Egyptian Virus Research Articles

Characterization and genetic analysis of recent and emergent virulent newcastle disease viruses in Egypt.

Extensive vaccination against Newcastle disease virus (NDV) induced more selective immune pressure from hosts that enhanced the evolutionary process of NDV. Herein, we characterized 13 recently isolated NDV isolates from vaccinated chicken flocks during 2014-2017. Sequence analysis of F gene showed the presence of 112 RRQKRF117 velogenic cleavage motif in 11 isolates, whereas the other two isolates (Ck/ME3/Eg/16 and Ck/ME5/Eg/16) showed the monobasic motif 112 GGRQGRL117 . Interestingly, isolate Ck/ME5/Eg/16 showed 100% and 99.82% nucleotide identity with the LaSota F gene hypervariable region and full-length gene, respectively. On the other hand, isolate Ck/ME3/Eg/16 revealed natural recombination with strains NDV/Ck/Egypt/3/2006 and NDV/Teal/VRLCU/Egypt/2015 that indicates re-emergence of that old strain. Interestingly, all 13 isolates showed high intracerebral pathogenicity (ICPI) and mean death time (MDT) despite the presence of lentogenic motif in both Ck/ME5/Eg/16 and Ck/ME3/Eg/16 isolates. Comparative analysis of F antigenic epitopes in our isolates with other published sequences from Egypt revealed high sequence conservation; recent isolates had one fixed amino acid substitution (K78R) and a novel V168I substitution, whereas a D170N substitution was detected in older strains (NDV-EG-35-2014 and NDV-KFR-B7-2012). Taken together, our results support the first isolation of virulent NDV isolates with a lentogenic motif; isolate Ck/ME5/Eg/16 might be generated in nature from LaSota live vaccine, whereas isolate Ck/ME3/Eg/16 is emergent from NDV/Ck/Egypt/3/2006. We conclude that the current diagnostic evaluation of the virulence of NDV isolates by characteristic amino acid residues at the F protein cleavage site is insufficient. There is a need to link virologic and epidemiologic data together, and routine and emergency LaSota vaccination protocols should be carefully and optimally applied, with regards to the timing and presence of co-infecting agents in the field.

Clinical evaluation of some sofosbuvir-based regimens for the treatment of hepatitis c in private healthcare sector in Egypt

Hepatitis C Virus has been a universal rising problem and the leading cause of liver cirrhosis and its related complications principally hepatic decompensation and hepatocellular carcinoma. The annual prevalence is estimated at 3–4 million subjects. Egypt is considered among the highest endemic seropositive areas globally having more than 5% related to the adult inhabitants. In Egypt, hepatitis C virus, genotype 4 is responsible for about 90% of the cases. In addition to their efficacy, DAA therapies target to significantly cut the cumulative total economic burden of HCV. The previous established and published studies related to new treatment regimens for hepatitis C virus in Egypt focused mainly on governmental hospitals/institutes, and nearly none focused on the private sector. This is a retrospective observational study focused on efficacy and safety evaluation of sofosbuvir (SOF) + ribavirin (RBV), SOF + daclatasvir (DCV), and SOF + daclatasvir (DCV) + RBV compared with SOF + pegylated interferon alfa (pegIFN) + RBV in the treatment of naive non-cirrhotic patients infected with hepatitis C virus in Egypt. The population in this study were 200 Egyptian patients, diagnosed with chronic hepatitis C genotype 4 who were non-cirrhotic, not diagnosed with hepatocellular carcinoma (HCC), and didn't have a liver transplant or co-infections. Those patients received treatment in private hospitals and clinics between 2014 and 2017. Results of this study showed that treatment with DAAs was associated with dramatic increase in SVR12 rate. The achieved SVR12 rates in this study were 91.7% for SOF + pegIFN + RBV, 75% for SOF + RBV, 96% for SOF + RBV + DCV, and 94% for SOF + DCV. Among the studied baseline patient characteristics, the viral load was found to be a significant independent predictor of the expected SVR12 rate. Safety assessment revealed that the most common side effect in this study were anaemia and thrombocytopenia. Anaemia was found to be significantly associated with regimens containing RBV and the initial haemoglobin level, while thrombocytopenia was found to be associated with the initial patient platelets count and pegINF containing regimen.

