A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian). The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.

Surveillance of avian influenza viruses in migratory birds in Egypt, 2003-09.

Migratory (particularly aquatic) birds are the major natural reservoirs for type A influenza viruses. However, their role in transmitting highly pathogenic avian influenza (HPAI) viruses is unclear. Egypt is a "funnel" zone of wild bird migration pathways from Central Asia and Europe to Eastern and Central Africa ending in South Africa. We sought to detect and isolate avian influenza viruses in migratory birds in Egypt. During September 2003-February 2009, the US Naval Medical Research Unit Number 3, Cairo, Egypt, in collaboration with the Egyptian Ministry of Environment, obtained cloacal swabs from 7,894 migratory birds captured or shot by hunters in different geographic areas in Egypt. Samples were processed by real-time reverse transcriptase PCR for detection of the influenza A matrix gene. Positive samples were processed for virus isolation in specific-pathogen-free embryonated eggs and isolates were subtyped by PCR and partial sequencing. Ninety-five species of birds were collected. Predominant species were Green-Winged Teal (Anas carolinensis; 32.0%, n=2,528), Northern Shoveler (Anas clypeata; 21.4%, n=1,686), and Northern Pintail (Anas acuta; 11.1%, n=877). Of the 7,894 samples, 745 (9.4%) were positive for the influenza A matrix gene (mainly from the above predominant species). Thirteen of the 745 (1.7%) were H5-positive by PCR (11 were low-pathogenic avian influenza and two were HPAI H5N1). The prevalences of influenza A was among regions were 10-15%, except in Middle Egypt (4%). Thirty-nine influenza isolates were obtained from PCR-positive samples. Seventeen subtypes of avian influenza viruses (including H5N1 and H7N7) were classified from 39 isolates using PCR and partial sequencing. Only one HPAI H5N1 was isolated in February 2006, from a wild resident Great Egret (Ardea alba). No major die-offs or sick migratory birds were detected during the study. We identified avian influenza virus subtypes not previously reported in Egypt. The HPAI H5N1 isolated or detected indicates that migratory birds may play a role in the dispersal of HPAI virus, but a detailed mechanism of this role needs to be elucidated.

Virus isolations and high population density implicate Culex antennatus (Becker) (Diptera: Culicidae) as a vector of Rift Valley Fever virus during an outbreak in the Nile Delta of Egypt.

In June, 2003, Egypt's hospital-based electronic disease surveillance system began to record increased cases of acute febrile illness from governorates in the Nile Delta. In response to a request for assistance from the Egyptian Ministry of Health and the World Health Organization (WHO), the U.S. Naval Medical Research Unit No. 3 (NAMRU-3) provided assistance in identifying the cause and extent of this outbreak. Testing of human clinical samples (n=375) from nine governorates in Egypt identified 29 cases of RVF viremia that spanned the period of June to October, and a particular focus of disease in Kafr el Sheikh governorate (7.7% RVF infection rate). Veterinary samples (n=101) collected during this time in Kafr el Sheikh and screened by immunoassay for RVFV-specific IgM identified probable recent infections in cattle (10.4%) and sheep (5%). Entomologic investigations that focused in rural, rice growing villages in the Sidi Salim District of Kafr el Sheikh during August-September, 2003, collected, identified, and tested host-seeking female mosquitoes for the presence of pathogenic viruses. Three isolates of RVF virus (RVFV) were obtained from 297 tested pools of female mosquitoes and all three RVFV isolates came from Cx. antennatus (Becker). While Cx. pipiens has been considered the primary vector of RVF virus in Egypt and is often the most common man-biting species found, Cx. antennatus was the dominant species captured at the 2003 outbreak location in Kafr el Sheikh governorate. This is the first time that Cx. antennatus has been found naturally infected with RVFV in Egypt.

Dengue hemorrhagic fever outbreak in children in Port Sudan.

