Genetic and virological characteristics of a reassortant avian influenza A H6N1 virus isolated from wild birds at a live-bird market in Egypt

The first detection of a human infection with avian influenza A/H6N1 virus in Taiwan in 2013 has raised concerns about this virus. During our routine surveillance of avian influenza viruses (AIVs) in live-bird markets in Egypt, an H6N1 virus was isolated from a garganey duck and was characterized. Phylogenetic analysis indicated that the Egyptian H6N1 strain A/Garganey/Egypt/20869C/2022(H6N1) has a unique genomic constellation, with gene segments inherited from different subtypes (H5N1, H3N8, H7N3, H6N1, and H10N1) that have been detected previously in AIVs from Egypt and some Eurasian countries. We examined the replication of kinetics of this virus in different mammalian cell lines (A549, MDCK, and Vero cells) and compared its pathogenicity to that of the ancestral H6N1 virus A/Quail/HK/421/2002(H6N1). The Egyptian H6N1 virus replicated efficiently in C57BL/6 mice without prior adaptation and grew faster and reached higher titers than in A549 cells than the ancestral strain. These results show that reassortant H6 AIVs might pose a potential threat to human health and highlight the need to continue surveillance of H6 AIVs circulating in nature.

Double-antibody-based nano-biosensing system for the onsite monitoring of SARS-CoV-2 variants

The fast and reliable diagnosis of COVID-19 is the foremost priority for promoting public health interventions. Therefore, double-antibody-based immunobiosensor chips were designed, constructed, and exploited for clinical diagnosis. Gold nanoparticles/tungsten oxide/carbon nanotubes (AuNPs/WO3/CNTs) were used as the active working sensor surface to support the chemical immobilization of a mixture of SARS-CoV-2 antibodies (anti-RBD-S and anti-RBD-S-anti-Llama monoclonal antibodies). The morphology and chemical functionalization of the fabricated disposable immunochips was characterized using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). After full assay optimization, the immunobiosensor showed a high sensitivity to detect SARS-CoV-2-S protein with limits of detection and quantification of 1.8 and 5.6 pg/mL, respectively. On the other hand, for the SARS-CoV-2 whole virus particle analysis, the detection and quantification limits were determined to be 5.7 and 17 pg/mL, respectively. The biosensor showed a highly selective response toward SARS-CoV-2, even in the presence of influenza, nontargeting human coronaviruses, and Middle East respiratory syndrome coronavirus (MERS-CoV). The immunochips exhibited distinct responses toward the variants of concern: B.1>C.36.3>Omicron> Delta> Alpha coronavirus variants. For biosensor validation, twenty-nine clinical specimens were analyzed, and the impedimetric responses were positively detected for two Delta samples, eighteen Omicron samples, and six B.1-type samples in addition to three negative samples. Eventually, the immunobiosensor was fabricated in the form of ready-to-use chips capable of sensitive detection of virus variants, especially variants of concern (VOC) and interest, in a specimen within 15 min. The chips provided instantaneous detection with the direct application of clinical samples and are considered a point-of-care device that could be used in public places and hot spots.

Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020-2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality

BACKGROUND

The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022.

METHODS

Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt.

RESULTS

A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively.

CONCLUSIONS

The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making.

Whole-Genome Sequence of a Human Monkeypox Virus Strain Detected in Egypt

Monkeypox virus has recently been detected in multiple countries. Two cases of monkeypox virus were reported in Egypt as part of an ongoing international outbreak. We report the whole-genome sequence of a monkeypox virus that was retrieved from the first confirmed case in Egypt. The virus was fully sequenced on the Illumina platform, and phylogenetic analysis demonstrated that the current monkeypox strain is closely related to clade IIb, which caused recent multicountry outbreaks.

