Our aim was to characterize the A/ck/Israeli/1055/2008 (H5N1) avian influenza virus that was isolated at the beginning of 2008, and to establish the phylogenetic relationship of this isolate to other H5N1 viruses that were recently isolated in adjacent countries. In light of a study of complete nucleotide sequences of all the genes we found that the isolate (year 2008) was closely related to the H5N1 viruses isolated in Egypt, Israel and Gaza in 2006. The Israeli isolate had the hemagglutinin-connecting peptide with a polybasic amino acid insertion. The most host-restriction sites of the 2008 isolate were typical of avian hosts, with one exception: K627 at the PB2 protein. As compared with previous local H5N1 isolates, a high mutation rate was found at the HA gene, which antigenic sites were under positive selection pressure.

Our aim was to establish the phylogenetic and genetic relationships among avian influenza viruses (AIV) recently isolated from poultry in Israel. During this study we analyzed complete nucleotide sequences of two envelope (hemagglutinin and neuraminidase) and six internal genes (polymerase B1, polymerase B2, polymerase A, nucleoprotein, nonstructural, and matrix) of 29 selected H9N2 and six internal genes of five H5N1 viruses isolated in Israel during 2000–2006. Comparative genetic and phylogenetic analyses of these sequences revealed that the local H5N1 viruses are closely related to H5N1 viruses isolated in European, Asian, and Middle Eastern countries in 2005–2006. The H9N2 Israeli isolates, together with viruses isolated in Jordan and Saudi Arabia formed a single group. Our data support the claim that during recent years a new endemic focus of H9N2 has been formed in the Middle East. The introduction of H5N1 and co-circulation of these two subtypes of AIV in this region may augment the risk of potentially pandemic strains emergence.

Since 2000, hundreds of H9N2 viruses have been isolated from all types of domestic birds. Although H9N2 is a low-pathogenicity virus, disease has been observed in all types of poultry in the field. Clinical signs ranged from very mild disease to high morbidity and mortality when the virus was associated with a secondary pathogen. Because of the wide range of the virus and the great losses it caused, initially a local vaccination program was implemented, but mass vaccination was quickly authorized. A local strain, isolated in 2002 was selected and is currently in use as an inactivated vaccine. An intensive operation is in progress to characterize the isolates. Several genes (hemagglutinin [HA], neuraminidase, nonstructural protein, nucleoprotein, and matrix) were sequenced, revealing three main groups: the first group included two isolates from 2000, the second group included isolates from 2001 to the beginning of 2003, and the third group included all isolates from 2003 to date. The differences between the second and third groups, in a part of the HA gene, ranged from 3.49% to 6.97% (average 4.57%) of the nucleotides. Similar differences were recorded in the other tested genes. These data could indicate the probable introduction of distinct progenitor viruses into the Israeli poultry population. Furthermore, sequencing of the HA protein of some Israeli isolates revealed the presence of L216 in the binding site; this finding was typical of the H9N2 viruses isolated from humans, which raises the possibility of an influence on host specificity and virulence.

During March 2006, an outbreak of highly pathogenic avian influenza (H5N1) occurred in multiple poultry farms in Israel. The epidemiologic investigation and review of outbreak mitigation efforts uncovered gaps in planning for and containing the outbreak, thus affording valuable lessons applicable to other countries in similar settings.

Highly pathogenic H5N1 avian influenza A viruses (AIV) have caused outbreaks among domestic poultry and wild aquatic birds in many Asian, European, and African countries since 1997. In March 2006 an avian H5N1 influenza A virus was isolated from poultry in Israel. In the present study we molecularly characterized the hemagglutinin (HA) and neuraminidase (NA) genes of eleven H5N1 viruses isolated from domestic poultry in Israel and Gaza in March–April 2006. Phylogenetic analysis of the HA and NA genes showed that the Israeli and Gazian viruses were closely related to viruses isolated in Egypt in 2006.

