Molecular epidemiology of COVID-19 epidemic in Ningxia, 2021

  Objective  To understand the molecular epidemiological characteristics of COVID-19 in Ningxia, and provide evidence for the surveillance, prevention and control of COVID-19.

  Methods  In this study, epidemiological investigation was conducted and Nasopharyngeal swab were collected from each COVID-19 case for RT-PCR and high throughput sequencing followed by phylogenic analysis and homology modeling using various bioinformatics tools.

  Results  There were 2 independent transmission chains in this COVID-19 epidemic in Ningxia. The average generation interval was 4 days and the median incubation period was 5.3 days (1.1−8.0 days). Three generation transmission occurred. The sequencing results showed that the epidemic was caused by the delta variant (B. 1.617.2). Compared with Wuhan reference strain (NC_045512), there were 45–50 nucleotide mutations in the genome sequences of the strains from 43 cases. There were 12 amino acid mutations in the spike (S) protein of SARS-CoV-2.

  Conclusion   This epidemic of COVID-19 was caused by the Delta variant, there is a risk that imported SARS-CoV-2 variants might cause local COVID-19 outbreaks. Continuous molecular surveillance for imported SARS-CoV-2 is essential in Ningxia.