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

Yekti Hediningsih; Mohammad Nurhafid; Endah Wahyuni; Dyah Ayu Kunti Hapsari; Purnomo Purnomo; Marwiyah Marwiyah; Hendrik Sulistiyanto; Ismi Farhati; Sekti Handayani; Wiwik Peni

doi:10.36990/hijp.v15i1.706

Authors

Yekti Hediningsih Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah; Universitas Muhammadiyah Semarang, Indonesia
Mohammad Nurhafid PT Artha Genetikalab Indonesia, Indonesia https://orcid.org/0000-0002-7648-6751
Endah Wahyuni Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Dyah Ayu Kunti Hapsari Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Purnomo Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Marwiyah Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Hendrik Sulistiyanto Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Ismi Farhati Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Sekti Handayani Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia
Wiwik Peni Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan Provinsi Jawa Tengah, Indonesia

DOI:

https://doi.org/10.36990/hijp.v15i1.706

Keywords:

Whole genome sequencing, Sequencing indicator, SARS CoV-2, Pool artic primer

Abstract

SARS CoV-2 is a virus that has spread to almost all countries in the world, including Indonesia. Whole genome sequencing is most appropriate for detecting several variants and gene mutations of SARS CoV-2. The purpose of this study was to identify and evaluate the entire SARS CoV-2 genome based on success and sequencing indicators at the Central Java Province Health Laboratory and Medical Device Testing Center. The survey method used in this study where samples were taken from several regions, namely Central Java, West Java, Banten and Jakarta. The analysis is based on fasta results from the Dragen COVID lineage analysis. The results showed that the proportion of success of the four working batches showed that the last two batches got a higher percentage than the first two batches. Pool artic primers used, namely versions V3 and V4 are strongly suspected as factors that influence the success where the V4 version shows better performance and is suitable for use in the whole genome sequencing of SARS CoV-2 at the Central Java Provincial Health Laboratory and Medical Device Testing Center. Several indicators are used as evaluation standards, namely cluster density, passing filter and Q30 which are adjusted to the instrument used.

Full-text of the article is available for this locale: Bahasa Indonesia.

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