Virology Journal

IntroductionThis paper sought to investigate the clinical characteristic differences between suspected and confirmed patients with COVID-19 from CT scan to prevent and treat this infectious disease, since the coronavirus outbreak in the world has seriously affected the quality of life. MethodsWe proposed to use a retrospective case-control study to give a comparison between suspected patients and confirmed patients in the clinical characteristics. Results(56%) patients were confirmed for COVID-19 from suspected 167 patients. We find that elder people were more likely to be infected by COVID-19. Among the confirmed 94 patients, 2 (2%) patients were admitted to an intensive care unit, and 0 (0%) patients died during the study period. We find that images of CT scan of patients with a COVID-19 are significantly different from patients without a COVID-19. ConclusionsTo our best knowledge, it is the first time to use the case-control design to study the coronavirus disease, since it is particularly appropriate for investigating infectious disease outbreaks. The clinical treatment experience in this study can supply a guideline for treating COVID-19 as the number of the infected patients is increasing in the world. Compared with other studies, we find that the mortality rate and the intensive care unit rate can be reduced if patients can be treated timely in the right identification and detection with nucleic acid testing and chest CT scan. Therefore, we recommend nucleic acid testing and chest CT scan for the clinical treatment practice from this successful clinical treatment study.

Most members of the genus Gammacoronavirus infect avian hosts, but far fewer viruses have been characterized than in the other coronavirus genera, leaving their diversity largely unclear. Pigeon gammacoronaviruses were previously detected by consensus PCR, but only partial sequences were determined. In this study, we comprehensively analyzed public RNA-seq datasets and reconstructed two nearly complete genomes of pigeon gammacoronaviruses. Molecular evolutionary analyses showed pigeon gammacoronaviruses belong to the subgenus Igacovirus, and their pairwise distances to the members of this subgenus meet the International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria, supporting their designation as a novel species in this subgenus. Notably, although nucleotide sequences are highly conserved gammacoronaviruses, their 3'-genomic region exhibited differences in gene organization among pigeon coronavirus variants. These findings expand our knowledge of the diversity of gammacoronaviruses.

The necrosis syndrome of freesia, first described in 1970 in Northern Europe, is still jeopardizing freesia cultivation all over the world. Although several viruses have been listed as possible causal agents, the etiology of the disease is still not clear and is possibly linked to a combination of different factors. In this study, a high-throughput sequencing virome analysis was performed on total RNA extracts derived from symptomatic freesia leaves; a novel virus putatively belonging to the recently ratified Konkoviridae family in the Bunyaviricetes class has been identified and characterized, for which we propose the name of freesia konkovirus 1 (FreKV-1). This family, officially listing only one genus and two species, has been expanded by exploring publicly available metatranscriptomic datasets through the Serratus Project Database and reconstructing new viral entities; the phylogenetic position of the Konkoviridae family has been investigated and new genera belonging to the family have been proposed. Moreover, a further previously unknown virus, putatively belonging to the Yueviridae family was partially characterized and its phylogenetic position was discussed. Overall, the analysis increased our knowledge of the number of viral agents infecting freesia and possibly involved in freesia necrosis syndrome.

Reptarenaviruses are viruses belonging to the genus Reptarenavirus within the family Arenaviridae, which infect snakes and cause inclusion body disease (IBD), a fatal condition characterized by behavioral abnormalities and wasting. Although many reptarenaviruses have been identified thus far, the phylogenetic gaps between reptarenaviruses and the other arenaviruses suggest the existence of yet-to-be-identified reptarenaviruses filling the gaps. In this study, we identified a novel reptarenavirus from publicly available RNA-seq data derived from Amazon coral snake (Micrurus spixii) and tentatively named it Amazon coral snake virus 1 (ACSV-1). We identified four ACSV-1 contigs containing the putative full-length open reading frames of the NP, GP, and L genes, as well as the partial Z gene. Phylogenetic analyses showed that ACSV-1 is highly divergent from known reptarenaviruses. The NP, GP, and L genes showed 48.3%, 42.3%, and 45.7% nucleotide sequence identities, respectively, with those of the closest relatives. Based on the International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria, ACSV-1 can be assigned to a novel species of virus within the genus Reptarenavirus. This study expands our understanding of the diversity and evolution of reptarenaviruses.