Comparative study between the efficacy of using sofosbuvir/daclatasvir and sofosbuvir/ledipasvir in treatment of hepatitis C virus in Egypt

Background Hepatitis C virus (HCV) infection is a global health care problem, with more than 170 million people infected worldwide. With the discovery of new direct-acting antiviral drugs, a new hope to get HCV cure has arisen. This work was designed to compare the efficacy between the use of sofosbuvir (SOF)/daclatasvir (DCV) and SOF/ledipasvir (LDV) in treatment of HCV. Patients and methods A total of 430 patients were enrolled into two groups: SOF/DCV group included 340 patients and SOF/LDV group included 90 patients. Each patient received treatment for 12–24 weeks. All patients were checked at each visit (at weeks 4, 8, 12, and 24) for the potential adverse events by a check-list questions, examinations, and laboratory tests. Check-list questions include headache, gastric upset, skin rash, and sleep disturbance. Results A total of 419 (97.4%) patients achieved sustained virologic response (SVR), and only 11 (2.5%) patients failed to achieve SVR. In SOF–DCV, 97.4%, and in SOF–LDV, 97.8% achieved SVR. Minor adverse events were mainly headache, sleep distribution, gastrointestinal tract disturbance, and skin rash, which were observed in 13.8% of patients in SOF–DCV group 20% in SOF–LDV group. Conclusion The use of the two regimens SOF/DCV and SOF/LDV yielded high success ratio for viral eradication with minimal tolerable adverse effects. These regimens of therapy have a great margin of safety with high efficacy.

Study the efficacy of sofosbuvir/daclatasvir in treatment of hepatitis C virus in Egypt

Objectives To evaluate the efficacy of combination therapy of sofosbuvir and daclatasvir with or without ribavirin as a treatment of chronic hepatitis C virus (HCV), estimated by the rate of achievement of sustained viral response 12 weeks. Background Direct-acting antiviral agents opened the gate to a new era for the management of HCV. These agents have shown high sustained viral response rates of ~90% in clinical trials, shorter therapies, less toxicity, and interferon-free regimens. Patients and methods This prospective, population-based study included 401 HCV-infected patients, 18–75 years of age, attending the Viral Hepatitis Unit of the National Committee for Control of Viral Hepatitis at Center of Cardiac and Digestive System, Sohag, who were divided into two groups: group I (easy to treat) was treated by sofosbuvir + daclatasvir for 3 months, and group II (difficult to treat) was treated by sofosbuvir + daclatasvir + ribavirin for 3 months. Results There was a high statistically significant difference between the studied groups regarding liver echo pattern, splenic size, fibrosis index based on the 4 factors, blood glucose, international normalized ratio, total bilirubin, serum albumin, aspartate transaminase, and platelet count (P 0.05). Conclusion The treatment regimen of sofosbuvir + daclatasvir with/without ribavirin for chronic HCV patients was of high efficacy.

Estimating Transmission Potential of H5N1 Viruses Among Humans in Egypt Using Phylogeny, Genetic Distance and Sampling Time Interval.

In 2014 and 2015, the number of human cases of H5N1 avian influenza virus infections had increased dramatically in Egypt. This increase might be related to increase in the transmission potential of the virus among humans. To clarify the cause of the increase in H5N1 human cases, we investigate the transmissibility of H5N1 viruses among humans via estimating the basic reproduction number R0 using nucleotide sequences and sampling dates of viruses. To this end, full-length hemagglutinin gene sequences of human and avian H5N1 influenza viruses isolated from 2006 to 2016 in Egypt were obtained from the NCBI influenza virus resource. Taking into account the phylogeny, genetic distance, sampling time difference among viruses, R0 was estimated to be 0.05 (95% CI: 0.01, 0.13) assuming that human-to-human transmissions occurred within a city, 0.23(95% CI: 0.14, 0.35) assuming human-to-human transmissions among cities. Our results indicate that human-to-human transmission of H5N1 viruses in Egypt is limited, and the large increase in human cases is likely attributed to other factor than increase in human-to-human transmission potential.

