Il-Hwan Kim

WODEM: wormhole attack defense mechanism in wireless sensor networks

The wormhole attack, which is accomplished by selectively relaying packets between two adversaries, can ruin routing and communication of the network without compromising any legitimate nodes. There have been a few countermeasures against the wormhole attack in generic ad hoc networks, but they are not appropriate for sensor networks since they require special devices (e.g. directional antenna) or put much overhead on each node. In this paper, we propose a new countermeasure against the wormhole attack for sensor networks, named WODEM. In WODEM, a few detector nodes equipped with location-aware devices and longer-lasting batteries detect wormholes, and normal sensor nodes are only required to forward control packets from the detector nodes. Therefore, WODEM is efficient in cost and energy. From the simulation results, we show that 10 detector nodes can detect a wormhole within the accuracy of 90% in a densely deployed sensor network.

Genetic diversity of spike, 3a, 3b and e genes of infectious bronchitis viruses and emergence of new recombinants in Korea.

The nucleotide sequences of a region including S1, S2, 3a, 3b and E genes of twenty-seven infectious bronchitis virus (IBV) isolates in Korea between 1990–2011 were determined and phylogenetic and computational recombination analyses were conducted. The sizes of coding regions of some genes varied among IBV isolates due to deletion or insertion of nucleotides; the nucleotide similarities of S1, S2, 3a, 3b and E genes among the 27 isolates were 75.9%–100.0%, 85%–100.0%, 64.0%–100.0%, 60.4%–100.0% and 83.1%–100.0%, respectively. According to phylogenetic analysis of S1 gene, the 27 isolates were divided into five genotypes, Mass, Korean-I (K-I), QX-like, KM91-like and New cluster 1. The phylogenetic trees based on the S2, 3a, 3b, E genes and S1-S2-3a-3b-E (S1-E) region nucleotide sequences did not closely follow the clustering based on the S1 sequence. The New cluster 1 prevalent during 2009 and 2010 was not found in 2011 but QX-like viruses became prevalent in 2011. The recombination analysis revealed two new S gene recombinants, 11036 and 11052 which might have been derived from recombinations between the New cluster 1 and QX-like viruses and between the K-I and H120 (vaccine) viruses, respectively. In conclusion, multiple IBV genotypes have co-circulated; QX-like viruses have recurred and new recombinants have emerged in Korea. This has enriched molecular epidemiology information of IBV and is useful for the control of IB in Korea.

Comparative Genomics of Korean Infectious Bronchitis Viruses (IBVs) and an Animal Model to Evaluate Pathogenicity of IBVs to the Reproductive Organs

The K-I and nephropathogenic K-II genotypes of infectious bronchitis virus (IBV) have been isolated since 1995 and 1990, respectively, in Korea and commercial inactivated oil-emulsion vaccines containing KM91 (K-II type) and Massachusetts 41 strains have been used in the field. To date, genomic analyses of Korean IBV strains and animal models to test the pathogenicity of Korean IBVs to the reproductive organs have been rare. In the present study, comparative genomics of SNU8067 (K-I type) and KM91 IBVs was performed, and an animal model to test the pathogenicity of SNU8067 was established and applied to vaccine efficacy test. The genome sizes of SNU8067 (27,708 nt) and KM91 (27,626 nt) were slightly different and the nucleotide and amino acid identities of the S1 (79%, 77%), 3a (65%, 52%), and 3b (81%, 72%) genes were lower than those of other genes (94%–97%, 92%–98%). A recombination analysis revealed that SNU8067 was a recombinant virus with a KM91-like backbone except S1, 3a, and 3b genes which might be from an unknown virus. An SNU8067 infection inhibited formation of hierarchal ovarian follicles (80%) and oviduct maturation (50%) in the control group, whereas 70% of vaccinated chickens were protected from lesions.

Multiplex nested RT-PCR for detecting avian influenza virus, infectious bronchitis virus and Newcastle disease virus

In this study, multiplex nested RT-PCR (mnRT-PCR) was applied to simultaneous detect multiplex PCR with the higher sensitivity of nested PCR that is required for avian influenza, infectious bronchitis and Newcastle disease virus using two steps of amplification. For the first PCR, primers that were specific for each virus were newly designed from the nucleoprotein gene of AIV, the nucleocapsid protein gene of IBV and the fusion protein gene of NDV to amplify products of 665, 386 and 236 nucleotides, respectively. The multiplex PCR step provides mass amplification using common primers, which increased markedly the sensitivity of the test. Non-specific reactions were not observed when other viruses and bacteria were used for evaluating the mnRT-PCR. As a field application, 172 samples were tested by RT-PCR and mnRT-PCR. Among these samples, the concordance rates for mnRT-PCR and the single conventional RT-PCR showed 98.9% (kappa=0.98) and 98.8% (kappa=0.96) similarity for IBV and AIV, respectively. As a result, it is recommended the multiplex nested PCR as an effective tool for detecting and studying the molecular epidemiology of various mixed infections of one or more of these viruses in poultry.

