TY - JOUR
T1 - Characterization of SARS-CoV-2 East Java isolate, Indonesia
AU - Rantam, Fedik Abdul
AU - Prakoeswa, Cita Rosita Sigit
AU - Tinduh, Damayanti
AU - Nugraha, Jusak
AU - Susilowati, Helen
AU - Wijaya, Andi Yasmin
AU - Puspaningsih, Ni Nyoman Tri
AU - Puspitasari, Dwiyanti
AU - Husada, Dominicus
AU - Kurniati, Neneng Dewi
AU - Aryati, Aryati
N1 - Funding Information:
The authors thank the entire staff of Dr Soetomo General Hospital and Airlangga University for providing the access and facilities to perform this study. We thank Dr Rer. Nat. Setyawan Purnomo Sakti, M.Eng., and Nike as staff of Electron Microscopy Unit, Brawijaya University, Malang, Indonesia, for the assistance in electron microscopy. We thank Abdul Hadi Furqoni, M.Si. for the involvement in this study. We thank Suryo Kuncorojakti, Ph.D and Dr. Alexander Patera Nugraha for the discussion of this study. We thank the entire subject involved in this study for participating in research and development of COVID-19 management.
Publisher Copyright:
© 2021 Rantam FA et al.
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - COVID-19
KW - Growth properties
KW - Infectious disease
KW - SARS-CoV-2
KW - Virus isolation
UR - http://www.scopus.com/inward/record.url?scp=85116024850&partnerID=8YFLogxK
U2 - 10.12688/f1000research.53137.1
DO - 10.12688/f1000research.53137.1
M3 - Article
C2 - 34621509
AN - SCOPUS:85116024850
SN - 2046-1402
VL - 10
JO - F1000Research
JF - F1000Research
M1 - 480
ER -
