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Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10−3 substitutions per year. Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.
Jiaxin Ling; Rachel A. Hickman; Jinlin Li; Xi Lu; Johanna F. Lindahl; Åke Lundkvist; Josef D. Järhult. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 During the Early Pandemic. Viruses 2020, 12, 1026 .
AMA StyleJiaxin Ling, Rachel A. Hickman, Jinlin Li, Xi Lu, Johanna F. Lindahl, Åke Lundkvist, Josef D. Järhult. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 During the Early Pandemic. Viruses. 2020; 12 (9):1026.
Chicago/Turabian StyleJiaxin Ling; Rachel A. Hickman; Jinlin Li; Xi Lu; Johanna F. Lindahl; Åke Lundkvist; Josef D. Järhult. 2020. "Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 During the Early Pandemic." Viruses 12, no. 9: 1026.
Ticks (order: Ixodida) are a highly diverse and ecologically important group of ectoparasitic blood-feeding organisms. One such species, the seabird tick (Ixodes uriae), is widely distributed around the circumpolar regions of the northern and southern hemispheres. It has been suggested that Ix. uriae spread from the southern to the northern circumpolar region millions of years ago and has remained isolated in these regions ever since. Such a profound biographic subdivision provides a unique opportunity to determine whether viruses associated with ticks exhibit the same evolutionary patterns as their hosts. To test this, we collected Ix. uriae specimens near a Gentoo penguin (Pygoscelis papua) colony at Neko harbour, Antarctica, and from migratory birds - the Razorbill (Alca torda) and the Common murre (Uria aalge) - on Bonden island, northern Sweden. Through meta-transcriptomic next- generation sequencing we identified 16 RNA viruses, seven of which were novel. Notably, we detected the same species, Ronne virus, and two closely related species, Bonden virus and Piguzov virus, in both hemispheres indicating that there have been at least two cross- circumpolar dispersal events. Similarly, we identified viruses discovered previously in other locations several decades ago, including Gadgets Gully virus, Taggert virus and Okhotskiy virus. By identifying the same or closely related viruses in geographically disjunct sampling locations we therefore provide evidence for virus dispersal within and between the circumpolar regions. In marked contrast, our phylogenetic analysis revealed no movement of the Ix. uriae hosts between the same locations. Combined, these data suggest that migratory birds are responsible for the movement of viruses at both the local and global scales.Author summary/ImportanceAs host populations diverge, so may those microorganisms, including viruses, that are dependent on those hosts. To examine this key issue in host-microbial evolution we compared the co-phylogenies of the seabird tick, Ixodes uriae, and their RNA viruses sampled from the far northern and southern hemispheres. Despite the huge geographic distance between them, phylogeographic analysis reveals that the same viruses were found both within and between the northern and southern circumpolar regions, most likely reflecting transfer by virus-infected migratory birds. In contrast, genomic data suggested that the Ix. uriae populations were phylogenetically distinct between the northern and southern hemispheres. This work emphasises the importance of migratory birds and ticks as vectors and sources of virus dispersal and introduction at both the local and global scales.
John H.-O. Pettersson; Patrik Ellström; Jiaxin Ling; Ingela Nilsson; Sven Bergström; Daniel González-Acuña; Björn Olsen; Edward C. Holmes. Circumpolar diversification of the Ixodes uriae tick virome. 2020, 1 .
AMA StyleJohn H.-O. Pettersson, Patrik Ellström, Jiaxin Ling, Ingela Nilsson, Sven Bergström, Daniel González-Acuña, Björn Olsen, Edward C. Holmes. Circumpolar diversification of the Ixodes uriae tick virome. . 2020; ():1.
Chicago/Turabian StyleJohn H.-O. Pettersson; Patrik Ellström; Jiaxin Ling; Ingela Nilsson; Sven Bergström; Daniel González-Acuña; Björn Olsen; Edward C. Holmes. 2020. "Circumpolar diversification of the Ixodes uriae tick virome." , no. : 1.
