Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia

Abstract

BackgroundThus far, Indonesia has recorded over 4,000,000 confirmed COVID-19 cases and 144,000 fatalities; 12.8% of cases have been in children under 18 years. Whole-genome viral sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been demonstrated to help differentiate hospital-acquired infection from community-acquired coronavirus disease 2019 (COVID-19) infection. Our study highlighted the use of WGS to investigate the origin of infection among pediatric oncology patients in Jakarta. The aim of our study was to evaluate clinical and laboratory characteristics and also the efficacy of using WGS to confirm hospital-acquired COVID-19 infection in a cluster of immunocompromised children within a single ward of a tertiary hospital in metropolitan Jakarta based on quasispecies, viral load, and admission dates.MethodReal-time reverse-transcription polymerase chain reaction (RT-PCR) from nasopharyngeal (NP) swabs was used to diagnose the patients and also guardians and healthcare workers (HCWs) in the ward, followed by WGS of RT-PCR positive cases to establish their phylogenetic relationships.ResultUsing WGS, we showed that SARS-CoV-2 transmission in a cluster of children with underlying malignancy was characterized by high similarity of whole virus genome, which suggests nosocomial transmission.

Promising use of immune cell‐derived exosomes in the treatment of SARS‐CoV‐2 infections

“…However, the most common mutants were found in the Spike‐D614G, N‐R203K, N‐G204R and NSP12‐P323L 8 . Further analysis of SARS‐CoV‐2 sequencing confirmed that multiple mutations in the genome concentrated in the open reading frame area and SPs 9–11 . The most important variants and mutations (https://covariants.org/) regarding viral infectivity were found in SPs at the position of 614 (D614G) (see Figure 1).…”

“… 8 Further analysis of SARS‐CoV‐2 sequencing confirmed that multiple mutations in the genome concentrated in the open reading frame area and SPs. 9 , 10 , 11 The most important variants and mutations ( https://covariants.org/ ) regarding viral infectivity were found in SPs at the position of 614 (D614G) (see Figure 1 ). As noticed, mutations in receptor binding protein (RBD) of the SPs enhance the stability of the virus structure and infectivity.…”

The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19)

“…Whole-genome sequencing (WGS) of SARS-CoV-2 can guide management of SARS-CoV-2 outbreaks. Several case studies of isolated hospital 12,13 and long-term care facility 14 outbreaks have demonstrated its role in establishing the source of the outbreak, transmission dynamics, and links. The greatest benefit of WGS for SARS-CoV-2 outbreak management accrues when the result is rapidly available (ie, within 5 days).…”

“…15 Limited access to WGS or reliance on data sharing from centralized models of sequencing for public health greatly influence its utility and the ability to influence infection control responses at a local level. [12][13][14] The objective of this study was to demonstrate the utility of real-time, on-site SARS-CoV-2 WGS.…”