Evaluation Of Bivalent Inactivated Infectious Bronchitis Viral Vaccine Prepared From Local Isolates

Infectious Bronchitis (IB) is currently one of the most important diseases in poultry flocks all over the world causes huge economic losses in poultry industry. Many IBV outbreaks associated with respiratory distress, nephropathy, and high mortalities were attributed to the circulation of new nephropathogenic IBV variant 2 strains. This study was conducted to development of bivalent inactivated IBV vaccine by using the local classical and variant isolates (KP279995/2014 and KP279998/2014 respectively) which isolated from poultry farms in Egypt as previous surveillance study during IBV outbreak from Al-Sharkia and Al-Qalubia governorates. The locally prepared vaccine formulated by using formalin for inactivation and MontanideTM ISA71 RVG as oil adjuvant. The prepared bivalent inactivated (IBV) vaccine was tested for sterility, safety and potency, the efficacy of the prepared vaccine was applied in specific pathogen free chicks (SPF) for monitoring the antibody titers by using of Enzyme Linked Immuno Sorbent Assay (ELISA) post vaccination with estimation of shedding parameters by Real-Time RT-PCR in challenging birds with 104.5EID50/dose challenge IBV strains (classical and/or variant). The results revealed that the prepared vaccine free from any bacterial or mycotic contamination also safe after double dose inoculation in SPF chicks. The efficacy of inactivated vaccine showed from 92% to 96% protection against homologous challenge based on assessment parameters. This confirms that poultry industry can be protected from IB disease if using locally isolates in preparing of inactivated vaccine which reduce the economic losses caused by IB infection viruses in Egypt.

Involvement of Egyptian Foods in Foodborne Viral Illnesses: The Burden on Public Health and Related Environmental Risk Factors: An Overview

Foodborne viral diseases are a major public health threat and pose a huge burden on the economies of both developed and developing countries. Enteric viruses are the causative agents of most foodborne illnesses and outbreaks. Egypt is classified by WHO among the regions with intermediate to high endemicity for various enteric viruses. This is manifested by the high prevalence rates of different enteric virus infections among Egyptian population such as Hepatitis A and E viruses, human rotaviruses, human noroviruses, human astroviruses, and human adenovirus. Recently, a number of foodborne gastroenteritis and acute hepatitis outbreaks have occurred in the US, Canada, Australia, and the European Union countries. Some of these outbreaks were attributed to the consumption of minimally processed foods imported from Egypt indicating the possibility that Egyptian foods may also be partially responsible for high prevalence of enteric virus infections among Egyptian population. In the absence of official foodborne-pathogen surveillance systems, evaluating the virological safety of Egyptian foods is a difficult task. In this review, we aim to provide a preliminary evaluation of the virological safety of Egyptian foods. A comprehensive review of prevalence studies on enteric virus infections shows hyperendemicity of several enteric viruses in Egypt and provides strong evidence of implication of Egyptian foods in these infections. We also address possible environmental risk factors that may lead to the contamination of Egyptian foods with enteric viruses. In addition, we describe potential obstacles to any plan that might be considered for improving the virological safety of Egyptian foods.

Genetic Analysis of Highly Pathogenic Avian Influenza H5N1 in West Delta Governorate

Avian influenza viruses became widely distributed in most Middle Eastern countries, causing high mortality rate and severe economic losses in poultry industry especially when complicated with other pathogens. The continuous evolution of highly pathogenic H5N1 avian influenza viruses (HPAI- H5N1) has resulted in multiple diverse groups based on their haemagglutinin (HA) sequences. In this study, samples from 40 broiler chicken farms during 2014 - 2017 were screened for HPAI- H5N1 Results showed that 15 flocks (37.5%) were positive for HPAI-H5 all of them non vaccinated . Furthermore, full sequencing of HA and NA gene for 3 isolates isolated during 2017 showed that the viruses were clustered with Egyptian viruses from clade 2.2.1.2 and closely related to viruses from neighboring countries.

Detection, isolation and characterization of cowpea mosaic virus in Egypt

Cowpea mosaic virus is among the most economically important viruses infecting cowpea. Incidence of infection was assessed in two governorates in Egypt, namely Alexandria and El Beheira. An overall infection rate of 6% in 200 collected samples was verified by ELISA indicating the presence, but not spread of the virus in selected areas. A CPMV isolate has been propagated in Kafr El Sheikh1 cowpea cultivar, followed by virus purification. Thin-section electron microscopy revealed cytopathological effects due to viral infection. Both CP S and CP L components of CPMV-egn coat protein of 37 kDa and 23 kDa were detected by SDS-PAGE. Following RNA purification, RNA1 (5000 bp) and RNA2 (3000 bp) were detected. Amplification of CPMV-egn coat protein gene (476 bp) and polymerase gene (716 bp) was followed by cloning and sequencing. Both sequences received accession numbers of KT456532 and KT456533 from Genbank, respectively. Phylogenetic analysis has revealed that the Egyptian CPMV-egn isolate shares more sequence homology to UK isolates, more than 2 Egyptian isolates reported earlier. However, CPMV-egn seems distinct from the closely related UK isolates. This observation may be an indication of genetic diversity of CPMV in Egypt.

