Pandemic potential of highly pathogenic avian influenza clade 2.3.4.4 A(H5) viruses.

The panzootic caused by A/goose/Guangdong/1/96-lineage highly pathogenic avian influenza (HPAI) A(H5) viruses has occurred in multiple waves since 1996. From 2013 onwards, clade 2.3.

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.

MChip, a low density microarray, differentiates among seasonal human H1N1, North American swine H1N1, and the 2009 pandemic H1N1.

Background: The MChip uses data from the hybridization of amplified viral RNA to 15 distinct oligonucleotides that target the influenza A matrix (M) gene segment. An artificial neural network (ANN) automates the interpretation of subtle differences in fluorescence intensity patterns from the microarray. The complete process from clinical specimen to identification including amplification of viral RNA can be completed in <8 hours for under US$10.

Antigenic and genetic diversity of highly pathogenic avian influenza A (H5N1) viruses isolated in Egypt.

Highly pathogenic avian influenza A virus (H5N1) has diverged antigenically and genetically since its initial detection in Asia in 1997. Viruses belonging to clade 2.2 in particular have been reported in numerous countries with the majority occurring in Egypt.

Single assay for simultaneous detection and differential identification of human and avian influenza virus types, subtypes, and emergent variants.

For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production.

Universal detection and identification of avian influenza virus by use of resequencing microarrays.

Zoonotic microbes have historically been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the appearance of some human infections have increased the concern of a possible new influenza pandemic, which highlights the need for broad-spectrum detection methods for rapidly identifying the spread or outbreak of all variants of avian influenza virus. In this study, we demonstrate that high-density resequencing pathogen microarrays (RPM) can be such a tool.

Oseltamivir resistance mutation N294S in human influenza A(H5N1) virus in Egypt.

In December 2006, three human specimens were received that were suspected positive for influenza A(H5N1). The specimens were tested using real time PCR. And the presence of A(H5N1) virus was confirmed in 2 patients (16F and 26M), The NA sequence from A(H5N1) positive specimens collected before and after antiviral therapy revealed a mutation (N294S) (N295S according to N1 numbering), previously associated with resistance to oseltamivir.

Genome analysis linking recent European and African influenza (H5N1) viruses.

To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates.

Global surveillance of emerging Influenza virus genotypes by mass spectrometry.

Background: Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.

Methods And Principal Findings: Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes.

Genetic characterization of HIV-1 strains circulating in Kazakhstan.

To determine the HIV-1 genetic diversity in Kazakhstan, 85 blood samples from HIV-seropositive donors were collected between 2001 and 2003. The study population consisted of 91.8% injecting drug users (IDUs); the remainder was infected sexually or iatrogenically.

Hepatitis E virus infection in work horses in Egypt.

Hepatitis E virus (HEV) is an important cause of hepatitis among young Egyptian adults with high seroprevalence rates seen in both rural areas of the Nile Delta and in suburban Cairo. Because natural antibodies to HEV have been detected in animals and zoonotic transmission is postulated, we surveyed work horses in Cairo for evidence of HEV exposure and viremia. Sera from 200 Cairo work horses were tested by ELISA for the presence of IgG anti-HEV antibody revealed a seropositivity of 13%.

Genetic forms of HIV Type 1 in the former Soviet Union dominate the epidemic in Azerbaijan.

A total of 125 strains collected in Azerbaijan between 1999 and 2002 from HIV seropositives were genetically classified. Of 84 strains classified using HMA, 91.6% were subtype A, 1.

Molecular epidemiology of HIV Type 1 in Ukraine: birthplace of an epidemic.

During the 1990s, HIV-1 spread rapidly through drug networks in Ukraine and from there throughout the former Soviet Union. To examine the origins of this epidemic, the genetics of HIV-1 in Ukraine were studied. Proviral DNA from PBMC was extracted and PCR amplified.

Prevalence and correlates of human immunodeficiency virus infection among female sex workers in Tashkent, Uzbekistan.

Objectives/goal: To assess prevalence of and correlates to human immunodeficiency virus (HIV) infection among female sex workers in Tashkent, Uzbekistan.

Study Design: Women participating in this cross-sectional study completed a questionnaire and HIV testing between April 2003 and March 2004. Logistic regression analyses determined correlation of variables to HIV infection.

PCR analysis of egyptian respiratory adenovirus isolates, including identification of species, serotypes, and coinfections.

Eighty-eight adenovirus (Ad) isolates and associated clinical data were collected from walk-in patients with influenza-like illness in Egypt during routine influenza surveillance from 1999 through 2002. Respiratory Ad distributions are geographically variable, and serotype prevalence has not been previously characterized in this region. Serotype identity is clinically relevant because it predicts vaccine efficacy and correlates strongly with both clinical presentation and epidemiological pattern.

HIV type 1 strains common in Europe, Africa, and Asia cocirculate in Yemen.

To determine the HIV-1 genetic diversity in Yemen, 19 strains collected from men and women were sequenced in pol and six of those were full genome sequenced; all were phylogenetically analyzed. Using the pol sequence data, nine (47.3%) were subtype B, six (31.

Outbreak of a West African recombinant of HIV-1 in Tashkent, Uzbekistan.

Objectives: This research describes the genetic diversity of HIV-1 in Uzbekistan.

Methods: During 2002 and 2003, blood from HIV-positive patients in Uzbekistan was collected, and part of the proviral pol gene and nearly full-length genomes were sequenced and analyzed.

Results: Among 142 Uzbek strains, most clustered genetically with the subtype A strain common in the former Soviet Union.