Background Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries. Methods The study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions. Results Ninety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. Conclusions Our study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes.

HighlightsMCL symptoms and signs may occur with various clinical features, from asymptomatic abdominal mass to acute abdomen.MCL should be considered as one of the differential diagnoses in acute abdomen and intraabdominal tumor cases in children.MCL has potential to grow and invade vital organs, therefore, resection/marsupialization is preferable for its management.

Background Since the COVID-19 pandemic was declared by the World Health Organization on March 11, 2020, routine clinical practices were affected, including pediatric surgery services. We aimed to compare pediatric surgery practices, including the number and types of surgery, either elective or emergency surgeries and outpatient services, before the outbreak and during the COVID-19 pandemic in our institution. Material and methods We retrospectively compared pediatric surgery practices, including elective and emergency surgeries, and outpatient services between the previous one-year period (March 2019–February 2020), the last three months of that period (December 2019–February 2020) before the outbreak, and the three months (March–May 2020) during the COVID-19 pandemic in our hospital. Results The frequency of elective surgeries during the pandemic was lower than during the last three months before the outbreak: 61 vs. 18 (~3-fold), 19 vs. 13 (~1.5-fold), 19 vs. 5 (~4-fold), and 30 vs. 15 (~2-fold) for digestive, neonate, urology and oncology cases, respectively. No laparoscopic procedures were performed during the pandemic compared with the one-year period before the outbreak (0 vs. 16 cases). The frequency of all emergency pediatric procedures before and during the COVID-19 pandemic was similar (29 vs. 20 cases, respectively). Moreover, a declining trend was also clearly apparent in the outpatient services during the pandemic compared with before the outbreak, both in the new and the established patients. Conclusions The pediatric surgery practices in our institution have been severely affected by the COVID-19 pandemic, including elective and outpatient services. This setback needs a comprehensive strategy to avoid morbidity from the neglected elective surgeries during the pandemic, including the proper comparison between the real risk of COVID-19 cross-infection and the benefits of elective procedures.

Background: Without early recognition and Kasai procedure, biliary atresia (BA) results in liver cirrhosis and leads to either transplantation or death at a young age. We aimed to characterize the liver histopathological findings for prediction of cirrhosis and survival in BA patients after Kasai surgery. Methods: We retrospectively reviewed all histopathological results for BA patients who underwent liver biopsy during Kasai surgery from August 2012 to December 2018 in Dr. Sardjito Hospital, Yogyakarta, Indonesia. Results: Fifty infants with BA were ascertained in our study, of whom 27 were males and 23 were females. The median age of Kasai procedure was 102.5 days (interquartile range (IQR), 75.75-142.25 days). There were 33 (66%) and 17 (34%) BA patients with and without liver cirrhosis, respectively, while the overall survival was 52%. The patients with a severe bile duct proliferation, severe cholestasis, and severe portal inflammation have a higher risk by 27-, 22-, and 19.3-fold, respectively, to develop liver cirrhosis compared with patients with a moderate/mild bile duct proliferation, moderate/mild/without cholestasis, and moderate/mild portal inflammation, respectively (p = 3.6 × 10 − 6 , 5.6 × 10 − 4 , and 1.6 × 10 − 3 , respectively), while the giant cell transformation was not associate with the development of liver cirrhosis (p = 0.77). The bile duct proliferation was strongly correlated with cholestasis and portal inflammation (p = 7.3 × 10 − 5 and 2 × 10 − 4 , respectively), and cholestasis was also significantly correlated with portal inflammation (p = 0.016). Interestingly, the age at Kasai procedure was strongly associated with the development of liver cirrhosis (p = 0.02), but not with the patients' survival (p = 0.33), while the degree of fibrosis and cholestasis were significantly correlated with the patients' survival, with HR of 3.9 (95% CI = 1.7-9.0; p = 0.017) and 3.1 (95% CI = 1.4-7.0; p = 0.016), respectively. Conclusions: Histopathological findings of bile duct proliferation, cholestasis, and portal inflammation can predict the liver cirrhosis development in patients with BA. Furthermore, degree of fibrosis and cholestasis affect the patients' survival following the Kasai operation.

BackgroundHirschsprung disease (HSCR) is a heterogeneous genetic disorder characterized by absence of ganglion cells along the intestines resulting in functional bowel obstruction. Mutations in neuregulin 1 (NRG1) gene have been implicated in some cases of intestinal aganglionosis. This study aims to investigate the contribution of the NRG1 gene to HSCR development in an Indonesian population.MethodsWe analyzed the entire coding region of the NRG1 gene in 54 histopathologically diagnosed HSCR patients.ResultsAll patients were sporadic non-syndromic HSCR with 53/54 (98%) short-segment and 1/54 (2%) long-segment patients. NRG1 gene analysis identified one rare variant, c.397G > C (p.V133 L), and three common variants, rs7834206, rs3735774, and rs75155858. The p.V133 L variant was predicted to reside within a region of high mammalian conservation, overlapping with the promoter and enhancer histone marks of relevant tissues such as digestive and smooth muscle tissues and potentially altering the AP-4_2, BDP1_disc3, Egr-1_known1, Egr-1_known4, HEN1_2 transcription factor binding motifs. This p.V133 L variant was absent in 92 non-HSCR controls. Furthermore, the rs7834206 polymorphism was associated with HSCR by case–control analysis (p = 0.037).ConclusionsThis study is the first report of a NRG1 rare variant associated with HSCR patients of South-East Asian ancestry and provides further insights into the contribution of NRG1 in the molecular genetic pathogenesis of HSCR.Electronic supplementary materialThe online version of this article (10.1186/s12887-018-1265-x) contains supplementary material, which is available to authorized users.