Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan.
J Infect Dev Ctries
; 15(10): 1376-1383, 2021 10 31.
Article
in English
| MEDLINE | ID: covidwho-1518653
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
ABSTRACT
INTRODUCTION:
The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed. The virus has been constantly mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS-CoV-2 have been defined globally. In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants.METHODOLOGY:
The real time PCR was performed on nasopharyngeal specimen to confirm SARS-CoV-2 with Orf 1ab and E gene as targets. The virus isolates were sequenced through oxford nanopore technology MinION platform. Isolates from the first and second wave of COVID-19 outbreak in Karachi were compared.RESULTS:
The overall positivity rate for PCR was 26.24% with the highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19.CONCLUSIONS:
Based on the present findings it is suggested that the locally transmitted virus from Karachi varies from those reported from other parts of Pakistan. Slight variability was also observed between viruses from the first and second wave. Variability in any potential vaccine target may result in failed trials, therefore information on any local viral variants is always useful for effective vaccine design and/or selection.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Nasopharynx
/
Genome, Viral
/
Nanopores
/
Whole Genome Sequencing
/
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
/
Randomized controlled trials
Topics:
Vaccines
/
Variants
Limits:
Adult
/
Female
/
Humans
/
Male
/
Middle aged
/
Young adult
Country/Region as subject:
Asia
Language:
English
Journal:
J Infect Dev Ctries
Journal subject:
Communicable Diseases
Year:
2021
Document Type:
Article
Affiliation country:
Jidc.14900
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