BackgroundSince mid-December 2019, a cluster of pneumonia-like diseases caused by a novel coronavirus, now designated COVID-19 by the WHO, emerged in Wuhan city and rapidly spread throughout China. Here we identify the clinical characteristics of COVID-19 in a cohort of patients in Shanghai. MethodsCases were confirmed by real-time RT-PCR and were analysed for demographic, clinical, laboratory and radiological features. ResultsOf 198 patients, the median duration from disease onset to hospital admission was 4 days. The mean age of the patients was 50.1 years, and 51.0% patients were male. The most common symptom was fever. Less than half of the patients presented with respiratory systems including cough, sputum production, itchy or sore throat, shortness of breath, and chest congestion. 5.6% patients had diarrhoea. On admission, T lymphocytes were decreased in 45.8% patients. Ground glass opacity was the most common radiological finding on chest computed tomography. 9.6% were admitted to the ICU because of the development of organ dysfunction. Compared with patients not treated in ICU, patients treated in the ICU were older, had longer waiting time to admission, fever over 38.5{degrees} C, dyspnoea, reduced T lymphocytes, elevated neutrophils and organ failure. ConclusionsIn this single centre cohort of COVID-19 patients, the most common symptom was fever, and the most common laboratory abnormality was decreased blood T cell counts. Older age, male, fever over 38.5{degrees}C, symptoms of dyspnoea, and underlying comorbidity, were the risk factors most associated with severity of disease.

BackgroundCoronavirus disease 19 (COVID-19) has become a global unprecedented pandemic infecting more than one millon people, which is declared by WHO as a international public health emergency. Eosinopenia may predict a poor prognosis of COVID-19. However, to date, there is no detailed analysis of the clinical characteristics of COVID-19 patients with eosinopenia. Research questionThe aim of this study was to describe clinical characteristics of COVID-19 patients with eosinopenia. Study Design and MethodsThis was a multi-center retrospective study conducted in three tertiary hospitals. A total of 59 patients with COVID-19 were reviewed from January 23, 2020 to March 10, 2020. We described clincial characteristics of patients with COIVD-19 and eosinopenia phenotype. ResultsThe median age of patients with COVID-19 was 39 years old, and 32 (54,2%) were male. Patients with severe type had higher proportions of dyspnea (50%) and gastrointestinal symptoms (50%) compared with mild or moderate patients. Laboratory findings indicated that lower counts of lymphocyte and eosnophils were observed in patients with severe type. Cough, sputum, and fatigue were more common symptoms in eosinopenia patients compared with non-eosinopenia patients. High proportion of comorbidities was observed in eosinopenia patients. Laboratory findings indicated that lymphocyte counts (median: 101 cells/l) in eosinopenia patients were significantly less than those of non-eosinopenia patients (median: 167 cells/l, p<0.001). The use of corticosteroids therapy in COVID-19 patients with eosinopenia were notably higher than those in patients with non-eosinopenia (50% vs 13.8%, respectively, p=0.005). Compared with parameters in non-eosinopenia patients, eosinopenia patients were more inclined to have less lymphocyte counts (OR value 6.566, 95%CI[1.101-39.173], p=0.039). InterpretationEosinopenia are very common in COVID-19 patient, particularly in severe patients. Common symptoms included fever, cough, sputum, and fatigue are frequent in eosinopenia patients. Eosinopenia may represent a novel phenotype in COVID-19, which needs further investigation.

