in 2017 and 2018 originated from an early 2017 strain. It is important to continue this surveillance of avian influenza viruses to monitor the evolution of circulating viruses.
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Suttie A, Deng YM, Greenhill AR, Dussart P, Horwood PF, Karlsson EA. Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 2019; 55:739-768. [PMID: 31428925 PMCID: PMC6831541 DOI: 10.1007/s11262-019-01700-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Avian influenza viruses (AIVs) circulate globally, spilling over into domestic poultry and causing zoonotic infections in humans. Fortunately, AIVs are not yet capable of causing sustained human-to-human infection; however, AIVs are still a high risk as future pandemic strains, especially if they acquire further mutations that facilitate human infection and/or increase pathogenesis. Molecular characterization of sequencing data for known genetic markers associated with AIV adaptation, transmission, and antiviral resistance allows for fast, efficient assessment of AIV risk. Here we summarize and update the current knowledge on experimentally verified molecular markers involved in AIV pathogenicity, receptor binding, replicative capacity, and transmission in both poultry and mammals with a broad focus to include data available on other AIV subtypes outside of A/H5N1 and A/H7N9.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
- School of Health and Life Sciences, Federation University, Churchill, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yi-Mo Deng
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew R Greenhill
- School of Health and Life Sciences, Federation University, Churchill, Australia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Erik A Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia.
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Hassan KE, El-Kady MF, El-Sawah AAA, Luttermann C, Parvin R, Shany S, Beer M, Harder T. Respiratory disease due to mixed viral infections in poultry flocks in Egypt between 2017 and 2018: Upsurge of highly pathogenic avian influenza virus subtype H5N8 since 2018. Transbound Emerg Dis 2019; 68:21-36. [PMID: 31297991 DOI: 10.1111/tbed.13281] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
For several years, poultry production in Egypt has been suffering from co-circulation of multiple respiratory viruses including highly pathogenic avian influenza virus (HPAIV) H5N1 (clade 2.2.1.2) and low pathogenic H9N2 (clade G1-B). Incursion of HPAIV H5N8 (clade 2.3.4.4b) to Egypt in November 2016 via wild birds followed by spread into commercial poultry flocks further complicated the situation. Current analyses focussed on 39 poultry farms suffering from respiratory manifestation and high mortality in six Egyptian governorates during 2017-2018. Real-time RT-PCR (RT-qPCR) substantiated the co-presence of at least two respiratory virus species in more than 80% of the investigated flocks. The percentage of HPAIV H5N1-positive holdings was fairly stable in 2017 (12.8%) and 2018 (10.2%), while the percentage of HPAIV H5N8-positive holdings increased from 23% in 2017 to 66.6% during 2018. The proportion of H9N2-positive samples was constantly high (2017:100% and 2018:63%), and H9N2 co-circulated with HPAIV H5N8 in 22 out of 39 (56.8%) flocks. Analyses of 26 H5, 18 H9 and 4 N2 new sequences confirmed continuous genetic diversification. In silico analysis revealed numerous amino acid substitutions in the HA and NA proteins suggestive of increased adaptation to mammalian hosts and putative antigenic variation. For sensitive detection of H9N2 viruses by RT-qPCR, an update of primers and probe sequences was crucial. Reasons for the relative increase of HPAIV H5N8 infections versus H5N1 remained unclear, but lack of suitable vaccines against clade 2.3.4.4b cannot be excluded. A reconsideration of surveillance and control measures should include updating of diagnostic tools and vaccination strategies.
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Affiliation(s)
- Kareem E Hassan
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany.,Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Magdy F El-Kady
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Azza A A El-Sawah
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Christine Luttermann
- Institute of Immunology Virology, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany
| | - Rokshana Parvin
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany.,Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Salama Shany
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany
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Guo F, Luo T, Pu Z, Xiang D, Shen X, Irwin DM, Liao M, Shen Y. Increasing the potential ability of human infections in H5N6 avian influenza A viruses. J Infect 2018; 77:349-356. [PMID: 30077579 DOI: 10.1016/j.jinf.2018.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 07/30/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Fucheng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Tingting Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Dan Xiang
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto M5S 1A8, Canada
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China; Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China .