SARS-CoV-2-Impedimetric Biosensor: Virus-Imprinted Chips for Early and Rapid Diagnosis

Due to the current global SARS-CoV-2 pandemic, rapid and accurate diagnostic tools are needed to prevent the spread of COVID-19 across the globe. An electrochemical sensing platform was constructed using CNTs/WO3-screen printed electrodes for imprinting the complete virus particles (SARS-CoV-2 particles) within the polymeric matrix to create viral complementary binding sites. The sensor provided high selectivity toward the target virus over other tested human corona and influenza respiratory interference viruses. The sensitivity performance of the sensor chips was evaluated using different viral concentrations, while the limits of detection and quantification were 57 and 175 pg/mL, respectively. Reaching this satisfied low detection limit (almost 27-fold more sensitive than the RT-PCR), the sensor was applied in clinical specimens obtained from SARS-CoV-2 suspected cases. Thus, dealing directly with clinical samples on the chip could be provided as a portable device for instantaneous and simple point of care in hospitals, airports, and hotspots.

Applying of SP, DC-Resistivity, DC-TDIP and TDEM soundings in high saline coastal aquifer

Four surface geophysical techniques were utilized to study the geological and hydrogeological settings of highly saline a coastal aquifer system to the north-east of River Nile Delta, Egypt. These techniques include SP, DC-Resistivity, TDIP and TDEM methods. The first target was to determine the geological stratification as a differentiation among clay, clayey, sand and sandy layers of high saline water. These techniques reflect that there is a complicated lateral and vertical difference in sediments along study area. The surface layers with depth down to ~120 m have low to medium content of clay that change with depth. Then, the second target was the differentiation laterally and vertically for salinity with depth down to ~250m as an interesting hydrogeological setting. These techniques reported that the sediments consist of thin and thick clay and silts, clayey sand, and sandy clay strata. Investigation depth was up to ~210m due to high salinity and clay content effect. At shallow depths, soil texture (down to ~100m and sometimes down to ~160m) consists of clay and silt with sand intercalation. The TEM data indicate a zone of less saline water and low clay content starting from ~40 to ~100m. There may be an evidence for a significant high to medium clay content after these depths down to ~250m. All four methods were calibrated with each other. Accordingly, good matching between the inversion model of TEMSs and composite logs of new drilled well was found, especially in lithological layers identifications. Also, this calibration confirmed that the area was complicated regarding the geological and hydrogeological conditions and the TDIP and TEM are the best methods in studying the environmental, geological and hydrogeological settings as primary important engineering implications for studying coastal highly saline aquifers.

Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients

Breast cancer (BC) incidence is progressively increasing in Egypt. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of its progression. To the best of our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients. Four hundred and nine cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies. TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in Tp53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, one drug response variant (p.P72R) in TP53 was detected in 8 samples. Furthermore, four novel variants were identified in JAK2, MTOR, KIT and EPHB. Further analysis, by Ingenuity Variant Analysis software (IVA), showed that PI3K/AKT signaling is altered in greater than 50% of Egyptian BC patients which implicates PI3K/AKT signaling as a therapeutic target. In this cohort, we shed the light on the most frequently detected somatic mutations and the most altered pathway in Egyptian BC patients.

P836 Long-term survival of a rare case of pseudoaneurysm of the mitral-aortic intervalvular fibrosa as a complication of endocarditis of a bicuspid aortic valve

Introduction

This is a case report of a rare condition of pseudoaneurysm of the mitral-aortic intervalvular fibrosa (P-MAIVF).

Case presentation

The patient was a 42-year-old Filipino gentleman. He first presented to us in 2014, for routine echocardiographic examination as a part of a preoperative assessment for a non-cardiac surgery. Patient was asymptomatic and had a history of bicuspid aortic valve, which was complicated by endocarditis in 2006, and was treated with antibiotics.