The avian influenza virus subtype H9N2 affects wild birds, domestic poultry, swine, and humans; it has circulated amongst domestic poultry in Israel during the last 6 years. The H5N1 virus was recorded in Israel for the first time in March 2006. Nonstructural (NS) genes and NS proteins are important in the life cycle of the avian influenza viruses. In the present study, NS genes of 21 examples of H9N2 and of two examples of H5N1 avian influenza viruses, isolated in Israel during 2000-2006, were completely sequenced and phylogenetically analyzed. All the H9N2 isolates fell into a single group that, in turn, was subdivided into three subgroups in accordance with the time of isolation; their NS1 and NS2 proteins possessed 230 and 121 amino acids, respectively. The NS1 protein of the H5N1 isolates had five amino acid deletions, which was typical of highly pathogenic H5N1 viruses isolated in various countries during 2005-2006. Comparative analysis showed that the NS proteins of the H9N2 Israeli isolates contained few amino acid sequences associated with high pathogenicity or human host specificity.

The partial nucleotide sequences of the hemagglutinin (HA) genes of 72 H9N2 influenza viruses isolated from chickens and turkeys in Israel during the period 2000-2005 were genetically analyzed. The isolates possessed the three types of amino acid motif -R-S-S-R/G-L-, -R-S-N-R/G-L-, and -R-S-K-R/G-L- at the cleavage site of HA. Phylogenetic analyses showed that all Israeli isolates belonged to the same group which further divided into three closely related sub-groups. The HA genes of these isolates were related to the HA gene of A/chicken/Germany/R45/98 isolated from chicken in Germany in 1998.

The first two isolates of H9N2 influenza virus were picked up from turkey and chicken hosts in May 2000, but the actual epizootic of the low pathogenicity avian influenza (LPAI) H9N2 virus started in December 2001, following a 1.5-year period of silence, during which the H10N7 and H6N3 influenza viruses were isolated sporadically. The outbreak of the H9N2 influenza began in northern Israel, from where the epizootic spread all over the country. Damage was relatively limited because of the widespread use of an inactivated vaccine. Single isolates were recorded in commercial ostrich and goose flocks, and in a wild pigeon. Apart from the routine serological tests, the diagnostics used the RT-PCR (reverse transcription polymerase chain reaction) test with type-specific primers related to the M and nucleoprotein (NP) genes, and a set of subtype-specific primers related to all the haemagglutinin (HA) and neuraminidase (NA) subtypes. All the primers were specially constructed. The part coding for N-terminus of the H chain of the HA gene of 61 out of 400 isolates was sequenced. The isolates showed a high rate of mutability, and differed distinctly from the H9 prototype strain; they belong to the same phylogenetic lineage divided into three sublineages, one of which exhibited a unique cleavage-site motif RSKR. The result indicates that two parallel evolutionary trends originated from the same local "prototype" isolate.

Avian reovirus (ARV) is a disease agent that causes economic losses in the poultry industry. The available vaccines do not confer full protection. One possible reason is the existence in the field of many virulent serotypes with no cross protection. Several ARV strains have been isolated in Israel in the last few years. In this study, we investigated the diversity of the sigma C protein of ARV because this is the most variable protein in the virus and it induces the production of neutralizing antibodies. Sigma C from two virulent isolates was sequenced, cloned, and expressed. The protein sequence differed from the attenuated vaccine strain (strain 1133) but was similar to a U.S. virulent strain (strain 1733). Those differences led to a change in the antigenic index of the protein, mainly at three sites. Sera of infected birds in a field trial and of birds in a controlled experiment vaccinated with the recombinant sigma C protein showed high titers in enzyme-linked immunosorbent assay to the recombinant protein and lower titers to the attenuated vaccine strain. This means that sigma C can be used as a diagnostic tool for the detection of antibodies relevant for protection and in the future as a subunit vaccine. The results of this study highlight the need to reconsider vaccinations against ARV in terms of the strains to be used and of the method of identifying protective antibodies transferred to progeny.

