Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia

Abstract

Introduction A global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health. Methods Data were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia. Results Phylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein). Conclusion Our findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health.

Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia

“…This trend aligns with previous studies that found Indonesia-associated variants (B.1.466.2 and B.1.470) were widespread before the Delta outbreak. These local variants were subsequently outcompeted by Delta lineages AY.23 and AY.24 [ 9 , 10 , 11 , 12 ].…”

“…Notably, the G142D mutation was observed in the BI, PVS, and BI + PVS groups ( Figure 4 ). It has been reported that this mutation is associated with a milder Delta infection in Makassar, Indonesia [ 11 ]. This mutation affects the super-site epitope in the NTD of the S protein, which binds to NTD-targeted neutralizing antibodies.…”

“…Previous analyses of SARS-CoV-2 Indonesia isolates have reported the temporal change in predominant lineages during the pre-Delta and Delta outbreaks, raising concerns about the rapid local transmission of SARS-CoV-2 variants [ 9 , 10 , 11 , 12 ]. However, more studies are warranted to characterize the mutations within the SARS-CoV-2 genome, which may be involved in infectivity and immune evasion, particularly associated with the Delta variants.…”

Development of a reverse transcription loop‐mediated isothermal amplification assay with novel quantitative pH biosensor readout method for SARS‐CoV‐2 detection

“…On the other hand, false‐negatives can occur due to mutations in the primer target region of the SARS‐CoV‐2 genome [24]. This study used the N gene that codes nucleocapsid protein as the target region because of its plentiful mRNA contents [14], yet further study needs to be done as another recent study at the same centre found a mutation at the N protein of all their samples [28]. Besides the ambiguity of the orange colour interpretation, the LoD difference between the colorimetric and gel electrophoresis methods in this study also shows the limitation of the colorimetric method.…”

Optimasi dan Evaluasi Whole Genome Sequencing SARS CoV-2 Di Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah

“…Whole genome sequencing mampu mendeteksi perubahan asam nukleat yang terjadi pada semua gen sehingga metode tersebut dijadikan sebagai metode monitoring perkembangan dan persebaran SARS CoV-2 di suatu wilayah. Beberapa penelitian menunjukan bahwa metode Whole Genome Sequencing berhasil dilakukan sebagai studi mengenai genome virus SARS CoV-2 untuk melihat mutasi, mapping persebaran hingga deteksi beberapa varian baru (Gunadi et al, 2020;Massi et al, 2022). Di Indonesia, metode whole genome sequencing masih sangat jarang sekali dilakukan.…”