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11
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Salaheldin AH, El-Hamid A, Elbestawy AR, Veits J, Hafez HM, Mettenleiter TC, Abdelwhab EM. Multiple Introductions of Influenza A(H5N8) Virus into Poultry, Egypt, 2017. Emerg Infect Dis 2018; 24. [PMID: 29470165 PMCID: PMC5938773 DOI: 10.3201/eid2405.171935] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
After high mortality rates among commercial poultry were reported in Egypt in 2017, we genetically characterized 4 distinct influenza A(H5N8) viruses isolated from poultry. Full-genome analysis indicated separate introductions of H5N8 clade 2.3.4.4 reassortants from Europe and Asia into Egypt, which poses a serious threat for poultry and humans.
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12
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Pu Z, Xiang D, Li X, Luo T, Shen X, Murphy RW, Liao M, Shen Y. Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Front Cell Infect Microbiol 2018; 8:414. [PMID: 30533399 PMCID: PMC6265602 DOI: 10.3389/fcimb.2018.00414] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/08/2018] [Indexed: 02/05/2023] Open
Abstract
Since 2013, the H7N9 avian influenza A virus (AIV) has caused human infections and to the extent of now surpassing H5N1. This raises an alarm about the potential of H7N9 to become a pandemic problem. Our compilation of the amino acid changes required for AIVs to cross the species-barrier discovers 58 that have very high proportions in both the human- and avian-isolated H7N9 viruses. These changes correspond with sporadic human infections that continue to occur in regions of avian infections. Among the six internal viral genes, amino acid changes do not differ significantly between H9N2 and H7N9, except for V100A in PA, and K526R, D627K, and D701N in PB2. H9N2 AIVs provide internal genes to H7N9. Most of the amino acid changes in H7N9 appear to come directly from H9N2. Seventeen amino acid substitutions appear to have fixed quickly by the 5th wave. Among these, six amino acid sites in HA1 are receptor binding sites, and PB2-A588V was shown to promote the adaptation of AIVs to mammals. The accelerated fixation of mutations may promote the adaptation of H7N9 to human, but need further functional evidence. Although H7N9 AIVs still cannot efficiently transmit between humans, they have the genetic makeup associated with human infections. These viruses must be controlled in poultry to remove the threat of it becoming a human pandemic event.
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Affiliation(s)
- Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dan Xiang
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Xiaobing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Tingting Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- *Correspondence: Yongyi Shen
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13
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Hu M, Yuan S, Ye ZW, Singh K, Li C, Shuai H, Fai N, Chow BKC, Chu H, Zheng BJ. PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. J Gen Virol 2017; 98:364-373. [PMID: 28113045 DOI: 10.1099/jgv.0.000717] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Substitutions in the PA N-terminus (PAN) of influenza A viruses are associated with viral pathogenicity. During our previous study, which identified PAN-V63I and -A37S/I61T/V63I/V100A substitutions as virulence determinants, we observed a severe decrease in virus growth and transcription/replication capacity posed by PAN-A37S/V100A substitution. To further delineate the significance of substitutions at these positions, we generated mutant H7N7 viruses bearing the substitutions PAN-A37S, -A37S/I61T, -A37S/V63I, -V100A, -I61T/V100A and -V63I/V100A by reverse genetics. Our results showed that all mutant viruses except PAN-V100A showed a significantly reduced growth capability in infected cells. At the same time, the PAN-A37S, -A37S/I61T and -A37S/V63I mutant viruses displayed decreased viral transcription and replication by diminishing virus RNA synthesis activity. Biochemical assays indicated that the substitutions PAN-A37S, -A37S/I61T and -A37S/V63I suppressed the polymerase and endonuclease activities when compared with those of the wild-type. Together, our results demonstrated that the PAN-A37S, -A37S/I61T and -A37S/V63I substitutions contributed to a decreased pathogenicity of avian H7N7 influenza A virus.