Effects of different NS genes of avian influenza viruses and amino acid changes on pathogenicity of recombinant A/Puerto Rico/8/34 viruses.

To examine the effects of the NS1 and NEP genes of avian influenza viruses (AIVs) on pathogenicity in mice, we generated recombinant PR8 viruses containing 3 different NS genes of AIVs. In contrast to the reverse genetics-generated PR8 (rPR8) strain and other recombinant viruses, the recombinant virus rPR8-NS(0028), which contained the NS gene of A/chicken/KBNP-0028/2000 (H9N2) (0028), was non-pathogenic to mice. The novel single mutations of 0028 NS1 to corresponding amino acid of PR8 NS1, G139D and S151T increased the pathogenicity of rPR8-NS(0028). The replacement of the PL motifs (EPEV or RSEV) of pathogenic recombinant viruses with that of 0028 (GSEV) did not reduce the pathogenicity of the viruses. However, a recombinant virus with an EPEV-grafted 0028 NS gene was more pathogenic than rPR8-NS(0028) but less than rPR8. The lower pathogenicity of rPR8-NS(0028) might be associated with the lower virus titer and IFN-β level in the lungs of infected mice, and be attributed to G139, S151 and GSEV-PL motif of NS1 gene of 0028. In conclusion we defined new amino acid residues of NS1 related to mice pathogenicity and the presence of pathogenic NS genes among low pathogenic AIVs may encourage continuous monitoring of their mammalian pathogenicity.

Effects of different polymerases of avian influenza viruses on the growth and pathogenicity of A/Puerto Rico/8/1934 (H1N1)-derived reassorted viruses.

We generated reassorted PR8 viruses containing six different combinations of avian influenza virus (AIV) polymerase genes from A/chicken/Korea/01310/2001 (H9N2) (01310) and A/chicken/Korea/KBNP-0028/2000 (H9N2) (0028) to examine the effects of the AIV polymerase genes PB1, PB2, and PA on replication efficiency in different host cells and pathogenicity in mice. The virus titers of the reassorted viruses possessing 01310 [rPR8-PB2(01310)] and 0028 [rPR8-PB2(0028)] PB2 genes were significantly higher than those of the others except the rPR8 virus in embryonated chicken eggs at 37°C, and those of avian polymerase reassorted viruses were significantly less than rPR8 in MDCK cells at 32 and 37°C. rPR8-PB2(01310), rPR8-PB2(0028), and rPR8-PA(0028) caused no body weight loss in BALB/c mice but rPR8-PA(01310), rPR8-PB1(01310), and rPR8-PB1(0028) caused mortality and significantly different body weight loss compared to those in the mock treatment. In contrast to rPR8-PB2(0028) and rPR8-PA(0028), rPR8-PB2(01310) was not isolated from infected mice, and rPR8-PB1(0028) was less pathogenic than rPR8-PB1(01310). We determined the amino acid residues that were specific to the less pathogenic polymerases. A comparison with those of pandemic 2009 H1N1, human fatal H5N1 and H7N9, and pathogenic AIVs to mice without adaptation revealed that they possessed the mammalian pathogenic constellation of polymerases. Thus, the novel polymerase genes and amino acid residues may be useful to understand the host-barrier overcome of AIVs in mice and to develop safer and efficacious vaccines.

H9N2 Avian Influenza Virus-Induced Conjunctivitis Model for Vaccine Efficacy Testing