Dengue fever (DF)/dengue hemorrhagic fever (DHF) has emerged as a global public health problem with countries in Asia and the Pacific sharing more than 70% of the disease burden. In 2004-2005 a total of 312 cases admitted to Pediatric and Sea Port Hospitals in Port Sudan were clinically diagnosed as DHF. The mortality rate recorded was 3.8% (n=12). Of the cases 73.4% were patients 5-15 years of age. A total of 91.2% of cases were admitted during May and June 2005 with 49.4% residing in the eastern region of Port Sudan. Dengue shock syndrome was observed in 37 of 312 (11.9%). All patients had thrombocytopenia with platelets count ranged from <100,000 to <150,000 cell/mm³. Of the 40 sera tested using RAPID-cassette test in the Khartoum Central Public Health Lab, 36 (90%) were dengue IgM positive. A subset of these sera (n=23) were sent to NAMRU-3 and confirmed by IgM-capture ELISA; 9 of 23 were PCR positive for dengue serotype 3.

Studies on West Nile virus infection in Egypt.

We conducted a prospective cohort study to determine prevalence and incidence of West Nile virus (WNV) in Egypt. Cohorts were established in Upper (UE), Middle (ME), and Lower (LE) Egypt. Additionally, a cross-sectional serosurvey was performed in the North (NS) and South (SS) Sinai. Cohorts were bled initially and 1 year later. Sera were tested for WNV-IgG by ELISA and positive sera were confirmed by plaque reduction neutralization test (PRNT). Sentinel chicken flocks placed in the above sites were bled monthly for virus isolation and serology. Mosquitoes were collected monthly from the above sites and tested for WNV. Human seroprevalence rates were 35%, 27%, 14%, 1% and 7% in UE, ME, LE, NS and SS, respectively. Seroconversion rates were 18%, 17% and 7% in UE, ME and LE, respectively; 49% of the seroconverters reported undiagnosed febrile illness. Sentinel chickens showed seroconversion in all study sites. WNV was isolated from both sentinel chickens and mosquitoes in cohort sites. This study demonstrates that WNV was actively circulating during the study period in different areas in Egypt and causing febrile illness in a considerable proportion of individuals in the study sites.

Isolation of cryptococcus, Candida, Aspergillus, Rhodotorula and nocardia from meningitis patients in egypt.

Meningitis occurs throughout Egypt and is largely attributed to bacterial pathogens, but there is little information on fungal etiologies of meningitis. We, therefore, investigated fungal infections among Egyptian patients with acute and subacute meningitis who tested negative for bacterial and viral agents. A total of 1000 cerebrospinal fluid (CSF) samples collected from nine governorates of Egypt during 1998-2002 were initially stained with Gram's, India ink, and lacto-phenol cotton-blue stains, and examined under light microscope to detect fungal elements. All CSF samples were cultured on brain heart infusion, Wickerham and Staib agar media for fungus isolation. CSF with suspected Cryptococcus neoformans infections were also tested by latex agglutination test for antigen detection. Species identification of selected isolates was carried out at the Mycotic Diseases Branch, CDC, Atlanta, Georgia, USA. Fungal agents were detected microscopically and by culture in 17 of 1000 (1.7%) CSF samples tested. Ten of 17 were identified as C. neoformans var grubii (serotype A), 4 as Candida albicans, and one each of Aspergillus candidus, Rhodotorula mucilaginosa (rubra) and Nocardia spp (actinomycetes). Out of the 17 cases with fungal CSF infection, 8 died (Cryptococcus-3, Candida-2, Aspergillus, Rhodotorula and Nocardia) and 2 suffered neurological sequelae. Of the 10 cryptococcal meningitis patients, 4 were HIV positive and one was diagnosed with lymphoma. To our knowledge, this is the first study on isolation of fungi other than Cryptococcus from CSF of Egyptian patients with acute/subacute meningitis. Consideration must now be given to cryptococcosis and candidiasis as potential etiologies of meningitis in Egypt.

Risk factors for brucellosis in Samarqand Oblast, Uzbekistan.