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Affiliation(s)
- Meng Hu
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Zi-Wei Ye
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kailash Singh
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, PR China
| | - Cun Li
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Huiping Shuai
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Ng Fai
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, PR China
| | - Hin Chu
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
| | - Bo-Jian Zheng
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
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14
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Ramos-Paredes J, Grijalva-Chon JM, Ibarra-Gámez JC. Virulence and genotypes of white spot syndrome virus infecting Pacific white shrimp Litopenaeus vannamei in north-western Mexico. JOURNAL OF FISH DISEASES 2017; 40:425-435. [PMID: 28105747 DOI: 10.1111/jfd.12598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
White spot syndrome virus (WSSV) has caused substantial global economic impact on aquaculture, and it has been determined that strains can vary in virulence. In this study, the effect of viral load was evaluated by infecting Litopenaeus vannamei with 10-fold serial dilution of tissue infected with strain WSSV Mx-H, and the virulence of four WSSV strains from north-western Mexico was assessed along with their variable number of tandem repeat (VNTR) genotypes in ORF75, ORF94 and ORF125. The LD50 of the Mx-H strain was a dilution dose of 10-7.5 ; the mortality titre was 109.2 LD50 per gram. In shrimp injected with 102.5 to 106.5 LD50 , no significant virulence differences were evident. Using mortality data, the four WSSV strains grouped into three virulence levels. The Mx-F strain (intermediate virulence) and the Mx-C strain (high virulence) showed more genetic differences than those observed between the Mx-G (low-virulence) and Mx-H (high-virulence) strains, in ORF94 and ORF125. The application of high-viral-load inocula proved useful in determining the different virulence phenotypes of the WSSV strains from the Eastern Pacific.
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Affiliation(s)
- J Ramos-Paredes
- Laboratorio de Análisis de Sanidad Acuícola, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, México
| | - J M Grijalva-Chon
- Laboratorio de Ecología Molecular, Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - J C Ibarra-Gámez
- Laboratorio de Análisis de Sanidad Acuícola, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, México
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15
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Cohen M, Fisher CJ, Huang ML, Lindsay LL, Plancarte M, Boyce WM, Godula K, Gagneux P. Capture and characterization of influenza A virus from primary samples using glycan bead arrays. Virology 2016; 493:128-35. [PMID: 27031581 PMCID: PMC4860064 DOI: 10.1016/j.virol.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 12/22/2022]
Abstract
Influenza A viruses (IAVs) utilize sialylated host glycans as ligands for binding and infection. The glycan-binding preference of IAV hemagglutinin (HA) is an important determinant of host specificity. Propagation of IAV in embryonated chicken eggs and cultured mammalian cells yields viruses with amino acid substitutions in the HA that can alter the binding specificity. Therefore, it is important to determine the binding specificity of IAV directly in primary samples since it reflects the actual tropism of virus in nature. We developed a novel platform for analysis of IAV binding specificity in samples that contain very low virus titers. This platform consists of a high-density flexible glycan display on magnetic beads, which promotes multivalent interactions with the viral HA. Glycan-bound virus is detected by quantifying the viral neuraminidase activity via a fluorogenic reporter, 2'-(4-methylumbelliferyl)-α-d-N-acetylneuraminic acid. This method eliminates the need for labeling the virus and significantly enhances the sensitivity of detection.
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Affiliation(s)
- Miriam Cohen
- Department of Pathology, Division of Comparative Pathology and Medicine, UC San Diego, La Jolla, CA, USA.
| | | | - Mia L Huang
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA, USA
| | - LeAnn L Lindsay
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, UC Davis, Davis, CA, USA
| | - Magdalena Plancarte
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, UC Davis, Davis, CA, USA
| | - Walter M Boyce
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, UC Davis, Davis, CA, USA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA, USA
| | - Pascal Gagneux
- Department of Pathology, Division of Comparative Pathology and Medicine, UC San Diego, La Jolla, CA, USA.