In November 1997, an outbreak of a neuroparalytic disease caused by West Nile (WN) virus was diagnosed in young goose flocks. Domestic geese were similarly affected in the late summer and fall of 1998, 1999, 2000 and 2001. WN viruses were also isolated from migratory and wild birds and horses in 1998–2001. A 1278 bp sequence of the envelope gene of 24 Israeli WN virus isolates was compared with those of seven isolates from Africa, Europe and New York. As a result, the Israeli isolates could then be grouped into two clusters. The 15 avian and three equine from 1997–2001 in the first cluster of viruses were shown to be identical to WN-NY99, while the second cluster comprised one goose isolate from 1998 and two goose and two pigeon isolates from 2000. These closely resembled the most recent Old World isolates, and indicate that at least two WN genotypes were co-circulating in the region during this time.

West Nile virus (WNV) was isolated in a flock of 1,200 migrating white storks that landed in Eilat, a town in southern Israel, on August 26, 1998. Strong, hot westerly winds had forced the storks to fly under considerable physical stress before reaching the agricultural land surrounding the town. Most of the flock were fledglings, <1 year old, which had hatched in Europe. Thirteen dead or dying storks were collected 2 days after arrival and submitted to the laboratory for examination. Four WNV isolates were obtained from their brains. Out of 11 storks tested six days after arrival, three had WNV-neutralizing antibodies. Comparative analysis of full-length genomic sequences of a stork isolate and a 1999 flamingo isolate from the USA showed 28 nucleotide (nt) (0.25%) and 10 amino acid (0.3%) changes. Sequence analysis of the envelope gene of the stork isolate showed almost complete identity with isolates from Israeli domestic geese in 1998 and 1999 and from a nonmigrating, white-eyed gull in 1999. Since these storks were migrating southwards for the first time and had not flown over Israel, we assume that they had become infected with WNV at some point along their route of migration in Europe.

Abstract: The recent epizootic of West Nile fever in Israel affected predominantly young domestic geese between three and eight weeks old. Clinically, the birds presented paralytic signs while morbidity and mortality were severe in affected flocks. The condition was encountered from early September through late November on goose farms located throughout the country. Losses incurred by goose flocks were sufficiently great as to warrant investigation of ways to protect young geese against the neurological form of the disease. We have conducted a series of vaccination trials in which three‐week old geese were immunized with an attenuated, commercial flavivirus vaccine derived from Israel turkey meningoencephalitis virus (TME). Birds were challenged two weeks later with a low Vero cell passage of West Nile virus by the intracerebral route. In a second group of experiments, inactivated and live TME vaccines were given in tandem at an interval of two weeks and challenged two weeks later. The third vaccination trial was based on West Nile virus (WNV) harvested from infant mouse brain, inactivated with formalin and oil adjuvanted. A single injection given either subcutaneously or intramuscularly resulted in 75% protection of the vaccinated groups, while two injections spaced two weeks apart resulted in 94% protection. Groups of geese, vaccinated at the farms and challenged under controlled conditions in the laboratory, showed levels of protection ranging from 39% to 72% for TME vaccine and 52% and 80% for WNV vaccine. The lower levels of protection are attributable to flocks being affected with intercurrent infections at the time of vaccination.

West Nile virus (WNV) caused disease outbreaks in Israel in the 1950s and the late 1970s. In 1998 an outbreak of WNV in goose farms and evidence of infection in dead migratory birds were reported. Consequently, human diagnostic services for WNV were resumed, including virus isolation, serology, and RT-PCR. Risk factors for infection were assessed by a serological survey in 1999, which revealed a seroprevalence of (a) 86% in people who had close contact with sick geese, (b) 28% in people in areas along bird migration routes, and (c) 27% in the general population. Following two fatal cases in Tel Aviv in September 1999 and one encephalitis case in the southern Eilot region, a regional serological survey was initiated there. The survey revealed two more WNV-associated acute encephalitis cases, an IgG seroprevalence of 51%, and an IgM seroprevalence of 22%. In the summer of 2000, acute cases of WN disease were identified in the central and northern parts of Israel, involving 439 people. The outbreak started in mid-August, peaked in September, and declined in October, with 29 fatal cases, primarily in the elderly. During the outbreak, diagnosis was based on IgM detection. Four virus isolates were subsequently obtained from preseroconverted frozen sera. Sequence and phylogenetic analysis of 1662 bases covering the PreM, M, and part of the E genes revealed two lineages. One lineage was closely related to a 1999 Israeli bird (gull) isolate and to a 1999 New York bird (flamingo) isolate, and the other lineage was closely related to a 1997 Romanian mosquito isolate and to a 1999 Russian human brain isolate.