Emergence and genetic analysis of variant pathogenic 4/91 (serotype 793/B) infectious bronchitis virus in Egypt during 2019.

Infectious bronchitis virus (IBV) affects both vaccinated and unvaccinated flocks worldwide, with a significant impact on the poultry industry. The aim of the present study is to characterize an emerging variant pathogenic IBV originating from field outbreaks in vaccinated Egyptian layer flock. Samples were collected from disease-suspected flock with a history of administration of live and inactivated IBV vaccines (Ma5 type). Virus propagation in embryonated chicken eggs (ECEs), after three successive passages, revealed typical IBV lesions such as curling and dwarfism. The reported isolate was identified by a real-time reverse transcriptase PCR assay targeting nucleocapsid (N) gene and, further characterized by full-length spike (S1) gene sequencing. Phylogenetic analysis revealed clustering of the isolated virus within 4/91 genotype of GI-13 lineage. Deduced amino acid sequences identity revealed 75–76% and 88–90% similarity with the currently used classic (H120, Ma5, and M41) and variant vaccine strains (4/91 and CR88) in Egypt, respectively. Recombination analysis gave an evidence for distinct patterns of origin for the studied isolate providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-13 lineage in the Egyptian field. The studied isolate (IBV/CK/EG/Fadllah-10/2019) emerged as a result of recombination between the variant group (Egy/var I genotype, GI-23 lineage) as a major parent and the CR88 variant vaccine strain (4/91 genotype, GI-13 lineage) as minor parent. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants which ascertain the importance of disease monitoring in vaccinated flocks as well as re-appropriation for the current vaccine strategies.Electronic supplementary materialThe online version of this article (10.1007/s11262-019-01693-9) contains supplementary material, which is available to authorized users.

Microalgae Biomass Application in Commercial Broilers Nutrition and Their Efficacy Against Challenge with Epidemic Newcastle Disease Virus in Egypt

Microalgae Biomass Application in Commercial Broilers Nutrition and Their Efficacy Against Challenge with Epidemic Newcastle Disease Virus in Egypt

Isolation of a Novel Reassortant Highly Pathogenic Avian Influenza (H5N2) Virus in Egypt.

Highly pathogenic avian influenza (HPAI) H5N1 and H5N8 have become endemic among domestic poultry in Egypt since 2006 and 2016, respectively. In parallel, the low pathogenic avian influenza H9N2 virus has been endemic since 2010. Despite the continuous circulation of these subtypes for several years, no natural reassortant has been detected so far among the domestic poultry population in Egypt. In this study, the HPAI (H5N2) virus was isolated from a commercial duck farm, giving evidence of the emergence of the first natural reassortment event in domestic poultry in Egypt. The virus was derived as a result of genetic reassortment between avian influenza viruses of H5N8 and H9N2 subtypes circulating in Egypt. The exchange of the neuraminidase segment and high number of acquired mutations might be associated with an alteration in the biological propensities of this virus.

Molecular characterization and genotyping of recent isolate of Infectious Bronchitis Virus (IBV) in Egypt

In this study a total number of 22 organ samples (including trachea, lung and kidney) from 22 broiler farms from northern Upper Egypt were collected from Mars 2017 to June 2018 from chickens showing clear clinical and pathological signs of Infectious Bronchitis. The samples were prepared and examined by real time RT-PCR for diagnosis of IBV. A total number of 11 samples were positive (50%) which were used for further isolation on SPF eggs by three blind serial passages. Positive samples that showed the pathogenic lesions of IB (curling and dwarfing of embryos) were collected and tested with real time RT-PCR (rRT-PCR) for more confirmation then a part from S1 gene sequence was amplified by RT-PCR and the product was sequenced and the data have been compared with other related IBV strains. The results indicate that the Egyptian virus in this study has an identity percent reached up to 89% with other recent Egyptian isolates. However, it reached 67% with classical vaccine strains like H120 and variant I like CR88 strain. The lowest identity was observed with M41 strain (59%) in this study. The phylogenetic tree compared to other isolates from Middle East and worldwide showed that this isolate is related to the IBV variant 2 group closely related to IBVEg/1265B/2012 strain and the Israeli strain IS/1494/06.