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16
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Feng Y, Guan W, Yuan B, Wang Y, Li Z, Song Y, Li S, Yang Z, Zhong N, Zhang Y, Xia X. Emergence of triple-subtype reassortants of fatal human H5N6 avian influenza virus in Yunnan, China. J Infect 2016; 72:753-756. [DOI: 10.1016/j.jinf.2016.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
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17
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Caglioti C, Selleri M, Rozera G, Giombini E, Zaccaro P, Valli MB, Capobianchi MR. In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. PLoS One 2016; 11:e0155661. [PMID: 27186639 PMCID: PMC4871468 DOI: 10.1371/journal.pone.0155661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/02/2016] [Indexed: 12/16/2022] Open
Abstract
In March/April 2009, a new pandemic influenza A virus (A(H1N1)pdm09) emerged and spread rapidly via human-to-human transmission, giving rise to the first pandemic of the 21th century. Influenza virus may be present in the infected host as a mixture of variants, referred to as quasi-species, on which natural and immune-driven selection operates. Since hemagglutinin (HA) and non-structural 1 (NS1) proteins are relevant in respect of adaptive and innate immune responses, the present study was aimed at establishing the intra-host genetic heterogeneity of HA and NS1 genes, applying ultra-deep pyrosequencing (UDPS) to nasopharyngeal swabs (NPS) from patients with confirmed influenza A(H1N1)pdm09 infection. The intra-patient nucleotide diversity of HA was significantly higher than that of NS1 (median (IQR): 37.9 (32.8–42.3) X 10−4 vs 30.6 (27.4–33.6) X 10−4 substitutions/site, p = 0.024); no significant correlation for nucleotide diversity of NS1 and HA was observed (r = 0.319, p = 0.29). Furthermore, a strong inverse correlation between nucleotide diversity of NS1 and viral load was observed (r = - 0.74, p = 0.004). For both HA and NS1, the variants appeared scattered along the genes, thus indicating no privileged mutation site. Known polymorphisms, S203T (HA) and I123V (NS1), were observed as dominant variants (>98%) in almost all patients; three HA and two NS1 further variants were observed at frequency >40%; a number of additional variants were detected at frequency <6% (minority variants), of which three HA and four NS1 variants were novel. In few patients multiple variants were observed at HA residues 203 and 222. According to the FLUSURVER tool, some of these variants may affect immune recognition and host range; however, these inferences are based on H5N1, and their extension to A(H1N1)pdm09 requires caution. More studies are necessary to address the significance of the composite nature of influenza virus quasi-species within infected patients.
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Affiliation(s)
- Claudia Caglioti
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
| | - Marina Selleri
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
| | - Gabriella Rozera
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
| | - Paola Zaccaro
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
| | - Maria Beatrice Valli
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, I.R.C.C.S., Rome, Italy
- * E-mail:
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18
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Tosh C, Nagarajan S, Kumar M, Murugkar HV, Venkatesh G, Shukla S, Mishra A, Mishra P, Agarwal S, Singh B, Dubey P, Tripathi S, Kulkarni DD. Multiple introductions of a reassortant H5N1 avian influenza virus of clade 2.3.2.1c with PB2 gene of H9N2 subtype into Indian poultry. INFECTION GENETICS AND EVOLUTION 2016; 43:173-8. [PMID: 27174088 DOI: 10.1016/j.meegid.2016.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/25/2016] [Accepted: 05/06/2016] [Indexed: 12/31/2022]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses are a threat to poultry in Asia, Europe, Africa and North America. Here, we report isolation and characterization of H5N1 viruses isolated from ducks and turkeys in Kerala, Chandigarh and Uttar Pradesh, India between November 2014 and March 2015. Genetic and phylogenetic analyses of haemagglutinin gene identified that the virus belonged to a new clade 2.3.2.1c which has not been detected earlier in Indian poultry. The virus possessed molecular signature for high pathogenicity to chickens, which was corroborated by intravenous pathogenicity index of 2.96. The virus was a reassortant which derives its PB2 gene from H9N2 virus isolated in China during 2007-2013. However, the neuraminidase and internal genes are of H5N1 subtype. Phylogenetic and network analysis revealed that after detection in China in 2013/2014, the virus moved to Europe, West Africa and other Asian countries including India. The analyses further indicated multiple introductions of H5N1 virus in Indian poultry and internal spread in Kerala. One of the outbreaks in ducks in Kerala is linked to the H5N1 virus isolated from wild birds in Dubai suggesting movement of virus probably through migration of wild birds. However, the outbreaks in ducks in Chandigarh and Uttar Pradesh were from an unknown source in Asia which also contributed gene pools to the outbreaks in Europe and West Africa. The widespread incidence of the novel H5N1 HPAI is similar to the spread of clade 2.2 ("Qinghai-like") virus in 2005, and should be monitored to avoid threat to animal and public health.