Tomato yellow leaf curl disease (TYLCD) is a major viral disease severely affecting tomato crops in the Mediterranean region, leading to reduced crop yield and significant economic losses. The disease is caused by monopartite begomoviruses belonging to the Geminiviridae family, primarily tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl virus (TYLCV), which often co-infect tomato plants, promoting the emergence of recombinant viral genomes. To investigate the diversity and evolutionary dynamics of these viruses, symptomatic plants collected from agricultural sites in Sicily between 2020 and 2022, along with archived plant samples from 1994 to 1999, were analyzed. For each collection site, leaves from symptomatic plants were pooled to form representative samples. Total nucleic acids were extracted and subjected to rolling circle amplification to enrich circular viral genomes. The amplified products were sequenced using Oxford Nanopore Technologies (ONT) long-read sequencing to obtain full-length viral genomes. Bioinformatic analyses revealed that archived samples exclusively contained TYLCSV-related sequences, confirming its historical predominance in Sicilian agroecosystems. Recent samples, by contrast, no longer contained TYLCV or TYLCSV parental genomes but were dominated by TYLCV-derived recombinants such as TYLCV-IS141- and TYLCV-IS76-like variants, indicating a temporal shift in the structure of the viral population. Furthermore, a distinct group of newly emerged recombinants, provisionally referred to as TYLCV-IMS54, was identified in the most recent samples. Their genome comprises a TYLCV backbone, a 54-nucleotide segment from TYLCSV located downstream of the stem-loop region, and an 341-nucleotide region derived from TYLCV-Mild. These results demonstrate the importance of continuous viral population monitoring through ONT-based sequencing to detect emerging variants that may influence disease management strategies in tomato crops and highlight the central role of recombination in shaping begomovirus populations. IMPACT STATEMENTTomato yellow leaf curl disease (TYLCD) is one of the most damaging viral diseases affecting tomato crops in the Mediterranean basin, yet the long-term dynamics of its causal agents and the role of recombination remain challenging due to the genome plasticity of these viruses. This study provides an updated and comprehensive picture of the begomovirus population structure in Sicily, a key agricultural region for tomato production, by analyzing both contemporary and historical plant samples. Through the application of ONT long-read sequencing combined with RCA and bioinformatic analyses, this research identified persistent recombinant genotypes including a distinct group of newly emerged recombinants, named TYLCV-IMS54. These findings expand current knowledge on the genetic variability and evolutionary processes shaping begomovirus populations in Sicilian agroecosystems. The detection of recombinant genomes highlights the enduring role of recombination in begomovirus diversification. By integrating sequencing data with population and phylogenetic analysis, this work offers valuable insights into the epidemiology and management of TYLCD in regions heavily impacted or newly colonized by these viral pathogens. The study also underscores the importance of continuous molecular surveillance using ONT-based platforms to enable early detection of emerging recombinant variants, with significant implications for plant virology, crop protection and agricultural biosecurity strategies. DATA SUMMARYRaw reads are deposited in the Sequence Read Archive (SRA) of NCBI (https://www.ncbi.nlm.nih.gov/sra) with BioProjects ID PRJNA1226414 and PRJNA1273745; the recombinant TYLCV-IMS54 sequence is available in GenBank with Accession Number PQ873011. Parental TYLCV-strains used in this study could be retrieved in GenBank with the following Acc. Nos: DQ144621 for TYLCV, NC_003828 for TYLCSV, KJ913682 for TYLCV-Mild. Recombinant strains could be retrieved in GenBank with the following Acc. Nos.: LN846609 for TYLCV-IS76 and AF271234 for TYLCMaV. The authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files.

1.Tamarillo or tree tomato (Solanum betaceum Cav.) is a fruit tree species of Andean origin with cultural and economic relevance in Colombia. However, the high incidence of complex viral diseases termed "virosis" in all tamarillo-growing regions of the country leads to huge production losses and seriously threatens its cultivation. The lack of effective treatments implies eradication as the only alternative in severe cases. In this work, we characterized the virome of eight tamarillo-growing locations across the Department of Narino (Colombia). By in-depth sequence analysis of RNA libraries, we confirmed the presence of up to four different virus species belonging to the genera Torradovirus, Potyvirus and Polerovirus in symptomatic tamarillo plants. These results represent the first report of torradovirus infection in tamarillo. Additionally, we identified a novel isolate of potato virus Y-Tamarillo (PVY-Tam) in Narino that could have originated in South America by a recent divergence of the PVYN lineage. We propose that length variability in the P3N-PIPO protein, which in the case of PVY-Tam contains two premature stop codons not identified in other PVY isolates, might be involved with host-specific adaptations. Our findings broaden the knowledge of tamarillo virosis in the Andean region, and overall, worldwide, thus offering new possibilities for developing effective diagnostic and control strategies.

Sobemovirus ryegrass mottle virus (RGMoV) is a single-stranded positive virus with a 30 nm viral particle size. It exhibits T=3 symmetry, with 180 coat protein (CP) subunits forming the virus structure. The RGMoV genome comprises five open reading frames, encoding P1, Px, a membrane-anchored 3C-like serine protease, a virus genome-linked protein, P16, an RNA-dependent RNA polymerase, and a coat protein. The RGMoV genome size varies, ranging from 4175 nt (MW411579.1) to 4253 nt (MW411579.1) in deposited sequences. An earlier deposited RGMoV complete genome sequence of 4212 nt length (EF091714.1) was utilized to develop an infectious complementary DNA (icDNA) construct for in vitro gRNA transcription from the T7 promoter. However, when the transcribed gRNA was introduced to oat plants, it failed to induce viral infection. This indicated the potential absence of certain sequences in either the 5 or 3 untranslated regions (UTR) or both. To resolve this, the complete sequence of the 3 UTR was determined through 3 end RACE, while the 5 UTR was identified using high-throughput sequencing (HTS) - 5 RACE-seq. Only the icDNA vector containing both newly identified UTR sequences proved infectious, resulting in classical viral infection symptoms and subsequent propagation of progeny viruses, exhibiting the ability to cause repeated infection in oat plants after at least one passage. The successful generation of the icDNA highlights the synergistic potential of utilizing both methods when one approach alone fails. Furthermore, this study demonstrates the reliability of HTS as a method for determining the complete genome sequence of viral genomes.