Echocardiography findings: Transthoracic echocardiography (TTE) showed a bicuspid aortic valve of no hemodynamic significance . A P-MAIVF was noted by Transesophageal echocardiography as a cavity expanding posteriorly into the left atrium from the left ventricular outflow tract, with a narrow neck at the junction of the aortic posterior cusp and the anterior mitral leaflet (Figure A). The cavity showed the characteristic expansion during ventricular systole, and collapse in diastole. Color flow showed the flow through the neck in systole and emptying during diastole (Figures C,D). There was mild mitral incompetence and no fistula was detected. Diagnosis was confirmed by cardiac magnetic resonance (Figure B).

Follow up

Because of the known complications of this condition, some of which are potentially fatal (such as rupture into the pericardium and tamponade), he was offered a surgical repair, which he had refused. Alternative conservative follow-up strategy was implemented and we had the opportunity to follow him for more than 5 years. During these years he was asymptomatic and uncomplicated. There was no change in the size of the pseudoaneurysm or its flow pattern.

Conclusion

This report demonstrates a rare case of P-MAIF as a complication of bicuspid aortic valve endocarditis and a long-term patient survival of a potentially fatal condition without corrective surgery.

Abstract P836 Figures A,B,C,D

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Dromedary Camels in Africa and Middle East

Dromedary camels are the natural reservoirs of the Middle East respiratory syndrome coronavirus (MERS-CoV). Camels are mostly bred in East African countries then exported into Africa and Middle East for consumption. To understand the distribution of MERS-CoV among camels in North Africa and the Middle East, we conducted surveillance in Egypt, Senegal, Tunisia, Uganda, Jordan, Saudi Arabia, and Iraq. We also performed longitudinal studies of three camel herds in Egypt and Jordan to elucidate MERS-CoV infection and transmission. Between 2016 and 2018, a total of 4027 nasal swabs and 3267 serum samples were collected from all countries. Real- time PCR revealed that MERS-CoV RNA was detected in nasal swab samples from Egypt, Senegal, Tunisia, and Saudi Arabia. Microneutralization assay showed that antibodies were detected in all countries. Positive PCR samples were partially sequenced, and a phylogenetic tree was built. The tree suggested that all sequences are of clade C and sequences from camels in Egypt formed a separate group from previously published sequences. Longitudinal studies showed high seroprevalence in adult camels. These results indicate the widespread distribution of the virus in camels. A systematic active surveillance and longitudinal studies for MERS-CoV are needed to understand the epidemiology of the disease and dynamics of viral infection.

Middle East respiratory syndrome coronavirus infection in non-camelid domestic mammals

Dromedary camels are natural host of the Middle East respiratory syndrome coronavirus (MERS-CoV). However, there are limited studies of MERS-CoV infection of other domestic mammals exposed to infected dromedaries. We expanded our surveillance among camels in Egypt, Tunisia, and Senegal to include other domestic mammalian species in contact with infected camels. A total of 820 sera and 823 nasal swabs from cattle, sheep, goats, donkeys, buffaloes, mules, and horses were collected. Swabs were tested using RT-PCR and virus RNA-positive samples were genetically sequenced and phylogenetically analysed. Sera were screened using virus microneutralization tests and positive sera (where available) were confirmed using plaque reduction neutralization tests (PRNT). We detected 90% PRNT confirmed MERS-CoV antibody in 35 (55.6%) of 63 sera from sheep collected from Senegal, two sheep (1.8%) of 114 in Tunisia and a goat (0.9%) of 107 in Egypt, with titres ranging from 1:80 to ≥1:320. We detected MERS-CoV RNA in swabs from three sheep (1.2%) of 254 and five goats (4.1%) of 121 from Egypt and Senegal, as well as one cow (1.9%) of 53 and three donkeys (7.1%) of 42 from Egypt. Partial sequences of the RT-PCR amplicons confirmed specificity of the results. This study showed that domestic livestock in contact with MERS-CoV infected camels may be at risk of infection. We recommend expanding current MERS-CoV surveillance in animals to include other livestock in close contact with dromedary camels. The segregation of camels from other livestock in farms and live animal markets may need to be considered.