Presence of bluetongue and epizootic hemorrhagic disease viruses in Egypt in 2016 and 2017

BTV and EHDV are closely-related orbiviruses that are transmitted between domestic and wild ruminants via the bites of hematophagous midges. Previous studies have reported seropositivity against BTV antibodies in sheep and goats in two Egyptian governorates (Beni Suef and Menoufia). However, no recent data are available on the BTV serotype(s) circulating in Egypt and the likely presence of EHDV has never been explored. This study investigated the presence of BTV and EHDV among cattle which had been found BTV-seropositive by ELISA method. These cattle living in proximity to sheep and goats previously found BTV-seropositive. These cattle displayed no clinical signs of BT but reproductive problems had been reported in herds. A total of 227 cattle blood samples were therefore collected in 2016 and 2017. Ninety-four of the 227 animals tested by a BTV ELISA were positive for BTV antibodies (41.4%). Of these 94 ELISA-positive cattle, only 83 EDTA-blood samples were available and therefore tested for BTV and EHDV genome detection by RT-PCR and sequencing.Of the cattle sampled in 2016, results revealed that two were RT-PCR-positive for BTV and seven for EHDV. Sequencing showed the presence of EHDV-1 and BTV-3 genome sequences. EHDV-1 S2 shared 99.5% homology with an EHDV-1 S2 from a strain isolated in 2016 in Israel. BTV-3 S2 and S8 sequences shared >99.8% nucleotide similarity with the BTV-3 Zarzis S2 and S8 sequences (Tunisian BTV, also detected in 2016). Of the 66 blood samples tested following their collection in 2017, they were all EHDV-negative by RT-qPCR while five were BTV- positive by RT-qPCR. However, attempts to identify the BTV serotype of these five samples were unsuccessful. Only part of BTV S8 was sequenced and it showed 79% nucleotide similarity with S8 of atypical BTV serotypes (particularly with BTV-26 and another BTV serotype strain isolated from a sheep pox vaccine). Overall, these findings demonstrate that both BTV and EHDV were circulating in Egypt in 2016 and 2017.

MOLECULAR ANALYSIS OF AVIAN INFECTIOUS BRONCHITIS VIRUS IN QALYOUBIA GOVERNORATE DURING 2017-2018

The regular updates of molecular studies of Avian Infectious Bronchitis Virus in Egypt become imperative specially with the ongoing emergence of new strains of infectious bronchitis virus (IBV) that worsen the situation in poultry farms and causing extensive economic losses. In our study, we collect samples from twenty broiler flocks range from 18 to 36 days of age and manifested severe respiratory signs with mortality up to 30%. The collected flocks located in Qalyoubia governorate during period between January 2017 to December 2018. IBV Screening in collected samples was conducted by real time rRT-PCR targeting the nucleoprotein (N) gene. A total of 12 out of 20 examined farms were positive for IBV with percentage of (60%). Five positive IBV isolates were selected for amplification and sequencing of 400 –bp targeting the hypervariable region-3 (HVR 3) of S1 protein. Phylogenetic analysis confirmed that these viruses were closely related to each other (90-98% identity) and were clustered to variant II (GI 23) viruses within the Egy/Var-Ⅱ subgroup. The amino acids homology showed (75% to 80% identity) between our Egyptian/Qal variants and the common vaccine used for IBV infection in Egyptian poultry farms.

Molecular pathogenic and host range determinants of reassortant Egyptian low pathogenic avian influenza H9N2 viruses from backyard chicken

ABSTRACTSince the introduction of H9N2 low pathogenic avian influenza virus in Egypt, it became an endemic disease causing considerable economic losses in different poultry sectors especially in the presence of other secondary bacterial and viral infections. The H9N2 viruses in Egypt are in continuous evolution that needs deep analysis for their evolution pattern based on the genetic constitutions of the pathogenic determinant genes (HA, PB2, PB1, PA, and NS). In this work, samples were collected from the backyard chickens from 3 Egyptian governorates. Five selected viruses were sequenced and analyzed for the hemagglutinin gene which showed genetic relatedness to the Asian G1 lineage group B, similar to the circulating H9N2 viruses in Egypt since 2013. The sequence for PB2, PB1, PA, HA and NS genes of the selected five viruses indicate a natural re-assortment event with recent Eurasian subtypes and similar to Egyptian H9N2 virus isolated from pigeon in Egypt during 2014. The Egyptian viruses of our study possess amino acids signatures including S42, V127, L550, L672 and V504 in the internal genes NS1, PA, and PB2, of respectively of an impact on virus transmission and replication. This work indicates that the H9N2 is in continuous evolution with alarming to the reassortment occurrence.