BackgroundThe pandemic of coronavirus disease 2019 (COVID-19) has become the first concern in international affairs as the novel coronavirus (SARS-CoV-2) is spreading all over the world at a terrific speed. The accuracy of early diagnosis is critical in the control of the spread of the virus. Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test. ObjectiveSummarize the baseline characteristics and laboratory examination results of hospitalized COVID-19 patients. Analyze the factors that could interfere with the early diagnosis quantitatively to support the timely confirmation of the disease. MethodsAll suspected patients with COVID-19 were included in our study until Feb 9th, 2020. The last day of follow-up was Mar 20th, 2020. Throat swab real-time RT-PCR test was used to confirm SARS-CoV-2 infection. The difference between the epidemiological profile and first laboratory examination results of COVID-19 patients and non-COVID-19 patients were compared and analyzed by multiple logistic regression. Receiver operating characteristic (ROC) curve and area under curve (AUC) were used to assess the potential diagnostic value in factors, which had statistical differences in regression analysis. ResultsIn total, 315 hospitalized patients were included. Among them, 108 were confirmed as COVID-19 patients and 207 were non-COVID-19 patients. Two groups of patients have significance in comparing age, contact history, leukocyte count, lymphocyte count, C-reactive protein, erythrocyte sedimentation rate (p<0.10). Multiple logistic regression analysis showed age, contact history and decreasing lymphocyte count could be used as individual factor that has diagnostic value (p<0.05). The AUC of first RT-PCR test was 0.84 (95% CI 0.73-0.89), AUC of cumulative two times of RT-PCR tests was 0.92 (95% CI 0.88-0.96) and 0.96 (95% CI 0.93-0.99) for cumulative three times of RT-PCR tests. Ninety-six patients showed typical pneumonia radiological features in first CT scan, AUC was 0.74 (95% CI 0.60-0.73). The AUC of patients age, contact history with confirmed people and the decreased lymphocytes were 0.66 (95% CI 0.60-0.73), 0.67 (95% CI 0.61-0.73), 0.62 (95% CI 0.56-0.69), respectively. Taking chest CT scan diagnosis together with patients age and decreasing lymphocytes, AUC would be 0.86 (95% CI 0.82-0.90). The age threshold to predict COVID-19 was 41.5 years, with a diagnostic sensitivity of 0.70 (95% CI 0.61-0.79) and a specificity of 0.59 (95% CI 0.52-0.66). Positive and negative likelihood ratios were 1.71 and 0.50, respectively. Threshold of lymphocyte count to diagnose COVID-19 was 1.53x109/L, with a diagnostic sensitivity of 0.82 (95% CI 0.73-0.88) and a specificity of 0.50 (95% CI 0.43-0.57). Positive and negative likelihood ratios were 1.64 and 0.37, respectively. ConclusionSingle RT-PCR test has relatively high false negative rate. When first RT-PCR test show negative result in suspected patients, the chest CT scan, contact history, age and lymphocyte count should be used combinedly to assess the possibility of SARS-CoV-2 infection.

ObjectiveTo compare the sex differences in the clinical findings among patients with severe coronavirus disease 2019 (COVID-19). MethodsWe retrospectively collected data of 47 patients diagnosed as severe type of COVID-19 from February 8 to 22, 2020, including demographics, illness history, physical examination, laboratory test, management, and compared differences between men and women. ResultsOf the 47 patients, 28 (59.6%) were men. The median age was 62 years, and 30 (63.8%) had comorbidities. The initial symptoms were mainly fever (34 [72.3%]), cough (36 [76.6%]), myalgia (5 [10.6%]) and fatigue (7 [14.9%]). Procalcitonin level was higher in men than in women (0.08 vs. 0.04ng/ml, p=0.002). N-terminal-pro brain natriuretic peptide increased in 16 (57.1%) men and 5 (26.3%) women (p=0.037). Five men (17.9%) had detected positive influenza A antibody, but no women. During 2-week admission, 5 (17.9%) men and 1 (5.3%) woman were reclassified into the critical type due to deterioration. Mortality was 3.6% in men and 0 in women respectively. Four (21.1%) women and one man (3.6%) recovered and discharged from hospital. ConclusionSex differences may exist in COVID-19 patients of severe type. Men are likely to have more complicated clinical condition and worse in-hospital outcomes as compared to women.