Abstract 4243: Genetic variants frequently detected in Egyptian breast cancer tumors: Comprehensive cancer panel by ion torrent DNA sequencing technology

Breast cancer is the leading cause of cancer-related death in women worldwide. In Egypt, it is the most common cancer among females and its incidence is progressively increasing with a great tendency to occur with advanced stages in younger ages. Due to the heterogeneity of breast cancer, it was classified into different subtypes, each exhibits a unique gene mutation profile, based on biological characteristics and on gene expression pattern. Therefore, further research is needed to investigate the unknown genetic mutations involved in the progression of that disease. This study aimed to sequence 409 exons of tumor suppressor genes and oncogenes to identify the frequency of the detected genetic mutations in breast cancer using Ion Comprehensive Cancer Panel. Forty-eight tissue samples of various breast cancer subtypes were collected from National Cancer Institute (NCI) outpatient clinic, Cairo University. Analysis revealed 191 exonic and splicing variants. In this paper, we will address the most frequently detected Egyptian genetic variants (in 31.25 % of cases or more) as well as other deleterious variants commonly associated with breast cancer. Most of the detected genetic variants were checked in 1000g, dbSNP and Exac All databases. Other variants were found at known hotspot sites. We reported fifty-one somatic and germline mutations in thirty-two genes; AKAP9, BUB1B, RPS6KA2, AURKB, FANCA, RNF213, FGFR4, KAT6B, NLRP1, KAT6A, PER1, ERBB4, IL6ST, PIK3CA, P53, AURKA, WRN, PALB2, PTEN, GATA3, AKT1, ERBB2 and KRAS. Only KAT6B incurred non-frameshift deletion and only GATA3 had frameshift insertion while KAT6A, ERBB4 and PTEN had frameshift deletion. All the identified variants were detected with different frequencies in each breast cancer subtype. Each sample harbored at least four mutations and the maximum number of mutations per sample was twelve. The current data showed that gene panels analyzed

by Next-Generation Sequencing (NGS) identifies large number of germline and somatic mutations that is crucial for understanding cancer predisposition and developing personalized or combination therapies that efficiently target the individual breast cancer-specific mutations.

Key words: Breast cancer, Somatic mutations, Germline mutations, Ion torrent sequencing, Targeted sequencing.

Note: This abstract was not presented at the meeting.

Citation Format: Abdel-Rahman N. Zekri, Osman Mansour, Samah A. Loutfy, Mohamed M. Hafez, M. Gomaa, Abeer Bahnassy, Mai M. Lotfy, Amira S. Youssef, Ola S. Ahmed, Mohammed Abouelhouda, Auhood Nassar. Genetic variants frequently detected in Egyptian breast cancer tumors: Comprehensive cancer panel by ion torrent DNA sequencing technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4243.

Avian influenza H5N1 vaccination efficacy in Egyptian backyard poultry

Raising backyard poultry under low biosecurity conditions is a common practice in Egypt. While vaccination is routinely applied in Egypt in commercial settings to curb the spread of avian influenza viruses, it remains less commonly used in backyard settings. We assessed the immunogenicity and protective efficacy of a H5N1 vaccine based on a contemporary Egyptian clade 2.2.1.2 virus among turkeys, ducks, geese, and chickens raised together in a backyard setting. Results showed that this vaccine elicits an immune response in all tested species reaching up to a hemagglutination inhibition titer of 10 log₂ after a booster dose. However, this response varied between species. When challenged, vaccinated birds survived and shed less virus in comparison with unvaccinated birds. However, unvaccinated ducks showed no symptoms of infection and survived the duration of the experiment. Moreover, vaccinated ducks shed more virus as compared to vaccinated birds of other species. Hence, we recommend avoiding mixing various species in the backyards of Egypt. Our data indicates that vaccination can be effective in the backyard setting in Egypt, although planning should consider the species covered.

Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt, August 2015 to January 2016

A cross-sectional study was conducted in Egypt to determine the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in imported and resident camels and bats, as well as to assess possible transmission of the virus to domestic ruminants and equines. A total of 1,031 sera, 1,078 nasal swabs, 13 rectal swabs, and 38 milk samples were collected from 1,078 camels in different types of sites. In addition, 145 domestic animals and 109 bats were sampled. Overall, of 1,031 serologically-tested camels, 871 (84.5%) had MERS-CoV neutralising antibodies. Seroprevalence was significantly higher in imported (614/692; 88.7%) than resident camels (257/339; 5.8%) (p < 0.05). Camels from Sudan (543/594; 91.4%) had a higher seroprevalence than those from East Africa (71/98; 72.4%) (p < 0.05). Sampling site and age were also associated with MERS-CoV seroprevalence (p < 0.05). All tested samples from domestic animals and bats were negative for MERS-CoV antibodies except one sheep sample which showed a 1:640 titre. Of 1,078 camels, 41 (3.8%) were positive for MERS-CoV genetic material. Sequences obtained were not found to cluster with clade A or B MERS-CoV sequences and were genetically diverse. The presence of neutralising antibodies in one sheep apparently in contact with seropositive camels calls for further studies on domestic animals in contact with camels.

Atropine-neostigmine mixture: a dose-response study

The dose-response relationship and the doses of atropine required to prevent neostigmine from lowering heart rates below baseline in 50 per cent (ED50) and 95 percent (ED95) of patients after antagonism of pancuronium-induced neuromuscular blockade were determined in 70 patients with neostigmine-atropine mixtures. Neostigmine 0.04 mg.kg-1 (group A, n = 35) or 0.06 mg.kg-1 (group B, n = 35) was randomly mixed with one of seven doses of atropine (ranging from 0.014 to 0.04 mg.kg-1) in group A and from 0.02 to 0.04 mg.kg-1 in group B), with dose-response curves for atropine being constructed for both groups 5 and 10 min after injection of the mixture. These dose-response curves were found to be parallel in both groups. The calculated ED50 and ED95 values of atropine were similar in both groups. The estimated ED50 doses of atropine in groups A and B at 5 min were 0.031 and 0.033 mg.kg-1 respectively, and at 10 min the ED50 doses were 0.037 and 0.037 mg.kg-1 respectively. The calculated ED95 doses of atropine in groups A and B at 5 min were 0.05 and 0.046 mg.kg-1, and at 10 min the ED95 doses were also similar, being 0.06 and 0.055 mg.kg-1 respectively. Under the conditions employed in this study it would seem that in order to prevent late reductions in heart rates, the appropriate doses of atropine when used with neostigmine should be greater than that commonly used.

Atropine-edrophonium mixture: a dose-response study

The dose-response and the doses required to prevent bradycardia in 50% (ED50) and 95% (ED95) of patients were determined for atropine after antagonism of pancuronium-induced neuromuscular blockade in 72 patients with edrophonium-atropine mixtures. Edrophonium 0.67 mg/kg (group A, n = 37) or 1.0 mg/kg (group B, n = 35) was randomly mixed with one of seven doses of atropine (ranging from 0.0125 to 0.0215 mg/kg in group A and from 0.02 to 0.04 mg/kg in group B); with dose-response curves for atropine being constructed for both groups 5 and 10 minutes after the injection of the mixture. These dose-response curves were found to be parallel in both groups. The calculated ED50 values of atropine were 1.6-2 times greater in group B, compared with those in group A. The estimated ED50 doses of atropine in groups A and B at 5 minutes were 0.018 and 0.029 mg/kg, respectively, and at 10 minutes, the ED50 doses were similar, being 0.016 and 0.032 mg/kg, respectively. The calculated ED95 doses of atropine in groups A and B at 5 minutes were 0.024 and 0.055 mg/kg, and at 10 minutes, the ED95 doses were also similar, being 0.027 and 0.05 mg/kg, respectively.