Characteristics of children with confirmed SARS-CoV-2 infection in Indonesia

SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia

Objective

The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tract microbiota might adversely affect the clinical condition of patients.

Methods

We utilized the Oxford Nanopore sequencing platform to analyze genetic variation of 43 samples of SARS-CoV-2 and 11 selected samples for 16S rRNA gene sequencing, using samples collected from May to August 2021.

Results

The prevalence of AY.23 (>82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Pseudomonas aeruginosa and Haemophilus parainfluenzae.

Conclusions

The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient.

Perioperative Management for Emergency Surgery in Pediatric Patients with COVID-19: Retrospective Observational Study

Background

The first wave of COVID-19 in 2020 created massive challenges in providing safe surgery for pediatric patients with COVID-19. Inevitably, emergency surgery and the unknown nature of the disease place a burden on the heavily challenged surgical services for pediatrics in a developing country. Lessons from the pandemic are important for future disaster planning.

Aim

To describe the characteristics of pediatric surgical patients with COVID-19 undergoing emergency surgery during the first wave and its perioperative narrative in a developing country.

Methods

The study was a multicenter retrospective descriptive study in eight Indonesian government-owned referral and teaching hospitals. The authors reviewed confirmed COVID-19 pediatric patients (≤18 years old) who underwent surgery. Institutional review board clearances were acquired, and data were evaluated in proportion and percentages. The writing of this paper follows the STROBE guidelines.

Results

About 7791 pediatric surgical cases were collected, 73 matched the study criteria and 24 confirmed cases were found. Cases were more common in females (58.3%), who were above 12 years old (37.5%) and who were asymptomatic (62.5%). Laparotomy (33.3%), general anesthesia (90.4%) and intubation (80.8%) were common, while use of video laryngoscopy (40%) and rapid sequence intubation (28.8%) were rare. The mean length of stay was 12 ±13.3 days, and in-hospital mortality was 8.3%.

Discussions

Lockdown and school closure were successful in protecting children, hence the low incidence of pediatric surgical cases with COVID-19 during the first wave. Many hospitals were unprepared to perform surgery for a droplet or airborne infectious disease, and COVID-19 testing was not available nationally in the early pandemic, hence the use of protective protection equipment  during these early pandemic times are often not efficient.

Conclusion

The incidence of COVID-19 in pediatric surgical patients is low. The rapidity and availability of preoperative testing for a new emerging disease are essential in a pandemic.

The Impact of Alpha Variant (B.1.1.7), Viral Load, and Age on the Clinical Course of Pediatric COVID-19 Patients

Objective The research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mainly consists of adult patients, leaving its impact on children understudied. This study aims to investigate the correlations between viral load, clinical course, age, and Alpha variant (B.1.1.7) in children.

Methods The study was conducted on children under the age of 18 years, who were admitted to Amasya University Sabuncuoglu Serefeddin Research and Training Hospital in Turkey between February and April 2021. ΔCt values, which were obtained by real-time polymerase chain reaction (PCR), were analyzed to estimate the viral loads of the patients. Alpha variant (B.1.1.7) positivity was determined by real-time PCR.

Results There was no difference between estimated viral loads of different clinical courses (p > 0.05), or between asymptomatic and symptomatic patients (p > 0.05). Viral loads were found to decrease with increasing age (p = 0.002). Also, a higher rate of symptomatic disease was found in children under the age of 4 years (p < 0.05). Alpha variant (B.1.1.7) was not found to be associated with severe disease in children (p > 0.05).

Conclusion Our results demonstrate higher viral loads and symptomatic disease in children under the age of 4 years. Alpha variant (B.1.1.7) was not found to be related to disease severity. There has not been a consensus on the vaccination of the pediatric population worldwide. More studies are needed to understand the viral kinetics of SARS-CoV-2 and its severity on children to build effective vaccination strategies in children as public health restrictions are eased.

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.