Dataset Information

Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country.

ABSTRACT:

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman.

Methods

We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID.

Findings

The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data.

Interpretation

Oman's robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.

SUBMITTER: Al-Mahruqi S

PROVIDER: S-EPMC7834852 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ObjectivesTo establish a hospital-based platform to explore the epidemiological and clinical characteristics of patients screened for COVID-19.DesignHospital-based surveillance.SettingThis study was conducted in four selected hospitals in Bangladesh during 10 June-31 August 2020.ParticipantsIn total, 2345 patients of all age (68% male) attending the outpatient and inpatient departments of surveillance hospitals with any one or more of the following symptoms within last 7 days: fever, cough, sore throat and respiratory distress.Outcome measuresThe outcome measures were COVID-19 positivity and mortality rate among enrolled patients. Pearson's χ2 test was used to compare the categorical variables (sign/symptoms, comorbidities, admission status and COVID-19 test results). Regression analysis was performed to determine the association between potential risk factors and death.ResultsCOVID-19 was detected among 922 (39%) enrolled patients. It was more common in outpatients with a peak positivity in second week of July (112, 54%). The median age of the confirmed COVID-19 cases was 38 years (IQR: 30-50), 654 (71%) were male and 83 (9%) were healthcare workers. Cough (615, 67%) was the most common symptom, followed by fever (493, 53%). Patients with diabetes were more likely to get COVID-19 than patients without diabetes (48% vs 38%; OR: 1.5; 95% CI: 1.2 to 1.9). The death rate among COVID-19 positive was 2.3%, n=21. Death was associated with age ≥60 years (adjusted OR (AOR): 13.9; 95% CI: 5.5 to 34), shortness of breath (AOR: 9.7; 95% CI: 3.0 to 30), comorbidity (AOR: 4.8; 95% CI: 1.1 to 21.7), smoking history (AOR: 2.2, 95% CI: 0.7 to 7.1), attending the hospital in <2 days of symptom onset due to critical illness (AOR: 4.7; 95% CI: 1.2 to 17.8) and hospital admission (AOR: 3.4; 95% CI: 1.2 to 9.8).ConclusionsCOVID-19 positivity was observed in more than one-third of patients with suspected COVID-19 attending selected hospitals. While managing such patients, the risk factors identified for higher death rates should be considered.