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Affiliation(s)
- Chakradhar Tosh
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
| | | | - Manoj Kumar
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Harshad V Murugkar
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | | | - Shweta Shukla
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Amit Mishra
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Pranav Mishra
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Sonam Agarwal
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Bharati Singh
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Prashant Dubey
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Sushil Tripathi
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
| | - Diwakar D Kulkarni
- ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India
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19
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Muzyka D, Pantin-Jackwood M, Starick E, Fereidouni S. Evidence for genetic variation of Eurasian avian influenza viruses of subtype H15: the first report of an H15N7 virus. Arch Virol 2015; 161:605-12. [PMID: 26650037 DOI: 10.1007/s00705-015-2629-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022]
Abstract
Since the first detection of H15 avian influenza viruses (AIVs) in Australia in 1979, only seven H15 strains have been reported. A new H15 AIV was detected in Ukraine in 2010, carrying the unique HA-NA subtype combination H15N7. This virus replicated efficiently in chicken eggs, and antisera against it reacted strongly with the homologous antigen, but with lower titers when using the reference Australian antigen. The amino acid motifs of the HA cleavage site and receptor-binding site were different from those in the Australian viruses. The new virus, together with an H15 virus from Siberia from 2008, constitutes a new clade of H15 AIV isolates.
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Affiliation(s)
- Denys Muzyka
- National Scientific Center, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Mary Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - Elke Starick
- Friedrich Loeffler Institute, Greifswald, Insel Riems, Germany
| | - Sasan Fereidouni
- Friedrich Loeffler Institute, Greifswald, Insel Riems, Germany. .,WESCA Wildlife Network, Greifswald, Germany. .,University of Veterinary Medicine Vienna, Research Institute of Wildlife Ecology, Vienna, Austria.
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20
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Wei K, Liu X. Phylogenetic Analysis and Functional Characterization of the Influenza A H5N1 PB2 Gene. Transbound Emerg Dis 2015; 64:374-388. [PMID: 25990872 DOI: 10.1111/tbed.12376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 12/23/2022]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses are endemic in poultry and cause continued inter-species transmission to human in Asia, such as China and Vietnam, leading to pandemic concerns and socio-economic challenges. Phylogenetic analysis of H5N1 viruses isolated from China and Vietnam during 2001-2012 showed that several geographically distinct sublineages have become established in these two countries. Subsequently, we reassigned HPAI H5N1 viruses into three distinct groups to reveal the intrasubtype reassortment. Apart from six reassortants detected here, we found that several viral strains showed signals for homologous recombination within PB2 and PB1 genes, suggestive of the fluidity of the H5N1 virus gene pool. Furthermore, sequenced-based analyses revealed that the viral polymerase displayed a higher level of genetic polymorphism but associated with lower substitution rate when compared with those of other gene segments. In addition, the selection pressure analysis indicated that purifying selection was predominant in eight genomic segments especially in the polymerase complex. However, the site-by-site analysis helped to detect 14 positively selected sites in the PB1, PA, HA, NA, MP and NS proteins. Despite the fact that PB2 protein of H5N1 viruses was highly conserved at the amino acid level, eleven adaptive mutations were still observed in the protein. Further comparative structural analysis of the K627E mutation indicated that there were no structural differences between the variants, which possessed either PB2-627E or PB2-627K. Transcriptomic analysis suggested the non-mitochondrial PB2 protein of H5N1 virus that forms a stable complex with the mitochondrial antiviral signalling protein (MAVS, also known as IPS-1, VISA or Cardif) can induce interferon-beta (IFN-β) expression, but the substitution (PB2-K627E) is not the sole determinant of the RIG-I-like receptors (RLR) signalling components induction in Calu-3 cells.
