key: cord-0775781-vu9eab5x authors: Wang, Jann-Tay; Lin, You-Yu; Chang, Sui-Yuan; Yeh, Shiou-Hwei; Hu, Bor-Hsian; Chen, Pei-Jer; Chang, Shan-Chwen title: The Role of Phylogenetic Analysis in Clarifying the Infection Source of a COVID-19 Patient date: 2020-04-08 journal: J Infect DOI: 10.1016/j.jinf.2020.03.031 sha: c0e8af4fa39ffc78bf6cfae77ff60cf4c8c292ee doc_id: 775781 cord_uid: vu9eab5x nan Previous reports indicated that the emergence of the novel coronavirus (SARS-CoV-2) infection (COVID-19) had raised global concern and was characterized as a pandemic event by the World Health Organization on March 11, 2020 [1] [2] [3] . Till March 18, 2020, it has spread to 146 countries, including Taiwan [4] . People in Taiwan and mainland China travel frequently, which put Taiwan at a great risk of acquiring an epidemic of COVID-19. Taiwan has been on constant alert and react rapidly to epidemics change from China ever since the severe acute respiratory syndrome (SARS) epidemic in 2003 and has done much effort on the containment of COVID-19 with success [5] . Till March 18, 2020, there are only 100 cases of COVID-19 noted in Taiwan, including 79 imported cases and 21 cases belonging to seven occasions of limited local transmission (six family clusters and two transmissions in social societies) [4] . To contain the epidemics of COVID-19, prevention from both import and export of contagious people is an essential intervention. It is also important to clearly clarify the infection source in order to initiate an efficient and successful contact tracing for the SARS-CoV-2 infected patients, and thereafter people exposed to the contagious patients could be quarantined to avoid further disease spreading. Here we present a COVID-19 patient whose infection source could not be completely clarified initially, and later was illuminated by using the phylogenetic analysis of the isolated virus. This 66-year-old Taiwanese woman was well before. She traveled to Dubai from January 29 to February 10, 2020, and Egypt from February 11 to February 21, 2020. When she stayed in Egypt, she ever participated an eight-day tourism on a Nile cruise boat. She returned to Taiwan via an international airline on February 21, 2020. She began to suffer from general malaise, myalgia, cold sweating, productive cough, and sore throat since February 18, 2020. She reported that there were another 16 persons in the same tourism group had similar symptoms at that time. Her symptoms persisted despite medication, prescribed on February 21 by a local medical doctor. On The most interesting point of this patient is where she contracted her COVID-19. By history, she is more likely to contract SARS-CoV-2 infection while travelling abroad. However, despite that the median incubation period of COVID-19 was 5.1 days, it might be as long as more than three weeks in some extreme cases [6, 7] . Therefore, an argument that she got the infection while she was in Taiwan couldn't be excluded completely. To clarify this argument, more virologic studies were conducted. Virus whole genome sequencing was conducted for the SARS-CoV-2 isolate (NTU03) from her throat swab collected on March 2, 2020. The derived NTU03 sequence was most similar to clade A2a with only 5 nucleotide differences, which included 2 synonymous mutations (Orf 1b/5410 CTA>TTA, and orf 3a/819 GTG>GTT), 2 nonsynonymous mutations (Orf 1b/799 G>V, and orf 3a/57Q>H), and a mutation within 5'UTR (Table) . An average of 12 nucleotide differences were observed between NTU03 and sequences of other clades, whereas an average of 10 nucleotide differences were observed with other previous viruses isolated from Taiwan. The phylogenetic analysis also reveals that the NTU03 belongs to clade A2a (Figure) . With the limited transmission clusters in Taiwan and the fact that NTU03 exhibits at least 8 unique nucleotide difference compared to other previously reported viruses from Taiwan, we conclude that it is much more probable that the present patient was infected during her travelling abroad. To our best knowledge, in late and its relationship to other viral sequences derived from case patients identified in Taiwan (red arrows). The phylogenetic tree was generated and modified for display purposes from Nextstrain (https://nextstrain.org/ncov) [9] , which uses genetic sequences and metadata from GISAID (https://www.gisaid.org/CoV2020/) and sequence submission date for the horizontal axis [10] . The phylogenetic tree was generated at 2020/03/09 6PM (GMT+8) with a total of 240 viral genomes sampled. UTR n/a n/a n/a orf1a 2772 TTC>TTT 924 F>F 4402 T T T T T T T T T C T T T T T T T T orf1a 4137 8782 C C C C C C C T T T T T C C C T C C orf1a 8517 AGC>AGT 2839 S>S T T T T T T T T T T T T T T T T orf1b 3780 CGT>CGC 1260 R>R CTC>CTT 1531 L>L 18603 T T T T T T T T C T T T T T T T T T orf1b 5136 CAT>CAC 1712 H>H CCT>TCT 1821 P>S 18975 T T T T T T T T A T T T T T T T T T orf1b 5508 GTT>GTA 1836 V>V orf8 32 ACA>ATA 11 T>I 28144 T T T T T T T C C C C C T T T C T T orf8 251 Emergence of a novel coronavirus causing respiratory illness from Wuhan Emergence of SARS-like Coronavirus in China: An Update Statement on the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV) Taiwan Centers for Disease Control Response to COVID-19 in Taiwan: Big data analytics, new technology, and proactive testing Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travelers from Wuhan The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application Egypt tires to reassure tourists as coronarivus spikes Nextstrain: real-time tracking of pathogen evolution TreeTime: Maximum-likelihood phylodynamic analysis were aligned and compared. MN908947 was used as the reference sequence, and orange shaded nucleotides indicated nucleotides different to the reference nucleotide, and grey shaded positions indicated lack of nucleotide information. The NTU01 and CDC03 are derived from the Case 3 patient, and CDC04 and CGMH1 are from the from the Case 4 patient orf3a 819 28688 T T T T T C T T T T T T T T T T T T N 415 TTG>CTG 139 L>LUTR n/a n/a n/a