key: cord-1039143-oj4bgpdz authors: Yan, Yan; Liu, Bin; Ding, Hui; Wang, Xu; Dai, Yaping; Ding, Difei; Yu, Hui; Sha, Mingchao; Lui, Chunyan; Chantsalmaa, Davgadorj; Qiu, Yuanwang; Huang, Lihua; Hu, Qinxue title: Characterizing COVID-19 severity, epidemiology and SARS-CoV-2 genotypes in a regional business hub of China date: 2020-08-25 journal: J Infect DOI: 10.1016/j.jinf.2020.08.031 sha: 49ca1bc0a223e3e83baaf0d1aab53a06a2accf41 doc_id: 1039143 cord_uid: oj4bgpdz nan To the Editor: We read with great interest the article of Sijia Tian et al 1 (http://nmdc.cn/coronavirus) as an information resource for scientists and clinicians. 2 However, it remains challenging to control and prevent this virus infection since information is rapidly evolving, and there are still many gaps that are not yet fully understood as to how this animal virus crossed species boundaries to infect humans. 3, 4 Based on epidemiological analyses and prediction, this highly contagious virus has a high probability of causing a recurrent epidemic in the 2020/2021 winter. 5 Therefore, to better control future outbreaks, it is important to understand SARS-CoV-2 transmission and pathogenesis by characterizing the clinical and epidemiological features of COVID-19 and the SARS-CoV-2 strains circulating locally and globally. In this retrospective study, we investigated COVID-19 disease severity, epidemiology and genotypes of SARS-CoV-2 in a regional business hub, Wuxi of China. Posterior oropharyngeal mucosal specimens of suspected patients were collected. We studied fifty-five COVID-19 patients (Ethics No. 2020-010-1) admitted to the hospital between January 25 and March 31, 2020. The clinical results showed 3 that most cases were mild illness (45/55, 81.8%) with the rest being severe (10/55, 18.2%), and were mainly imported (Generation one cases (G1) = 35, 63.6%) and occurred mainly in January and February of 2020 after the implement of monitoring and quarantine measures. The cases in March were significantly decreased, and most source cases were from neighboring provinces (Wuhan, Henan, Anhui, and Shanghai) and foreign countries (USA, Germany, Japan, and Philippines) ( Fig. 1A and 1B) . High incidence of severe illness was found in G1 (6/35, 17.1%) and G2 group (4/15, 26.7%). Nearly 32.7% (18/55) cases (G2 plus G3 groups) were attributable to household transmission, and 3.6% (2/55) G2 had no clear community contact history ( Fig. 1B and 1C ). Among the total cases, 58.2% (32/55) were male, and men (7/32, 21.9%) also had a higher proportion of severe cases than females (3/23, 13.0%) (Fig. 1C ). The main infection group was 20-44 years old (17/55, 30.9%). The proportion of severe cases with comorbidities (8/10, 80%) was ~4-fold greater than that of mild cases (10/45, 22.2%) (Fig. 1E ), while 60% (6/10) severe cases occurred in over 55 years old (Fig. 1F ). The average age (53.4 ± 6.6) of severely ill patients was significantly higher than all patients' average age (41.6 ± 2.6) (p=0.038). Concerning SARS-CoV-2 transmission and pathogenesis, current knowledge is limited. Coronaviruses are prone to mutations because they are single-stranded RNA viruses. 6 It is probable that these viruses would undergo mutations over time that could substantially change their features. 6, 7 SARS-CoV-2 genomes of different pandemic locations inside 6, 7 and outside of China 8 have become available. It is crucial to monitor protein mutations in viruses, which refers to changes in the 4 sequence of amino acids of SARS-CoV-2 genome. According to the changes in the genomic base and amino acid sequences, the mutation time point of a virus can be traced. 9 If the amount of data is sufficient, the development can be traced from the perspective of space and time. 2 Such information, in combination with the clinical outcomes of infected individuals, may help design prevention and treatment strategies. There are several standards for the classification of SARS-CoV-2 epidemic strains at home and abroad. 7, 8 We adopted Tang's analysis and classification method which was developed to analyze 103 available whole-genome sequences from the early stage of the SARS-CoV-2 outbreak. 7 According to Tang's analysis, S-type and L-type subtypes were prevalent at the early period of the SARS-CoV-2 outbreak, and the L-type dominated the epidemic in Wuhan in the early period (~70%), but the frequency subsequently decreased since early January 2020. 7 Tang's study has been confirmed by Forster et al 8 strains were related to mild outcome), we performed multiple alignment analyses to identify the subtype of Wuxi prevalent strains. Similar to that observed in most foreign countries, the genotype of Wuxi strains from patients was L-type subtype regardless of severe or mild outcome, and this subtype could be found in many foreign countries as of April 2020 ( Fig. 2A) . We also found that the S-type was an epidemic strain in Beijing (BJ, January 29, 2020) and Wuhan (WH, January 25, 2020). Homology comparison of the analyzed sequences indicated that the nucleotide identity was 99.7% between the S-and L-type subtype reference strains. The nucleotide and amino acid mutations of SARS-CoV-2 Wuxi strains that appeared in ORF1a (nt 8782, T8517C) were synonymous, whereas the mutation that appeared in ORF8 (nt 28144, C251T, S84L) was nonsynonymous, compared with S-type subtype reference sequences (Fig.2B ). In conclusion, our findings have revealed the clinical features of COVID-19 and 6 the genotypes of SARS-CoV-2 in a regional business hub during the lockdown period, providing a key reference for implementing such study locally and globally to understand SARS-CoV-2 transmission and pathogenesis. The authors declare no competing interest. Nucleotide and amino acid sequences of Wuxi strains and reference strains are shown as single letters or dots when they are the same. Characteristics of COVID-19 infection in Beijing A novel coronavirus outbreak of global health concern Transmission of 2019-nCoV infection from an asymptomatic contact in Germany The proximal origin of SARS-CoV-2 Potential impact of seasonal forcing on a SARS-CoV-2 pandemic Mutations, recombination and insertion in the evolution of 2019-nCoV On the origin and continuing evolution of SARS-CoV-2 Phylogenetic network analysis of SARS-CoV-2 genomes The global spread of 2019-nCoV: a molecular evolutionary analysis. Pathogens and global health We thank Xike Zhou for providing technical support.