OBJECTIVES: This study was conducted to identify the potential risk factors for human brucellosis infection in Samarqand, Uzbekistan. METHODS: Clinically identified cases admitted to different hospitals during 2004-2006 (N=144), and age-, sex- and residence-matched control patients (N=288) with other unrelated conditions, were included in this study. Structured questionnaires were completed and consent forms signed. Patients and controls were tested on site for Brucella infection by standard tube agglutination test and culture. Statistical analyses were performed with Stata software for univariate and multivariate analysis. RESULTS: Among the 144 patients with confirmed brucellosis, 137 (95.1%) owned farm animals, 135 (93.8%) were from rural areas, and 119 (82.6%) were enrolled during the animal breeding season. Multivariate analysis indicated that brucellosis was highly associated with contact with aborted animals (adjusted matched odds ratio (AMOR) 87.19, 95% confidence interval (CI) 9.36-911.85; p<0.001), slaughtering/butchering animals (AMOR 35.35, 95% CI 6.25-199.77; p<0.001) in the household, consumption of raw milk (AMOR 54.13, 95% CI 1.98-1476.13; p=0.018), and being in a family that had brucellosis sharing the same exposure (AMOR 15.93, 95% CI 1.37-184.97; p=0.027). CONCLUSIONS: To reduce the burden of brucellosis in Samarqand Oblast, veterinary services should be improved. Also public health education programs should be increased. Implementing these measures will minimize exposure to infected farm animals and reduce the risk of infection.

Adverse response of non-indigenous cattle of European breeds to live attenuated Smithburn Rift Valley fever vaccine.

Three hundred eighteen European cows and 115 buffaloes were vaccinated with locally prepared Smithburn vaccine, of which, 100 cows and 20 buffaloes were pregnant. Twenty-eight cows aborted within 72 days post-vaccination, buffaloes did not abort. Blood samples collected 77 days post-vaccination from aborted cows, 17 pregnant cows, 5 pregnant buffaloes, and 32 non-pregnant cows. Sera were tested by ELISA for anti-RVF IgM and IgG. All aborted cows were strongly positive for IgG. Five of 17 cows and two of five buffaloes that did not abort were IgG positive. The percentage of IgM positives in aborted cows was 25% and 0% in non-aborted cows. The percentage of IgG positives in pregnant non-aborted cows was lower than in non-pregnant cows. The percentage of IgG positives of non-pregnant cows was lower than pregnant aborted cows. Virus was isolated from one aborted fetus. The nucleotide sequence of fetus virus was compared to Smithburn of Onderstepoort, local Smithburn and virus isolates from 1993 to 1994 and 1977 RVF outbreaks. The nucleotide sequences of Onderstepoort and Egyptian Smithburn vaccines were almost identical. The sequences of 1993-1994 isolates were identical to 1977 outbreak virus. Virus from the fetus had two mutations; it is apparently a variant that is genetically distant from local Smithburn and Onderstepoort vaccines. Fetus virus was genetically distant from virus of 1993/1994 and 1977 outbreaks. In conclusion, antibody response to vaccination with local Smithburn had occurred in some, but not all the cows and buffaloes. Virus isolation from the fetus suggests in utero transmission of used vaccine virus, which resulted in high abortions in European cows.

HIV type 1 strains from East and West Africa are intermixed in Sudan.

The genetic subtypes of HIV-1 in the Sudan epidemic have not been characterized. Here we report the partial sequencing and analysis of 30 strains collected from HIV-1-positive patients and blood donors in Khartoum in 1998 and 1999. From analysis of partial pol and env sequences, it was determined that 50% were subtype D and 30% were subtype C. Of interest, some subtype D clustered with those from East Africa whereas others joined subtype D from West Africa. Subtype A, subtype B, and three unique recombinants were also found, some partially unclassifiable. One unclassified strain matched another reported previously from the Democratic Republic of Congo. Sudan borders nine other African countries, and has suffered more than 20 years of civil strife with large population displacements. The intermixing of HIV-1 subtypes previously separated in Africa may be occurring there, with the potential to generate novel new strains by recombination.