COVID-19 epidemic monitoring after non-pharmaceutical interventions: The use of time-varying reproduction number in a country with a large migrant population

Wahaibi, Adil Al; Manji, Abdullah Al; Maani, Amal Al; Rawahi, Bader Al; Harthy, Khalid Al; Alyaquobi, Fatma; Al-Jardani, Amina; Petersen, Eskild; Abri, Seif Al

doi:10.1016/j.ijid.2020.08.039

Cited by 29 publications

(38 citation statements)

References 32 publications

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“…All confirmed cases underwent epidemiological investigations and included the information of each patient’s demography (age, gender, residency, and nationality), epidemiology (source of infection if known, date of onset, primary case [infector] or secondary case [infected], and designation [cluster or sporadic]). The data were then analyzed to find out the relationship between the patients using the Epicontact R library; further the description of the methods is found in a recent article by Al Wahaibi et al (2020) .…”

Section: Methodsmentioning

confidence: 99%

“…The first confirmed cases of COVID-19 was reported in Oman on 24 February of two Omani nationals who returned from a visit to Iran. Initially, a steady increase in the number of imported confirmed cases was observed in the following weeks, with the first suspected case of local transmission reported on March 23, 2020 in Mutrah, a city within Muscat, the capital of Oman ( Al Wahaibi et al, 2020 ). To date, the number of infected cases has increased to more than 115,000 and approximately 1200 deaths ( Ministry of Health, Oman, 2020 ) were recorded.…”

Section: Introductionmentioning

confidence: 99%

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

Al-Mahruqi

Wahaibi

Khan

et al. 2021

International Journal of Infectious Diseases

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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 wholegenome 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.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Al-Mahruqi

Wahaibi

Khan

et al. 2021

International Journal of Infectious Diseases

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“…These approaches have been applied to the COVID-19 pandemic to gather information about the key epidemiological parameters and quantify the effects of NPIs by looking at deviations from expected and/or initial trends [24] , [46] , [124] , [125] , [126] , [127] , [129] , [130] , [131] , [132] , [133] , [134] . Let’s dive into some details.…”

Section: Epidemic Modelsmentioning

confidence: 99%

“…Authors in Refs. [46] , [126] , [129] , [131] adopt and/or extend the approach developed in [155] , [156] to estimate

. This method is readily available in Python and R and is called EpiEstim .…”

Section: Epidemic Modelsmentioning

confidence: 99%

Non-pharmaceutical interventions during the COVID-19 pandemic: A review

2021

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Infectious diseases and human behavior are intertwined. On one side, our movements and interactions are the engines of transmission. On the other, the unfolding of viruses might induce changes to our daily activities. While intuitive, our understanding of such feedback loop is still limited. Before COVID-19 the literature on the subject was mainly theoretical and largely missed validation. The main issue was the lack of empirical data capturing behavioral change induced by diseases. Things have dramatically changed in 2020. Non-pharmaceutical interventions (NPIs) have been the key weapon against the SARS-CoV-2 virus and affected virtually any societal process. Travels bans, events cancellation, social distancing, curfews, and lockdowns have become unfortunately very familiar. The scale of the emergency, the ease of survey as well as crowdsourcing deployment guaranteed by the latest technology, several Data for Good programs developed by tech giants, major mobile phone providers, and other companies have allowed unprecedented access to data describing behavioral changes induced by the pandemic. Here, I review some of the vast literature written on the subject of NPIs during the COVID-19 pandemic. In doing so, I analyze 348 articles written by more than 2518 of authors in the first 12 months of the emergency. While the large majority of the sample was obtained by querying PubMed, it includes also a hand-curated list. Considering the focus, and methodology I have classified the sample into seven main categories: epidemic models, surveys, comments/perspectives, papers aiming to quantify the effects of NPIs, reviews, articles using data proxies to measure NPIs, and publicly available datasets describing NPIs. I summarize the methodology, data used, findings of the articles in each category and provide an outlook highlighting future challenges as well as opportunities.

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“…Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), first emerged in December 2019 in Wuhan, China, and spread rapidly across the world. In Oman, the first imported case was diagnosed on 24 February 2020 ( Wahaibi et al, 2020 ). Until mid-August 2020, there was ongoing community transmission, with a total of 79,701 confirmed cases of SARS-CoV-2 infection and 488 deaths in Oman.…”

Section: Introductionmentioning

confidence: 99%