The prediction of Influenza A/H3N2 Vaccine Efficacy using samples obtained from Indonesian Hajj pilgrims in 2013

Abstrak Latar Belakang: Vaksinasi merupakan salah satu cara efektif dalam mengontrol dan mengurangi beban penyakit yang disebabkan oleh Influenza. Akan tetapi, efikasi vaksin bisa bervariasi jika strain yang digunakan untuk vaksin berbeda dengan strain yang bersirkulasi di dunia. Hal ini menunjukan pentingnya melakukan analisa prediksi efikasi vaksin. Pada studi ini, prediksi efikasi vaksin Influenza A/H3N2 dilakukan berdasarkan perhitungan antigenic distance strain vaksin WHO dengan virus influenza yang berasal dari jemaah Haj iIndonesia pada tahun 2013. Metode: Sekuensing gen HA dilakukan terhadap dua sampel tersimpan yang terkonfirmasi positif Influenza A/ H3N2 yang berasal dari jemaah Haji Indonesia tahun 2013. Pepitope Calculator digunakan untuk menghitung antigenic distance dari dua strain virus influenza dan dilanjutkan dengan perhitungan Pepitope value. Vaksin strain yang direkomendasikan oleh WHO; A/Texas/50/2012, A/Switzerland/9715293/2013, A/HongKong/4801/2014 dan dua virus yang diambil dari jemaah Haji Indonesia pada tahun 2013 dianalisa pada studi ini. Hasil: Prediksi efikasi vaksin yang direkomendasikan WHO tahun 2013 (A/Texas/50/2012) dengan sampel yang berasal dari jemaah Haji Indonesia tahun 2013 menunjukkan hasil lebih rendah dibandingkan dengan strain vaksin untuk musim flu pada tahun selanjutnya. Hasil ini sesuai dengan hasil analisis filogenetik dan perbandingan asam amino dimana sampel pada studi ini berkerabat lebih dekat dengan strain vaksin untuk musim flu selanjutnya dengan perbedaan asam amino yang lebih sedikit di bagian epitope protein HA dibandingkan dengan vaksin tahun 2013. Kesimpulan: Perhitungan efikasi vaksin menggunakan antigenic distance antara strain vaksin WHO dan virus yang menginfeksi jemaah haji Indonesia pada tahun 2013 menunjukkan hasil yang rendah. (Health Science Journal of Indonesia 2018;9(1):1-7) Keywords: Efikasi vaksin, Influenza A/H3N2, jemaah Haji, Indonesia Abstract Background: Influenza vaccination is an effective approach to control and reduce the disease burden of influenza viruses. However, the efficacy of influenza vaccine varies every year due to the different antigenic distance between vaccine and the circulating influenza strains globally and therefore necessitates the study of vaccine efficacy (VE). This study describes the prediction of Influenza A/H3N2 VE based on antigenic distances WHO vaccine strains and the virus obtained from Indonesian Hajj pilgrims in 2013. Methods: Coding between Sequence of HA gene of Influenza A/H3N2 virus was obtained from archival samples of Indonesian Hajj Pilgrims in 2013. Pepitope value calculation using Pepitope Calculator to measure the antigenic distance of HA sequences of two influenza strains was implemented. The HA sequences of WHO vaccine strains: A/ Texas/50/2012, A/Switzerland/9715293/2013, A/HongKong/4801/2014 and two influenza viruses from Indonesian Hajj pilgrims in 2013 were analyzed. Results: This study predicted that influenza vaccine strain recommended by WHO for 2013 (A/Texas/50/2012) have low efficacy to the influenza virus obtained from Indonesian Hajj Pilgrim in 2013 while showing higher efficacy to vaccine strain recommended for the following year. This result was in line with phylogenetic analysis and amino acid differences in which the samples in this study were grouped together with vaccine strain in following years and had less amino acid differences in epitope located in HA protein compared with 2013 vaccine strain. Conclusion: The prediction of VE using the antigenic distance measurement between WHO vaccine strain and Indonesian Hajj pilgrim collected in 2013, is considered low. (Health Science Journal of Indonesia 2018;9(1):1-7) Keywords: Vaccine efficacy, influenza A/H3N2 virus, Hajj pilgrim, Indonesi

Frequency of D222G and Q223R Hemagglutinin Mutants of Pandemic (H1N1) 2009 Influenza Virus in Japan between 2009 and 2010

