Helicobacter pylori virulence genes in the five largest islands of Indonesia

BACKGROUND: It remains unclear whether the low incidence of gastric cancer in Indonesia is due to low infection rates only or is also related to low Helicobacter pylori pathogenicity. We collected H. pylori strains from the five largest islands in Indonesia and evaluated genetic virulence factors. METHODS: The genotypes of H. pylori virulence factors were determined by polymerase chain reaction (PCR)-based sequencing. Histological severity of the gastric mucosa was classified into 4 grades, according to the updated Sydney system. RESULTS: A total of 44 strains were analyzed. Forty-three (97.7 %) were cagA-positive: 26 (60.5 %) were East-Asian-type-cagA, 9 (20.9 %) were Western-type-cagA, and 8 (18.6 %) were novel ABB-type, most of which were obtained from Papuan. EPIYT sequences were more prevalent than EPIYA sequences (P = 0.01) in the EPIYA-B motif of all types of cagA. The majority of cagA-positive strains (48.8 %, 21/43) had a 6-bp deletion in the first pre-EPIYA region. Subjects infected with East-Asian-type-cagA strains with a 6-bp deletion had significantly lower inflammation and atrophy scores in the corpus than those infected with Western-type-cagA strains (both P = 0.02). In total, 70.4 % of strains possessed the vacA s1m1 genotype and 29.5 % were m2. All strains from peptic ulcer patients were of the iceA1 genotype, which occurred at a significantly higher proportion in peptic ulcer patients than that in gastritis patients (55.3 %, P = 0.04). The double positive genotype of jhp0562/β-(1,3)galT was predominant (28/44, 63.6 %), and subjects infected with this type had significantly higher inflammation scores in the corpus than those with the jhp0562 negative/β-(1,3)galT positive genotype (mean [median]; 1.43 [1] vs. 0.83 [1], P = 0.04). There were significant differences in cagA and pre-EPIYA cagA type, oipA status, and jhp0562/β-(1,3)galT type among different ethnic groups (P < 0.05). CONCLUSIONS: In addition to a low H. pylori infection rate, the low incidence of gastric cancer in Indonesia might be attributed to less virulent genotypes in predominant strains, which are characterized by the East-Asian-type-cagA with a 6-bp deletion and EPIYT motif, a high proportion of m2, dupA negative or short type dupA, and the jhp0562/β-(1,3)galT double positive genotype

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Are Intentions or Actions More Important? Well, It's Not That Simple

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North Sumatran Malay Folktales: Its Structure, Social Function and Meaning

This study is a descriptive-qualitative analysis that uses the techniques of observation, interviews and written documents. The Systemic Functional Linguistic (SFL) approach based on the principle of semiotics is used in this study. The data analysis consists of folktales found in North Sumatra, that is, “Batu Belah Batu Betangkup”, “Putri Kuau” and “Sri Putih Cermin”. By using the SFL approach this study describes the structure, social function, and meaning of North Sumatran Malay folktales. From the analysis it is found that the structure, function and meaning of all the three NSM folktales are similar. The material and verbal processes found in the texts of the folktales depict life in the palace and the everyday life of North Sumatran Malay society in the past as well as in the present. North Sumatran Malay texts are the representation of culture and meaning in which the value of of North Sumatran Malay society are inherent. Keywords: folklore, “Batu Belah Batu Betangkup”, “Putri Kuau”, “Sri Putih Cermin”, systemic functional linguistics, North Sumatran Malay values Abstrak Kajian ini merupakan penelitian deskriptif-kualitatif yang menggunakan teknik pengamatan, wawancara dan kepustakaan. Pendekatan Linguistik Sistemik Fungsional (LSF) yang berdasarkan prinsip semiotik digunakan dalam kajian ini. Data kajian terdiri daripada cerita rakyat yang terdapat di Sumatera Utara, iaitu “Batu Belah Batu Betangkup” , “Putri Kuau” dan “Sri Putih Cermin” . Dengan menggunakan LSF kajian akan mengungkapkan struktur, fungsi sosial, dan makna cerita rakyat Melayu Sumatera Utara (MSU). Daripada analisis didapati struktur, ketiga-tiga cerita rakyat MSU ini memiliki struktur, fungsi, dan makna yang mirip. Proses material dan verbalnya yang terdapat dalam teks cerita rakyat menunjukkan cerminan kehidupan istana dan sehari-hari masyarakat Melayu Sumatera Utara baik yang terjadi pada zaman dahulu maupun masa kini. Teks Melayu Sumatera Utara mewakili budaya dan makna sebagai nilai yang dijunjung dan dijiwai oleh masyarakatnya. Keywords: cerita rakyat, “Batu Belah Batu Betangkup” , “Putri Kuau” , “Sri Putih Cermin” , linguistik fungsional sistemik, nilai Melayu Sumatera Utara</jats:p

Waris Pengganti dalam Peraturan Keluarga Indonesia

Tulisan ini bertujuan untuk mengetahui aturan ahli waris pengganti dalam peraturan keluarga di Indonesia dan relevansinya dalam menyelesaikan masalah kontemporer. Menggunakan metode studi pustaka dengan melakukan pendekatan kualitatif. Secara tersurat tidak ditemukan kata ahli waris pengganti dalam Al-Qur’an dan Hadits. Sedangkan di Indonesia dikenal istilah ini karena sudah dicantumkan pada pasal 185 Kompilasi Hukum Islam. Salah satu pendapat yang dikeluarkan oleh M. Yahya Harahap menyatakan bahwa cucu dapat menggantikan posisi orang tuanya yang lebih dahulu meninggal dari kakek untuk mendapatkan harta warisan. Hazairin berpendapat bahwa Allah mengadakan mawali untuk seseorang dari harta peninggalan orangtua dan keluarga dekat. Jika yang menjadi pewaris orangtua, maka ahli waris atau mawali adalah anaknya. Dalam hal ini ahli waris pengganti merupakan tindakan alternatif yang memberikan mashlahat dalam pembagian harta warisan</jats:p