Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens
Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-Co...
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-02-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/14/3/461 |
| _version_ | 1797441118090035200 |
|---|---|
| author | Pragya D. Yadav Nivedita Gupta Varsha Potdar Sreelekshmy Mohandas Rima R. Sahay Prasad Sarkale Anita M. Shete Alpana Razdan Deepak Y. Patil Dimpal A. Nyayanit Yash Joshi Savita Patil Triparna Majumdar Hitesh Dighe Bharti Malhotra Jayanthi Shastri Priya Abraham |
| author_facet | Pragya D. Yadav Nivedita Gupta Varsha Potdar Sreelekshmy Mohandas Rima R. Sahay Prasad Sarkale Anita M. Shete Alpana Razdan Deepak Y. Patil Dimpal A. Nyayanit Yash Joshi Savita Patil Triparna Majumdar Hitesh Dighe Bharti Malhotra Jayanthi Shastri Priya Abraham |
| author_sort | Pragya D. Yadav |
| collection | DOAJ |
| description | Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung specimens of both passages. The successful isolation of the virus from hamster specimens with Vero CCL-81 was observed with cytopathic effect in infected cells and high viral load in the cell suspension. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequences, suggesting intact pathogenicity of the virus isolate. Our data demonstrated successful isolation of the Omicron variant with the in vivo method first followed by in vitro method. The virus isolate could be used in the future to explore different aspects of the Omicron variant. |
| first_indexed | 2024-03-09T12:19:22Z |
| format | Article |
| id | doaj.art-f0608ba6969e4a81a7f1f212f7da1f52 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T12:19:22Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-f0608ba6969e4a81a7f1f212f7da1f522023-11-30T22:43:47ZengMDPI AGViruses1999-49152022-02-0114346110.3390/v14030461Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical SpecimensPragya D. Yadav0Nivedita Gupta1Varsha Potdar2Sreelekshmy Mohandas3Rima R. Sahay4Prasad Sarkale5Anita M. Shete6Alpana Razdan7Deepak Y. Patil8Dimpal A. Nyayanit9Yash Joshi10Savita Patil11Triparna Majumdar12Hitesh Dighe13Bharti Malhotra14Jayanthi Shastri15Priya Abraham16Indian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box 4911, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaGenestrings Diagnostic Centre Pvt. Ltd., 3, MMTC, Geetanjali Enclave, New Delhi 110017, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaViral Research and Diagnostic Laboratory, Sawai Man Singh Medical College, Jaipur 302004, IndiaViral Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai 400011, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaDue to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung specimens of both passages. The successful isolation of the virus from hamster specimens with Vero CCL-81 was observed with cytopathic effect in infected cells and high viral load in the cell suspension. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequences, suggesting intact pathogenicity of the virus isolate. Our data demonstrated successful isolation of the Omicron variant with the in vivo method first followed by in vitro method. The virus isolate could be used in the future to explore different aspects of the Omicron variant.https://www.mdpi.com/1999-4915/14/3/461SARS-CoV-2OmicronB.1.1.529isolationSyrian hamstercell culture |
| spellingShingle | Pragya D. Yadav Nivedita Gupta Varsha Potdar Sreelekshmy Mohandas Rima R. Sahay Prasad Sarkale Anita M. Shete Alpana Razdan Deepak Y. Patil Dimpal A. Nyayanit Yash Joshi Savita Patil Triparna Majumdar Hitesh Dighe Bharti Malhotra Jayanthi Shastri Priya Abraham Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens Viruses SARS-CoV-2 Omicron B.1.1.529 isolation Syrian hamster cell culture |
| title | Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens |
| title_full | Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens |
| title_fullStr | Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens |
| title_full_unstemmed | Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens |
| title_short | Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens |
| title_sort | isolation and genomic characterization of sars cov 2 omicron variant obtained from human clinical specimens |
| topic | SARS-CoV-2 Omicron B.1.1.529 isolation Syrian hamster cell culture |
| url | https://www.mdpi.com/1999-4915/14/3/461 |
| work_keys_str_mv | AT pragyadyadav isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT niveditagupta isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT varshapotdar isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT sreelekshmymohandas isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT rimarsahay isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT prasadsarkale isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT anitamshete isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT alpanarazdan isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT deepakypatil isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT dimpalanyayanit isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT yashjoshi isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT savitapatil isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT triparnamajumdar isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT hiteshdighe isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT bhartimalhotra isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT jayanthishastri isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens AT priyaabraham isolationandgenomiccharacterizationofsarscov2omicronvariantobtainedfromhumanclinicalspecimens |