SUMMARY. Clinical signs such as respiratory signs, egg drop, and mortality have been reported in field cases of low pathogenic avian influenza by H9N2 avian influenza virus (AIV) but have rarely been reproduced by the virus alone. Thus, virus reisolation rates and titers in tissues were measured for vaccine efficacy testing. In the present study, we established a clinical sign-based vaccine efficacy test by reproduction of highly frequent conjunctivitis (77.8%–90%) via binocular instillation of an H9N2 virus (01310 strain, 1 × 106 EID50/10 µl for each eye). Specific-pathogen-free chickens were assigned to vaccine and control groups, and the vaccine group was inoculated intramuscularly with a commercial H9N2 inactivated oil emulsion vaccine. The chickens were challenged by 01310 via binocular instillation at 2 and 4 wk postvaccination (WPV). The positive rates of conjunctivitis and virus reisolation were significantly different between the vaccine and control groups (conjunctivitis at 2 WPV, 0% vs. 77.8%, and at 4 WPV, 0% vs. 80%). Vaccine antibody was detected in tears as well as in serum samples of the vaccine group before challenge. The conjunctivitis model may be useful for efficacy testing of AI vaccine due to a clinical symptom-based read of results, but further efficacy testings with different types, doses of AI vaccines, and challenge viruses will be required to complete the evaluation of our model. RESUMEN. Modelo de conjuntivitis inducida por el virus de la influenza aviar H9N2 para la evaluación de la eficacia de vacunas. Los signos clínicos tales como signos respiratorios, caída de la producción de huevo y mortalidad han sido reportados en casos de campo del virus de la influenza aviar de baja patogenicidad H9N2, pero rara vez se han reproducido estos signos con la inoculación única de este virus. Por lo tanto, se midieron los porcentajes de aislamiento del virus y los títulos en los tejidos para evaluar la eficacia de la vacuna. En el presente estudio, se ha establecido una evaluación basada en los signos clínicos para evaluar la eficacia de las vacunas mediante la reproducción de la conjuntivitis que es frecuente (77.8%–90%) mediante la instilación en los dos ojos de un virus H9N2 (cepa 01310, con un título de 1 × 106 dosis infectantes 50% en embrión de pollo por 10 µl, inoculadas en cada ojo). Aves libres de patógenos específicos se asignaron a los grupos vacunados y controles, las aves del grupo vacunado fueron inoculadas por vía intramuscular con una vacuna inactivada comercial emulsionada en aceite con el subtipo H9N2. Los pollos fueron desafiados por instilación en los dos ojos con la cepa 01310 a las dos y cuatro semanas después de la vacunación. Los porcentajes de aves con conjuntivitis y de aislamiento del virus fueron significativamente diferentes entre los grupos de aves vacunadas y controles (presencia de conjuntivitis a las dos semanas después de la vacunación fue de cero por ciento contra 77.8%, respectivamente y a las cuatro semanas después de la inoculación fue de cero por ciento contra 80%, respectivamente). Se detectaron anticuerpos contra la vacuna en las lágrimas, así como en las muestras de suero del grupo vacunado antes del desafío. Este modelo utilizando el desarrollo de la conjuntivitis puede ser útil para las evaluación de la eficacia de las vacunas de influenza aviar debido a la detección de los signos clínicos, pero se requiere llevar a cabo pruebas de eficacia adicionales con diferentes tipos y dosis de vacunas contra la influenza aviar y con virus de desafío distintos para completar la evaluación de este modelo.

Characterization of mutations associated with the adaptation of a low-pathogenic H5N1 avian influenza virus to chicken embryos.

Migratory waterfowls are the most common reservoir for avian influenza virus (AIV), thus viral adaptation is required for efficient replication in land fowls. To date, low pathogenic (LP) H5 subtype AIVs have been isolated from migratory waterfowls, and the adaptation of these viruses to land fowls might lead to the generation of highly pathogenic AIVs. Thus, A/wild duck/Korea/50-5/2009 (H5N1) LPAIV was passaged 20 times through embryonated chicken eggs (ECEs), and the resulting genetic and phenotypic changes were investigated. The pathogenicities of the early (50-5-E2) and final passage (50-5-E20) strains to chicken embryos were similarly high, but the 50-5-E20 titer was 100 times higher than that of 50-5-E2. 50-5-E20 showed 8 amino acid changes in PA (1), HA (4), NA (1), M1 (1) and M2 (1), with different frequencies among influenza A viruses (0-99.6%). The relevance of these changes, except H103Y in HA, to viral replication remains unknown. To investigate the roles of internal genes and mutations in HA and NA in viral replication, four recombinant viruses possessing combinations of HA and NA genes of 50-5-E2 and 50-5-E20 with 6 internal genes of PR8 were generated through reverse genetics. The embryo pathogenicities of the H5N1 recombinant viruses carrying internal PR8 genes were reduced, and the titers of the recombinant viruses with 50-5-E20 HA were higher than those with 50-5-E2 HA. Therefore, the identified mutations might be useful as chicken adaptation markers for the generation of high growth H5N1 recombinant viruses in ECEs.

Analysis of buffer replacement policies for WWW proxy

The advent of the Web service brought out the explosive growth of Internet, which necessitates a scheme to reduce the network traffic. Caching is a popular method in reducing such traffic, and it is widely used in many Web servers, clients, and proxy servers. Since an object of Web service is accessed as a whole, the caching scheme for such object must be different from others that usually treat a piece of an object as a unit of caching. In this paper, we propose caching schemes for variable size objects. Performance of the proposed schemes are explored through trace-driven simulation studies.

Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene

The polymerase of avian influenza A virus (AIV) is a heterotrimer composed of PB2, PB1, and PA. PB2 plays a role in overcoming the host barrier; however, the genetic prerequisites for avian PB2 to acquire mammalian pathogenic mutations have not been well elucidated. Previously, we identified a prototypic avian PB2 that conferred non-replicative and non-pathogenic traits to a PR8-derived recombinant virus when it was used to infect mice. Here, we demonstrated that key amino acid mutations (I66M, I109V, and I133V, collectively referred to as MVV) of this prototypic avian PB2 increase the replication efficiency of recombinant PR8 virus carrying the mutated PB2 in both avian and mammalian hosts. The MVV mutations caused no weight loss in mice, but they did allow replication in infected lungs, and the viruses acquired fatal mammalian pathogenic mutations such as Q591R/K, E627K, or D701N in the infected lungs. The MVV mutations are located at the interfaces of the trimer and are predicted to increase the strength of this structure. Thus, gaining MVV mutations might be the first step for AIV to acquire mammalian pathogenicity. These results provide new insights into the evolution of AIV in birds and mammals.