Background & AimsThe coronavirus disease 2019 (COIVD-19) caused by SARS-CoV-2 has been characterized as a pandemic, which causes a serious public health challenge in the world. A very large group of patients infected by HBV has been reported worldwide, especially in China. In order to answer whether specific treatment strategy on the patients coinfected with HBV and SARS-CoV-2, it requires profound understanding of the clinical characteristics on those patients. However, the impacts of SARS-CoV-2 infection on HBV patients remain largely unknown.Approach & ResultsIn this retrospective investigation, we included 123 COVID-19 patients admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from January 5 to March 7, 2020. All enrolled patients are the laboratory confirmed COVID-19 pneumonia cases according to the criteria reported previously. A total of 123 patients were analyzed for their Clinical records, laboratory results including the diagnosis of HBV infection and liver function. Among 123 confirmed COVID-19 patients, the mean age was 51 years old and 59.3% were females (73/123). Fifteen were previously HBV infected patients, 66.7% of them were males (10/15), patients with HBV infection appeared to have a higher incidence of liver cirrhosis and an increased level of total bilirubin. Seven (46.7%) patients with HBV infection were defined as severe cases, while the severity rate was 24.1% for the patients without HBV infection (26/108). The mortality of patients with HBV infection was 13.3% (2/15) compared to 2.8% (3/108) for the patients without HBV infection.ConclusionsSARS-CoV-2 infection may cause Live function damage in COVID-19 cases and the patients with HBV infection are likely to have more severe disease outcome.
Xiaoping Chen; Qunqun Jiang; Zhiyong Ma; Jiaxin Ling; Wenjia Hu; Qian Cao; Pingzheng Mo; Rongrong Yang; Shicheng Gao; Xien Gui; Yong Xiong; Jinlin Li; Yongxi Zhang. Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection. 2020, 1 .
AMA StyleXiaoping Chen, Qunqun Jiang, Zhiyong Ma, Jiaxin Ling, Wenjia Hu, Qian Cao, Pingzheng Mo, Rongrong Yang, Shicheng Gao, Xien Gui, Yong Xiong, Jinlin Li, Yongxi Zhang. Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection. . 2020; ():1.
Chicago/Turabian StyleXiaoping Chen; Qunqun Jiang; Zhiyong Ma; Jiaxin Ling; Wenjia Hu; Qian Cao; Pingzheng Mo; Rongrong Yang; Shicheng Gao; Xien Gui; Yong Xiong; Jinlin Li; Yongxi Zhang. 2020. "Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection." , no. : 1.
ObjectivesComorbidities have significant indications for the disease outcome of COVID-19, however which underlying diseases that contribute the most to aggravate the conditions of COVID-19 patients is still largely unknown. SARS-CoV-2 viral clearance is a golden standard for defining the recovery of COVID-19 infections. To dissect the underlying diseases that could impact on viral clearance, we enrolled 106 COVID-19 patients who were hospitalized in the Zhongnan Hospital of Wuhan University, Wuhan, China between Jan 5 and Feb 25, 2020.MethodologyWe comprehensively analyzed demographic, clinical and laboratory data, as well as patient treatment records. Survival analyses with Kaplan-Meier and Cox regression modelling were employed to identify factors influencing the viral clearance negatively.ResultsWe found that increasing age, male gender, and angiotensin-converting enzyme 2 (ACE2) associated factors (including hypertension, diabetes, and cardiovascular diseases) adversely affected the viral clearance. Furthermore, analysis by a random forest survival model pointed out hypertension, cortisone treatment, gender, and age as the four most important variables.ConclusionsWe conclude that patients at old age, males, and/or having diseases associated with high expression of ACE2 will have worse prognosis during a COVID-19 infections.
Xiaoping Chen; Wenjia Hu; Jiaxin Ling; Pingzheng Mo; Yongxi Zhang; Qunqun Jiang; Zhiyong Ma; Qian Cao; Liping Deng; Shihui Song; Ruiying Zheng; Shicheng Gao; Hengning Ke; Xien Gui; Åke Lundkvist; Jinlin Li; Johanna F Lindahl; Yong Xiong. Hypertension and Diabetes Delay the Viral Clearance in COVID-19 Patients. 2020, 1 .
AMA StyleXiaoping Chen, Wenjia Hu, Jiaxin Ling, Pingzheng Mo, Yongxi Zhang, Qunqun Jiang, Zhiyong Ma, Qian Cao, Liping Deng, Shihui Song, Ruiying Zheng, Shicheng Gao, Hengning Ke, Xien Gui, Åke Lundkvist, Jinlin Li, Johanna F Lindahl, Yong Xiong. Hypertension and Diabetes Delay the Viral Clearance in COVID-19 Patients. . 2020; ():1.
Chicago/Turabian StyleXiaoping Chen; Wenjia Hu; Jiaxin Ling; Pingzheng Mo; Yongxi Zhang; Qunqun Jiang; Zhiyong Ma; Qian Cao; Liping Deng; Shihui Song; Ruiying Zheng; Shicheng Gao; Hengning Ke; Xien Gui; Åke Lundkvist; Jinlin Li; Johanna F Lindahl; Yong Xiong. 2020. "Hypertension and Diabetes Delay the Viral Clearance in COVID-19 Patients." , no. : 1.