BACKGROUND: In April 2009, a novel swine-derived influenza A virus (H1N1pdm) emerged and rapidly spread around the world, including Japan. It has been suggested that the virus can bind to both 2,3- and 2,6-linked sialic acid receptors in infected mammals, in contrast to contemporary seasonal H1N1 viruses, which have a predilection for 2,6-linked sialic acid. METHODS/RESULTS: To elucidate the existence and transmissibility of α2,3 sialic acid-specific viruses in H1N1pdm, amino acid substitutions within viral hemagglutinin molecules were investigated, especially D187E, D222G, and Q223R, which are related to a shift from human to avian receptor specificity. Samples from individuals infected during the first and second waves of the outbreak in Japan were examined using a high-throughput sequencing approach. In May 2009, three specimens from mild cases showed D222G and/or Q223R substitutions in a minor subpopulation of viruses infecting these individuals. However, the substitutions almost disappeared in the samples from five mild cases in December 2010. The D187E substitution was not widespread in specimens, even in May 2009. CONCLUSIONS: These results suggest that α2,3 sialic acid-specific viruses, including G222 and R223, existed in humans as a minor population in the early phase of the pandemic, and that D222 and Q223 became more dominant through human-to-human transmission during the first and second waves of the epidemic. These results are consistent with the low substitution rates identified in seasonal H1N1 viruses in 2008

Proportion of influenza cases in severe acute respiratory illness in Indonesia during 2008-2009

Aim: To access the proportion of Influenza which caused SARI casesMethods: From April 2008 until March 2009, 549 samples of nasal and throat swabs were collected from SARI patients from eight hospitals in eight provinces in Indonesia. The samples were analyzed for Influenza by real-time RT-PCR method using several specific primers for influenza A (A/H1N1, A/H3N2 and A/H5N1) and Influenza B. The sequence of these primers was provided by CDC, Atlanta.Results: We found 516 (94%) of the specimens testing results were not infl uenza A or B viruses. There was 21 (4%) cases caused by influenza A and 12 (2%) caused by influenza B. From the influenza A cases, one case of SARI was caused by A/H1N1, two cases were A/H5N1, 17 cases were A/H3N2 and one case was unsubtypeable Influenza A.Conclusion: The majority of SARI cases were not caused by influenza viruses. From this surveillance the most common influenza  A related to SARI is A/H3N2. Facts of the avian influenza virus A/H5N1 cases have been found in Indonesia and the spread of novel virus influenza A/H1N1 in 2009 raised our concern about the importance of SARI surveillance. (Med J Indones 2010; 19:264-7)Keywords: influenza, severe acute respiratory illness</p

STUDI PEMETAAN AWAL DNA Mycobacterium tuberculosis COMPLEX SECARA Spoligotyping PADA HASIL ISOLASI DAHAK PASIEN TUBERKULOSIS PARU DARI 10 IBU KOTA PROPINSI (BAGIAN I)

Abstract. Mapping TB genotype of Mycobacterium tuberculosis (Mtb) is an important study to identify their distribution or characteristic and also may lead to improve control of the disease. This study conducted a preliminary mapping of the tubercle bacilli which had been circulating in Indonesia. Cultures of DNA isolated from TB patients at urban areas in 16 provinces in Indonesia, are chosen based on TB Case Detection Rate (CDR) 2006 from Indonesia Directorate General of Communicable Disease Control and Environment Health (Ministry of Health), were analyzed by spoligotyping for strain differentiation. In this first part, the analyzed result only came from urban areas in 10 provinces, i.e. Palembang, Bandar Lampung, Serang, Jakarta, Bandung, Surabaya, Banjarmasin, Makassar, Pontianak and Ambon. Sample were 269 DNA from 294 isolates collected from sputum of suspect TB patients with sputum-smear positive (SS+) and age above 15 years old. All samples were obtained from peripheral health laboratory in each province. The procedure collection is accordance to Indonesia DOTs guidelines (AFB smears) and samples were transported from those 10 areas to Bacteriology Laboratory at CBPRD. Sputum was taken for culture in liquid media MGIT Bactec 960 and solid media Lowenstein Jensen. The DNAs from positive liquid media MGIT Bactec 960 were isolated and analyzed by spoligotyping to identify the spoligo pattern. The spoligotyping results converted into octal format within Words &amp; Excel spreadsheets and compared to International Spoligotype-database (SpolDB4). The previous study (Parwati et.al.) found some differences geographical distribution between Beijing genotype strain of tubercle bacilli in West Indonesia compare to East Indonesia, and the same pattern was also found in this study. Furthermore, the results in this study showed the differences in spoligo pattern of Mtb complex at 10 urban areas in West, Middle and East Indonesia. The percentage of Beijing strain family in the samples from West Indonesia showed around 26.61% (31.48% in Sumatra, 28.83% in Java and 16.98% in Kalimantan); from the Middle Indonesia around 25.93%; and none were found in samples from the East Indonesia. The SpolDB4 pattern also showed that the majority of isolates belonged to major clades of M.tuberculosis, i.e. the East African-Indian (EAI); Haarlem (H), Latin American-Mediterranean (LAM), the Central and Middle Eastern Asian (CAS); U = undefined; T = T family; and the MANU/ Manu family. We also found some isolates of Mycobacterium bovis. There were no significant association showed between genotype families and gender, but strong significant association found with ethnics and geography. Further confirmation of the results is still ongoing (k value; RFLP and MIRU-VNTR). As conclusion, this study constituted a first attempt to describe the preliminary mapping of genetic population structure of the tubercle bacilli circulating in Indonesia.   Key words: preliminary mapping, Mtb complex, spoligotyping, Beijing genotype strain, SpolDB