Novel H5N1 highly pathogenic avian influenza viruses in Egypt: characterization, zoonotic potential and vaccination studies

The current study investigated the prevalence and genetic diversity of highly pathogenic avian influenza (HPAI) viruses in non-vaccinated backyard chicken flocks in Qalubia governorate during the period 2012-2014. Results revealed the emergence of two novel H5N1 HPAI viruses, designated A/Chicken/Egypt/D2296E/2012 (CH/E12) and A/Chicken/Egypt/D2296H/2014 (CH/H14). Phylogenetic analysis of the hemagglutinin (HA) genes revealed that CH/E12 belongs to the predominant subclade 2.2.1.2, meanwhile CH/H14 provides an empiric evidence for the ongoing circulation of the 2.2.1.1 viruses, which were thought to have disappeared from Egypt since 2011. In addition, genetic analysis revealed that CH/E12 and CH/H14 retained the amino acid substitutions which characterize the subclade 2.2.1.2 and 2.2.1.1, respectively. However, the HA-receptor binding residues of the two viruses carried numerous substitutions, suggesting a preferable binding to human type receptors. Vaccination-challenge studies were conducted under standard laboratory conditions using three commercially available vaccines. Results revealed that the hemagglutination inhibition (HI) titers as well as the levels of protection conferred by each vaccine were positively correlated with the HA identity between the vaccine and challenge viruses. The antigenically related (90.8–96.2%) A/swan/Hungary/4999/2006 and A/chicken/Egypt/18-H/09 vaccine strains provided the highest (86.6–93.3%) protection, meanwhile the antigenically distinct (78.3–81%) A/chicken/Mexico/232/1994 H5N2 vaccine strain provided the lowest level of protection (80–83.3%) against lethal challenge. These findings highlight the significance of backyard chickens as a constant reservoir of HPAI H5N1 viruses in Egypt and raise the need for monitoring the prevalence of H5N1 viruses in backyard chicken flocks in order to understand the virus evolution and to select the proper vaccination strategy.

Time to raise the concern for central nervous system tuberculosis and human immunodeficiency virus in Egypt? Multiple central nervous system tuberculoma: a case report

Central nervous system (CNS) tuberculoma is a rare serious form of tuberculosis. AIDS and the other immunosuppressive causes are the major risk factors for CNS tuberculomas. We present a case of multiple CNS tuberculomas in an almost healthy patient with no history of symptoms of immunosuppression or signs of focal deficits. A high index of suspicion is needed to diagnose CNS tuberculomas, especially with the rising incidence of HIV in Egypt.

Genetic and antigenic characterization of avian influenza H9N2 viruses during 2016 in Iraq.

BackgroundLittle is known about the antigenic and genetic characteristics of influenza A viruses circulating in poultry in Iraq.ObjectiveThis study describes the genetic and antigenic characteristics of the detected avian influenza H9N2 viruses in Iraq during 2016.MethodsFull genome sequences of two H9N2 viruses isolated from chickens in Iraq during 2016 were assembled. Antigenic analyses of Iraqi H9N2 viruses and contemporary H9N2 isolates from Lebanon and Egypt were performed by hemagglutination inhibition assay.ResultsPhylogenetic analysis of surface glycoproteins and internal segments (PB2, PA, NP, M, and NS) indicated that the Iraqi H9N2 viruses were closely related to G1-like lineage of H9N2 viruses isolated from Pakistan and Iran indicating possible epidemiological links. The PB1 segments of the current characterized H9N2 viruses were not related to any of the previously characterized H9N2 viruses and closely similar to H7N7 virus detected in chickens in Germany in 2015. Multiple genetic determinants for virulence and mammalian transmission were characterized in the characterized H9N2 viruses in Iraq. The antigenic analysis showed a close relationship between H9N2 viruses in Iraq and contemporary H9N2 viruses in Egypt and Lebanon. Like H9N2 viruses, Iraqis H9N2 virus bound to human-like receptor rather than avian-like receptor thus represent a public health risk.ConclusionActive surveillance of avian influenza virus in poultry and migratory birds should be adopted to monitor the genesis and emergence of new viruses in Iraq.

Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016–2018

ABSTRACT Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016–2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.