Scientific Reports 5: Article number: 10942; published online: 01 June 2015; updated: 23 February 2016 This Article contains typographical errors in Table 2 where ‘Week 2 (N = 32)’ was incorrectly given as ‘Week (N = 2)’.

/pdf/correction-corrigendum-the-serum-profile-of-hypercytokinemia-539iu0xf8h.pdf

Correction: Corrigendum: The Serum Profile of Hypercytokinemia Factors Identified in H7N9-Infected Patients can Predict Fatal Outcomes

Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

/pdf/nextstrain-real-time-tracking-of-pathogen-evolution-1vkingd0mr.pdf

Nextstrain: real-time tracking of pathogen evolution.

Favipiravir (T-705; 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) is an anti-viral agent that selectively and potently inhibits the RNA-dependent RNA polymerase (RdRp) of RNA viruses. Favipiravir was discovered through screening chemical library for anti-viral activity against the influenza virus by Toyama Chemical Co., Ltd. Favipiravir undergoes an intracellular phosphoribosylation to be an active form, favipiravir-RTP (favipiravir ribofuranosyl-5'-triphosphate), which is recognized as a substrate by RdRp, and inhibits the RNA polymerase activity. Since the catalytic domain of RdRp is conserved among various types of RNA viruses, this mechanism of action underpins a broader spectrum of anti-viral activities of favipiravir. Favipiravir is effective against a wide range of types and subtypes of influenza viruses, including strains resistant to existing anti-influenza drugs. Of note is that favipiravir shows anti-viral activities against other RNA viruses such as arenaviruses, bunyaviruses and filoviruses, all of which are known to cause fatal hemorrhagic fever. These unique anti-viral profiles will make favipiravir a potentially promising drug for specifically untreatable RNA viral infections.

https://www.jstage.jst.go.jp/article/pjab/93/7/93_PJA9307B-02/_pdf

Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase

Zoonotic spillover, which is the transmission of a pathogen from a vertebrate animal to a human, presents a global public health burden but is a poorly understood phenomenon. Zoonotic spillover requires several factors to align, including the ecological, epidemiological and behavioural determinants of pathogen exposure, and the within-human factors that affect susceptibility to infection. In this Opinion article, we propose a synthetic framework for animal-to-human transmission that integrates the relevant mechanisms. This framework reveals that all zoonotic pathogens must overcome a hierarchical series of barriers to cause spillover infections in humans. Understanding how these barriers are functionally and quantitatively linked, and how they interact in space and time, will substantially improve our ability to predict or prevent spillover events. This work provides a foundation for transdisciplinary investigation of spillover and synthetic theory on zoonotic transmission.

/pdf/pathways-to-zoonotic-spillover-5230h7thxs.pdf

Pathways to zoonotic spillover

Background During the spring of 2013, a novel avian-origin influenza A (H7N9) virus emerged and spread among humans in China. Data were lacking on the clinical characteristics of the infections caused by this virus. Methods Using medical charts, we collected data on 111 patients with laboratory-confirmed avian-origin influenza A (H7N9) infection through May 10, 2013. Results Of the 111 patients we studied, 76.6% were admitted to an intensive care unit (ICU), and 27.0% died. The median age was 61 years, and 42.3% were 65 years of age or older; 31.5% were female. A total of 61.3% of the patients had at least one underlying medical condition. Fever and cough were the most common presenting symptoms. On admission, 108 patients (97.3%) had findings consistent with pneumonia. Bilateral ground-glass opacities and consolidation were the typical radiologic findings. Lymphocytopenia was observed in 88.3% of patients, and thrombocytopenia in 73.0%. Treatment with antiviral drugs was initiated in 108 patients (97.3%)...

/pdf/clinical-findings-in-111-cases-of-influenza-a-h7n9-virus-4vbey1hih5.pdf

Clinical findings in 111 cases of influenza A (H7N9) virus infection

Background The first identified cases of avian influenza A(H7N9) virus infection in humans occurred in China during February and March 2013. We analyzed data obtained from field investigations to describe the epidemiologic characteristics of H7N9 cases in China identified as of December 1, 2013. Methods Field investigations were conducted for each confirmed case of H7N9 virus infection. A patient was considered to have a confirmed case if the presence of the H7N9 virus was verified by means of real-time reverse-transcriptase–polymerase-chain-reaction assay (RT-PCR), viral isolation, or serologic testing. Information on demographic characteristics, exposure history, and illness timelines was obtained from patients with confirmed cases. Close contacts were monitored for 7 days for symptoms of illness. Throat swabs were obtained from contacts in whom symptoms developed and were tested for the presence of the H7N9 virus by means of real-time RT-PCR. Results Among 139 persons with confirmed H7N9 virus infectio...

/pdf/epidemiology-of-human-infections-with-avian-influenza-a-h7n9-3ac2l85fx0.pdf

Epidemiology of Human Infections with Avian Influenza A(H7N9) Virus in China

Qun Li, M.D., Lei Zhou, M.D., Minghao Zhou, Ph.D., Zhiping Chen, M.D., Furong Li, M.D., Huanyu Wu, M.D., Nijuan Xiang, M.D., Enfu Chen, M.P.H., Fenyang Tang, M.D., Dayan Wang, M.D., Ling Meng, M.D., Zhiheng Hong, M.D., Wenxiao Tu, M.D., Yang Cao, M.D., Leilei Li, Ph.D., Fan Ding, M.D., Bo Liu, M.D., Mei Wang, M.D., Rongheng Xie, M.D., Rongbao Gao, M.D., Xiaodan Li, M.D., Tian Bai, M.D., Shumei Zou, M.D., Jun He, M.D., Jiayu Hu, M.D., Yangting Xu, M.D., Chengliang Chai, M.D., Shiwen Wang, M.D., Yongjun Gao, M.D., Lianmei Jin, M.D., Yanping Zhang, M.D., Huiming Luo, M.D., Hongjie Yu, M.D., M.P.H., Lidong Gao, M.D., Xinghuo Pang, M.D., Guohua Liu, M.D., Yuelong Shu, Ph.D., Weizhong Yang, M.D., Timothy M. Uyeki, M.D., M.P.H., M.P.P., Yu Wang, M.D., Fan Wu, M.D., and Zijian Feng, M.D., M.P.H.

https://www.chinacdc.cn/kjxm/zxkyjz/201305/P020130522555712064160.pdf

Preliminary Report: Epidemiology of the Avian Influenza A (H7N9) Outbreak in China

/pdf/close-contacts-infected-cases-and-the-trends-of-sars-cov-2-34hkjknq.pdf

Furong Li

Papers

Epidemiology of Human Infections with Avian Influenza A(H7N9) Virus in China

Preliminary Report: Epidemiology of the Avian Influenza A (H7N9) Outbreak in China

Close Contacts, Infected Cases, and the Trends of SARS-CoV-2 Omicron Epidemic in Shenzhen, China