Characterization of SARS-CoV-2 East Java isolate, Indonesia [version 1; peer review: 2 approved]
Fedik Abdul Rantam,
Cita Rosita Sigit Prakoeswa,
Damayanti Tinduh,
Jusak Nugraha,
Helen Susilowati,
Andi Yasmin Wijaya,
Ni Nyoman Tri Puspaningsih,
Dwiyanti Puspitasari,
Dominicus Husada,
Neneng Dewi Kurniati,
Aryati Aryati
Affiliations
Fedik Abdul Rantam
Research Center for Vaccine Technology and Development, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, 60132, Indonesia
Cita Rosita Sigit Prakoeswa
Professioal Education and Research, Dr. Soetomo General Academic Hospital, Faculty of Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia
Damayanti Tinduh
Research and Development Board, Dr. Soetomo General Hospital, Surabaya, East Java, 60132, Indonesia
Jusak Nugraha
Clinical Pathology Department, Dr. Soetomo General Hospital, Faculty of Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia
Helen Susilowati
Research Center for Vaccine Technology and Development, Institute of Tropical Disease, Airlangga University, Surabaya, East Java, 60132, Indonesia
Andi Yasmin Wijaya
Faculty of Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia
Ni Nyoman Tri Puspaningsih
Bioresource Engineering Group in Research Center for Bio-Molecule Engineering (BIOME), Airlangga University, Surabaya, East Java, 60132, Indonesia
Dwiyanti Puspitasari
Pediatrics Department, Dr. Soetomo General Hospital, Surabaya, East Java, 60132, Indonesia
Dominicus Husada
Pediatrics Department, Dr. Soetomo General Hospital, Surabaya, East Java, 60132, Indonesia
Neneng Dewi Kurniati
Clinical Microbiology Department, Dr. Soetomo General Hospital, Surabaya, East Java, 60132, Indonesia
Aryati Aryati
Clinical Pathology Department, Dr. Soetomo General Hospital, Faculty of Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia
Background: Incidents of SARS-CoV-2 in East Java increased steadily, and it became the second epicenter in Indonesia. The COVID-19 pandemic caused a dire multisectoral crisis all around the world. This study investigates and characterizes local isolates from East Java, Indonesia. Methods: There were 54 patients suspected with SARS-COV-2 infection and 27 patients were COVID-19 positive. Virus isolates were obtained from COVID-19 inpatients’ nasopharyngeal swabs at the Dr Soetomo Teaching Hospital, Surabaya. There were only three isolates (#6, #11, #35) with good growth characteristics. Serial blind passage and cytopathic effect observation in the Vero E6 cell line were performed for virus isolation. Confirmation of the SARS-CoV-2 infection was proven by means of reverse transcriptase-polymerase chain reactions using SARS-CoV-2 specific primers, scanning electron microscopy, and scanning transmission electron microscopy examination. Whole genome sequencing was performed using ARTIC protocol. Furthermore, SARS-CoV-2 characterization was identified through a western blot using rabbit serum immunized with inactive SARS-CoV-2 vaccine and human natural COVID-19 infection serum. Results: Spike gene analysis of three samples (#6, #11, #35) found that the D614G mutation was detected in all isolates, although one isolate exhibited the D215Y and E484D mutation. Based on whole genome analysis, those three isolates were included in clade 20A, and two isolates were included in lineage B.1.6 with one isolate belongs to lineage B.1.4.7. Conclusion: Based on molecular characterization and immunogenicity of SARS-CoV-2 East Java, Indonesia showed high titer and it has mutation in some regions.