Turkey meningoencephalitis (TME) is a paralytic epornitic disease of turkeys caused by turkey meningoencephalitis virus (TMEV), an arthopod-borne flavivirus belonging to the Ntaya serogroup VI. A TMEV specific RT-PCR was compared with classical techniques for TMEV diagnosis, which include virus isolation in 8-day-old chicken embryonated eggs and suckling mice, on 17 TME flocks with neurological signs that occurred during the fall of 1997. In 11/17 flocks both the RT-PCR and the virus isolation methods detected virus, in 4/17 flocks a negative diagnosis was obtained by both methods, and two flocks were positive by RT-PCR only. In four flocks RT-PCR only detected virus after inoculation into embryonated eggs or suckling mice. There was a dose response effect in the yield of the RT-PCR product. Direct examination of turkey brains yielded bands of low to medium intensity. Use of RT-PCR after embryo and/or mouse inoculation resulted in products of far greater intensity. Thus, RT-PCR can be successfully used to amplify TMEV RNA in the brains of diseased turkeys but a negative result would require egg and mouse inoculation for enrichment of virus prior to RT-PCR.

Lake Kinneret (Israel), which currently supplies 30% of the national water demands (of which 50% is for domestic purposes), is also utilized for commercial fishery, recreation, and tourism. The measures taken to prevent pollution include, among others, sewage and fish pond waste removal, and burial of industrial and household solid wastes at established garbage dumps. On January 13, 1985, hundreds of dead and moribund gulls (Larus ridibundus) were observed on the shoreline and water surface at the northwest part of the lake, and around the northern garbage dump site. Sick birds exhibited signs that the nervous system was involved, i.e., paralysis of the wings and of the feet, and limberneck. Routine analyses ruled out the possibility that the poisoning was due to pesticides or an infective agent. Botulism intoxication was suspected and type C-botulism toxin was identified in the serum of moribund birds. This is the first record of a botulism outbreak in waterfowl in Israel. The total mortality was approximately 3000-4000 gulls, of which 1200 dead birds were collected and burnt. Investigations revealed that at a garbage dump situated in the vicinity of the lake, waste products of a chicken slaughter house were not buried as required by formal regulations. Examination of lake water, sediments, and vegetation for possible contamination by botulism toxin were negative. The implications of the outbreak on the environment are discussed.

The incidence of Campylobacter jejuni/coli was examined in five flocks of broilers monitored from hatch to slaughter, in feed and water and in litter samples. A total of 1440 samples from 720 broilers was examined. Campylobacter spp. were not isolated from broiler chicks at 1 day of age and were only isolated from one broiler chick in one flock at 1 week of age. In three flocks Campylobacter spp. were isolated from all chicks sampled at 4 weeks of age. In the fourth flock all chicks sampled were negative until 8 weeks of age when all were positive. The fifth flock remained negative throughout the 8 weeks of its life. Campylobacter spp. were not found in 20 samples of food and water. Of 20 litter samples they were found in only two. Eleven broiler flocks were examined only at slaughter. Twenty-four caecal samples were examined from each flock. In three flocks no Campylobacter spp. were isolated, in one flock one broiler chick was positive and in seven flocks from 58% to 100% of sampled broilers were positive. A total of 146 isolates was typed; 123 were C. jejuni and 23 C. coli, these belonged to 46 serotypes. In some flocks several serotypes were identified, some of them were not found again on further examinations of the same flocks during the growing period.