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Emerg Infect Dis ; 27(1): 196-204, 2021 01.
Article in English | MEDLINE | ID: covidwho-993249


Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinical, and epidemiologic data from 50 patients, who accounted for 53.8% of total reported case-patients as of February 28, 2020. We performed whole-genome sequencing to determine phylogenetic relationship and transmission dynamics of severe acute respiratory syndrome coronavirus 2 infections. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. The estimated time to the most recent common ancestor of local coronavirus disease outbreak was December 24, 2019, with an evolutionary rate of 3.04 × 10-3 substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.

COVID-19/epidemiology , COVID-19/virology , Disease Outbreaks , Adult , Aged , Aged, 80 and over , COVID-19/transmission , Cluster Analysis , Disease Hotspot , Evolution, Molecular , Female , Hong Kong/epidemiology , Humans , Male , Middle Aged , Mutation , Phylogeny , Phylogeography , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viroporin Proteins/genetics , Whole Genome Sequencing , Young Adult
Int J Mol Sci ; 21(15)2020 Jul 29.
Article in English | MEDLINE | ID: covidwho-693630


To control the COVID-19 pandemic and prevent its resurgence in areas preparing for a return of economic activities, a method for a rapid, simple, and inexpensive point-of-care diagnosis and mass screening is urgently needed. We developed and evaluated a one-step colorimetric reverse-transcriptional loop-mediated isothermal amplification assay (COVID-19-LAMP) for detection of SARS-CoV-2, using SARS-CoV-2 isolate and respiratory samples from patients with COVID-19 (n = 223) and other respiratory virus infections (n = 143). The assay involves simple equipment and techniques and low cost, without the need for expensive qPCR machines, and the result, indicated by color change, is easily interpreted by naked eyes. COVID-19-LAMP can detect SARS-CoV-2 RNA with detection limit of 42 copies/reaction. Of 223 respiratory samples positive for SARS-CoV-2 by qRT-PCR, 212 and 219 were positive by COVID-19-LAMP at 60 and 90 min (sensitivities of 95.07% and 98.21%) respectively, with the highest sensitivities among nasopharyngeal swabs (96.88% and 98.96%), compared to sputum/deep throat saliva samples (94.03% and 97.02%), and throat swab samples (93.33% and 98.33%). None of the 143 samples with other respiratory viruses were positive by COVID-19-LAMP, showing 100% specificity. Samples with higher viral load showed shorter detection time, some as early as 30 min. This inexpensive, highly sensitive and specific COVID-19-LAMP assay can be useful for rapid deployment as mobile diagnostic units to resource-limiting areas for point-of-care diagnosis, and for unlimited high-throughput mass screening at borders to reduce cross-regional transmission.

Betacoronavirus/genetics , Colorimetry/methods , Coronavirus Infections/diagnosis , Mass Screening/economics , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Betacoronavirus/isolation & purification , COVID-19 , Colorimetry/economics , Coronavirus Infections/virology , Humans , Limit of Detection , Nasopharynx/virology , Nucleic Acid Amplification Techniques/methods , Pandemics , Pneumonia, Viral/virology , Point-of-Care Systems , RNA, Viral/metabolism , SARS-CoV-2 , Viral Load