SummaryBackgroundViral clearance is one important indicator for the recovery of SARS-CoV-2 infected patients. Previous studies have pointed out that suboptimal T and B cell responses can delay viral clearance in MERS-CoV and SARS-CoV infected patients. The role of leukomonocytes in viral clearance of COVID-19 patients is not yet well defined.MethodsFrom January 26 to February 28, 2020, an observational study was launched at the Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China. We enrolled 25 laboratory-confirmed COVID-19 patients, whose throat-swab specimens were tested positive for SARS-CoV-2 infection by qRT-PCR. To investigate the factors that contribute to the viral clearance, we comprehensively analyzed clinical records, counts of lymphocyte subsets including CD3+, CD4+, CD8+ T cells, B cells and NK cells in the patients who successfully cleared SARS-CoV-2, and compared to those that failed to, after a standardized treatment of 8-14 days.FindingsIn 25 enrolled COVID-19 patients, lymphopenia was a common feature. After the treatment, 14 out of the 25 enrolled patients were tested negative for SARS-CoV-2. The patients that cleared the infection had restored the numbers of CD3+, CD4+, CD8+ T cells and B cells as compared to the still viral RNA positive patients, while the recovered patients had a higher count of leukomonocytes.ConclusionsBy comparison of leukomonocytes counts in COVID-19 patients at different stages of the disease, we found that CD3+, CD4+, CD8+ T cells and B cells appear to play important roles in viral clearance. The restoration of leukomonocytes counts from peripheral blood can be used as prognosis for the recovery of an COVID-19 infection. We propose that restoration of leukomonocytes counts can be added to the COVID-19 diagnostic guidance as a criterion for releasing and discharging patients.
Xiaoping Chen; Jiaxin Ling; Pingzheng Mo; Yongxi Zhang; Qunqun Jiang; Zhiyong Ma; Qian Cao; Wenjia Hu; Shi Zou; Liangjun Chen; Lei Yao; Mingqi Luo; Tielong Chen; Liping Deng; Ke Liang; Shihui Song; Rongrong Yang; Ruiying Zheng; Shicheng Gao; Xien Gui; Hengning Ke; Wei Hou; Åke Lundkvist; Yong Xiong. Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients. 2020, 1 .
AMA StyleXiaoping Chen, Jiaxin Ling, Pingzheng Mo, Yongxi Zhang, Qunqun Jiang, Zhiyong Ma, Qian Cao, Wenjia Hu, Shi Zou, Liangjun Chen, Lei Yao, Mingqi Luo, Tielong Chen, Liping Deng, Ke Liang, Shihui Song, Rongrong Yang, Ruiying Zheng, Shicheng Gao, Xien Gui, Hengning Ke, Wei Hou, Åke Lundkvist, Yong Xiong. Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients. . 2020; ():1.
Chicago/Turabian StyleXiaoping Chen; Jiaxin Ling; Pingzheng Mo; Yongxi Zhang; Qunqun Jiang; Zhiyong Ma; Qian Cao; Wenjia Hu; Shi Zou; Liangjun Chen; Lei Yao; Mingqi Luo; Tielong Chen; Liping Deng; Ke Liang; Shihui Song; Rongrong Yang; Ruiying Zheng; Shicheng Gao; Xien Gui; Hengning Ke; Wei Hou; Åke Lundkvist; Yong Xiong. 2020. "Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients." , no. : 1.
This study shows that only a single introduction of SINV into a new geographical area is required for spread and establishment, provided that the requisite vector(s) and reservoir(s) of epizootological and epidemiological importance are present. Furthermore, we present the first report of recombination between two strains of SINV in nature. Our study increases the knowledge on new introductions and dispersal of arboviruses in general and of SINV in particular.
Jiaxin Ling; Teemu Smura; Jan O. Lundström; John H.-O. Pettersson; Tarja Sironen; Olli Vapalahti; Åke Lundkvist; Jenny C. Hesson. Introduction and Dispersal of Sindbis Virus from Central Africa to Europe. Journal of Virology 2019, 93, e00620-19 .
AMA StyleJiaxin Ling, Teemu Smura, Jan O. Lundström, John H.-O. Pettersson, Tarja Sironen, Olli Vapalahti, Åke Lundkvist, Jenny C. Hesson. Introduction and Dispersal of Sindbis Virus from Central Africa to Europe. Journal of Virology. 2019; 93 (16):e00620-19.
Chicago/Turabian StyleJiaxin Ling; Teemu Smura; Jan O. Lundström; John H.-O. Pettersson; Tarja Sironen; Olli Vapalahti; Åke Lundkvist; Jenny C. Hesson. 2019. "Introduction and Dispersal of Sindbis Virus from Central Africa to Europe." Journal of Virology 93, no. 16: e00620-19.