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Affiliation(s)
- K Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - X Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
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21
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Arafa AS, Naguib MM, Luttermann C, Selim AA, Kilany WH, Hagag N, Samy A, Abdelhalim A, Hassan MK, Abdelwhab EM, Makonnen Y, Dauphin G, Lubroth J, Mettenleiter TC, Beer M, Grund C, Harder TC. Emergence of a novel cluster of influenza A(H5N1) virus clade 2.2.1.2 with putative human health impact in Egypt, 2014/15. ACTA ACUST UNITED AC 2015; 20:2-8. [PMID: 25860390 DOI: 10.2807/1560-7917.es2015.20.13.21085] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A distinct cluster of highly pathogenic avian influenzaviruses of subtype A(H5N1) has been found to emergewithin clade 2.2.1.2 in poultry in Egypt since summer2014 and appears to have quickly become predominant.Viruses of this cluster may be associated withincreased incidence of human influenza A(H5N1) infectionsin Egypt over the last months.
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Affiliation(s)
- A S Arafa
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, Egypt
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22
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Molecular epidemiology and evolution of A(H1N1)pdm09 and H3N2 virus during winter 2012-2013 in Beijing, China. INFECTION GENETICS AND EVOLUTION 2014; 26:228-40. [PMID: 24911284 DOI: 10.1016/j.meegid.2014.05.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/12/2014] [Accepted: 05/30/2014] [Indexed: 12/12/2022]
Abstract
In order to evaluate the epidemiology of influenza A and its surface antigens (haemagglutinin [HA] and neuraminidase [NA]) for molecular epidemiology and evolution analysis during winter 2012-2013 in Beijing, China, we worked within the framework of the Chinese National Influenza Center and collected nasal swabs of patients presenting with influenza-like illness. We found that both A(H1N1)pdm09 (46.8%) and H3N2 (53.2%) viruses were the predominant strains during the 2012-2013 influenza epidemic. The peak phase started at the second week of 2013 and lasted about 1month. We obtained HA and NA sequences of viruses from 44 patients by using Sanger sequencing. None of the strains had the oseltamivir resistance site H274Y. Phylogenetic analysis of 29 A(H1N1)pdm09 viruses showed a genetic drift from the vaccine strain A/California/07/2009 with mutations (H155Q/R and L178I) at the antigenic sites Ca and Sa of HA; the strains were classified into genetic groups 6 and 7 because of the presence of D114N, S160G, S202T, and A214T mutations in HA. H3N2 viruses formed seasonal phylogenetic clusters representative for each season from 2000 to 2013; 15 of the 2012-2013 H3N2 strains were assigned to the A/Victoria/361/2011 genetic clade with mutations at the antigenic sites A, B and C of HA, including R158K/G, N161S, Q172H, and N294K; the 2012-2013 strains with V239I, S61N, T64I, and A214S HA mutations were classified into subgroup 3C. The mutation of potential N-linked glycosylation residues at the antigenic sites of HA and around the enzymatic active center of NA may have increased viral pathogenicity by masking antigenic sites from immune recognition. Our data suggest that influenza vaccines are generally effective, but still provide suboptimal protection due to antigenic variation. This study increases the understanding of influenza A viruses in humans and is informative for future vaccine strain selection.
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Avian influenza: mixed infections and missing viruses. Viruses 2013; 5:1964-77. [PMID: 23921843 PMCID: PMC3761236 DOI: 10.3390/v5081964] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/20/2013] [Accepted: 07/23/2013] [Indexed: 02/05/2023] Open
Abstract
A high prevalence and diversity of avian influenza (AI) viruses were detected in a population of wild mallards sampled during summer 2011 in California, providing an opportunity to compare results obtained before and after virus culture. We tested cloacal swab samples prior to culture by matrix real-time PCR, and by amplifying and sequencing a 640bp portion of the hemagglutinin (HA) gene. Each sample was also inoculated into embryonated chicken eggs, and full genome sequences were determined for cultured viruses. While low matrix Ct values were a good predictor of virus isolation from eggs, samples with high or undetectable Ct values also yielded isolates. Furthermore, a single passage in eggs altered the occurrence and detection of viral strains, and mixed infections (different HA subtypes) were detected less frequently after culture. There is no gold standard or perfect reference comparison for surveillance of unknown viruses, and true negatives are difficult to distinguish from false negatives. This study showed that sequencing samples prior to culture increases the detection of mixed infections and enhances the identification of viral strains and sequences that may have changed or even disappeared during culture.
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