Studi Pemetaan Awal Dna Mycobacterium Tuberculosis Complex Secara Spoligotyping Pada Hasil Isolasi Dahak Pasien Tuberkulosis Paru Dari 10 Ibu Kota Propinsi (Bagian I)

. Mapping TB genotype of Mycobacterium tuberculosis (Mtb) is an important study to identify their distribution or characteristic and also may lead to improve control of the disease. This study conducted a preliminary mapping of the tubercle bacilli which had been circulating in Indonesia. Cultures of DNA isolated from TB patients at urban areas in 16 provinces in Indonesia, are chosen based on TB Case Detection Rate (CDR) 2006 from Indonesia Directorate General of Communicable Disease Control and Environment Health (Ministry of Health), were analyzed by spoligotyping for strain differentiation. In this first part, the analyzed result only came from urban areas in 10 provinces, i.e. Palembang, Bandar Lampung, Serang, Jakarta, Bandung, Surabaya, Banjarmasin, Makassar, Pontianak and Ambon. Sample were 269 DNA from 294 isolates collected from sputum of suspect TB patients with sputum-smear positive (SS+) and age above 15 years old. All samples were obtained from peripheral health laboratory in each province. The procedure collection is accordance to Indonesia DOTs guidelines (AFB smears) and samples were transported from those 10 areas to Bacteriology Laboratory at CBPRD. Sputum was taken for culture in liquid media MGIT Bactec 960 and solid media Lowenstein Jensen. The DNAs from positive liquid media MGIT Bactec 960 were isolated and analyzed by spoligotyping to identify the spoligo pattern. The spoligotyping results converted into octal format within Words &amp; Excel spreadsheets and compared to International Spoligotype-database (SpolDB4). The previous study (Parwati et.al.) found some differences geographical distribution between Beijing genotype strain of tubercle bacilli in West Indonesia compare to East Indonesia, and the same pattern was also found in this study. Furthermore, the results in this study showed the differences in spoligo pattern of Mtb complex at 10 urban areas in West, Middle and East Indonesia. The percentage of Beijing strain family in the samples from West Indonesia showed around 26.61% (31.48% in Sumatra, 28.83% in Java and 16.98% in Kalimantan); from the Middle Indonesia around 25.93%; and none were found in samples from the East Indonesia. The SpolDB4 pattern also showed that the majority of isolates belonged to major clades of M.tuberculosis, i.e. the East African-Indian (EAI); Haarlem (H), Latin American-Mediterranean (LAM), the Central and Middle Eastern Asian (CAS); U = undefined; T = T family; and the MANU/ Manu family. We also found some isolates of Mycobacterium bovis. There were no significant association showed between genotype families and gender, but strong significant association found with ethnics and geography. Further confirmation of the results is still ongoing (k value; RFLP and MIRU-VNTR). As conclusion, this study constituted a first attempt to describe the preliminary mapping of genetic population structure of the tubercle bacilli circulating in Indonesia

Hemagglutination assay using chicken, guinea pig, and horse erythrocytes with or without α2,3 sialidase treatment.

<p>Hemagglutination assay using chicken, guinea pig, and horse erythrocytes with or without α2,3 sialidase treatment.</p

Alignment of the amino acid sequences including D187E, D222G, and Q223R mutants within the receptor binding site of H1N1pdm hemagglutinin.

<p>E187, G222, and R223 variants obtained from three clinical specimens (#1, #2, and #3) from the first wave of the outbreak. Three clinical nasal swabs were each subjected to RNA extraction, RT-PCR, and TA cloning. More than one hundred clones per specimen were sequenced using conventional Sanger technology. Positions 187, 222, and 223 are shown in bold and are underlined.</p

Frequency distribution of N119, D125, E187, G222, and R223 variants within the HA receptor binding site of viruses obtained from clinical specimens infected with influenza A viruses.

<p>Frequency distribution of N119, D125, E187, G222, and R223 variants within the HA receptor binding site of viruses obtained from clinical specimens infected with influenza A viruses.</p