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EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324519


Since the outbreak of 2019 novel coronavirus (2019-nCoV) at the hardest-hit city of Wuhan, the fast-moving spread has killed over three hundred people and infected more than ten thousands in China1. There are more than one hundred cases outside of China, affecting a dozen of countries globally2. The genome sequence of 2019-nCoV has been reported and fast diagnostic kits, effective treatment as well as preventive vaccines are rapidly being developed3. Initial fast-growing confirmed cases triggered lock-down of Wuhan as well as nearby cities in Hubei Province. Mathematical models have been proposed by scientists around the world to project the numbers of infected cases in the coming days 4,5. However, major factors such as transportation and cultural customs have not been weighed enough. Our model is not set out for precise prediction of the number of infected cases, rather, it is meant for a glance of the dynamics under a public epidemic emergency situation and of different contributing factors. We hope that our model and simulation would provide more insights and perspective information to public health authorities around the globe for better informed prevention and containment solution.

EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324516


Background: SARS-CoV-2 has become a pandemic and researchers have built phylogenetic trees to trace the spread of the virus. However, the accumulation rate of variations and mutational hotspots remain largely unclear. Results: We collected more than 3,100 SARS-CoV-2 genome sequences from GISAID and profiled the landscape of whole genome variations. We detected 2,096 single nucleic variants (SNVs) and seven short deletions. 1,224 of them (58.4%) are missenses variation, altering the corresponding residues. We found the accumulation rate of SNVs in the current spreading situation is 6.36e-2/day. We found 15 missenses SNVs are extremely high frequent (existing in more than 100 genome sequences, p < 1e-5), effecting ORF1ab , S , ORF3a , M , ORF8 , and N . Moreover, one frequent substitution at locus 23,403 changes the 614 th amino acid of spike glycoprotein from D to G, potentially effecting the functions of this key protein. Conclusion: Our study provided the genome-wide mutation landscape of SARS-CoV-2. We found the continent specific mutational patterns and 15 missenses high frequent SNVs effecting 6 genes of the virus, may promoting the adaption of the virus during evolving.

Innovation (N Y) ; 1(1): 100006, 2020 May 21.
Article in English | MEDLINE | ID: covidwho-833425


BACKGROUND: The Chinese government implemented a metropolitan-wide quarantine of Wuhan city on 23rd January 2020 to curb the epidemic of the coronavirus COVID-19. Lifting of this quarantine is imminent. We modelled the effects of two key health interventions on the epidemic when the quarantine is lifted. METHODS: We constructed a compartmental dynamic model to forecast the trend of the COVID-19 epidemic at different quarantine lifting dates and investigated the impact of different rates of public contact and facial mask usage on the epidemic. RESULTS: We projected a declining trend of the COVID-19 epidemic if the current quarantine strategy continues, and Wuhan would record the last new confirmed cases in late April 2020. At the end of the epidemic, 65,733 (45,722-99,015) individuals would be infected by the virus, among which 16,166 (11,238-24,603, 24.6%) were through public contacts, 45,996 (31,892-69,565, 69.7%) through household contact, and 3,571 (2,521-5,879, 5.5%) through hospital contacts (including 778 (553-1,154) non-COVID-19 patients and 2,786 (1,969-4,791) medical staff). A total of 2,821 (1,634-6,361) would die of COVID-19 related pneumonia in Wuhan. Early quarantine lifting on 21st March is viable only if Wuhan residents sustain a high facial mask usage of ≥85% and a pre-quarantine level public contact rate. Delaying city resumption to mid/late April would relax the requirement of facial mask usage to ≥75% at the same contact rate. CONCLUSIONS: The prevention of a second epidemic is viable after the metropolitan-wide quarantine is lifted but requires a sustaining high facial mask usage and a low public contact rate.

SSRN; 2020.
Preprint | SSRN | ID: ppcovidwho-577


Background: Various forms of model have been applied to predict the trend of the epidemic since the outbreak of COVID-19 at the hardest-hit city of Wuhan. br b

Quant Biol ; 8(3): 238-244, 2020.
Article in English | MEDLINE | ID: covidwho-754125


BACKGROUND: Various models have been applied to predict the trend of the epidemic since the outbreak of COVID-19. METHODS: In this study, we designed a dynamic graph model, not for precisely predicting the number of infected cases, but for a glance of the dynamics under a public epidemic emergency situation and of different contributing factors. RESULTS: We demonstrated the impact of asymptomatic transmission in this outbreak and showed the effectiveness of city lockdown to halt virus spread within a city. We further illustrated that sudden emergence of a large number of cases could overwhelm the city medical system, and external medical aids are critical to not only containing the further spread of the virus but also reducing fatality. CONCLUSION: Our model simulation showed that highly populated modern cities are particularly vulnerable and lessons learned in China could facilitate other countries to plan the proactive and decisive actions. We shall pay close attention to the asymptomatic transmission being suggested by rapidly accumulating evidence as dramatic changes in quarantine protocol are required to contain SARS-CoV-2 from spreading globally. SUPPLEMENTARY MATERIALS: The supplementary materials can be found online with this article at 10.1007/s40484-020-0215-4.