Protein structures are central to understanding the diversity and biological function of RNA viruses. However, few experimentally validated structures of RNA viruses are currently available. To address this gap, we established the RNA Viral Protein Structure Database (RVPSD) that comprises diverse RNA viral protein structures predicted using AlphaFold2. RVPSD integrates taxonomic classification, viral nucleotide and protein sequences, functional annotations, and predicted three-dimensional protein structures to support a systematic exploration of the RNA viral proteomes. Currently, RVPSD comprises a total of 154,716 AlphaFold2-predicted RNA viral protein structures from 5,263 RNA virus species, with 84.9% exhibiting high pLDDT scores (>70) and representing a large-scale and comprehensive resource for RNA viral protein structures. RVPSD also provides a user-friendly web interface, with advanced search, sequence- and structure-based retrieval, interactive 3D visualization, and access and downloading structural data, enabling researchers to perform comparative structural analyses and functional annotation of viral "dark matter".

BackgroundDefining the clinical features and associated outcomes of patients diagnosed with corona virus disease (COVID-19) is fundamental to improving our understanding and adequate management of this illness. The aim of this study was to identify the demographic data, underlying comorbidities and the mortality related factors of hospitalized patients with COVID-19 in Upper Egypt. Patients and methods1064 cases consecutively admitted to isolation hospitals in Upper Egypt. All cases had confirmed COVID-19 infection. The electronic records of the patients were retrospectively revised and the demographic data, clinical manifestations, qSOFA score on admission and 30 days-outcome (ICU admission, death, recovery, referral or still in hospital) were analyzed. Overall cumulative survival in all patients and those > or < 50 years were calculated. Results49.2% of the study population were males and 50.8% were females with mean age 49.4{+/-}17.8 years-old. On admission, 83.9% were stable with qSOFA score <1, 3% required non-invasive mechanical ventilation, and 2.1% required O2 therapy. Within 30 days, 203 cases (19.1%) required admission to ICU. Death was recorded in 11.7% of cases, 28.7% recovered, 40.5% referred and 19.2% were still under treatment. Determinants of ICU admission and survival in the current study were age > 50, respiratory rate > 24/minute, SaO2 < 89%, qSOFA >1 and need for O2 therapy or NIV. The cumulative survival was 75.3% with the mean survival was 28.1, and 95.2% overall survival was recorded in those aged [&le;]50 years. ConclusionsAge older than 50 years old, those with pre-existing DM, initial qSOFA score, requirement for O2 therapy and NIV from the first day of hospital admission may be associated with unfavorable 30 days- in hospital outcome of COVID-19.

Nidoviruses (the order Nidovirales) are positive strand RNA viruses, and the order currently contains 14 families, 48 genera, and 130 species. Novel nidoviruses have been identified in a variety of animal hosts, but many phylogenetic gaps remain, suggesting the presence of yet-to-be-identified viruses. In this study, we identified a novel nidovirus from publicly available RNA-seq data obtained from the blood of the common chameleon (Chamaeleo chamaeleon recticrista [Boettger, 1880]), and tentatively named it common chameleon nidovirus 1 (CCNV-1). Phylogenetic analysis showed that CCNV-1 is clustered with a member of the family Nanhypoviridae and some unclassified viruses designated as arteriviruses. Further, CCNV-1 genetically distinct from known viruses, exhibiting 50.9% amino acid identity in the RdRp sequence to its closest relative, Jingmen rodent arterivirus 1. Thus, this study provides novel insights into the diversity of nidoviruses.

Marseilleviruses are a group of double-strand DNA viruses that infect amoeba within the Nucleocytoviricota phylum and are ubiquitous in water and soil globally. Here, we report four novel strains isolated from mangroves in Guangdong province, China, namely, futianmevirus, futianmfvirus, dashavirus str. E, and xiwanvirus. Viral particles presented about 220[~]240 nm icosahedrally shaped capsids and were wrapped by membranes to form giant vesicles. Based on stability assays, viral particles were halotolerant and acid-tolerant, but sensitive to chloroform and high temperature, while giant vesicles conferred thermal and acid/alkaline resistance to particles. Genomics and phylogenetic analyses showed that the four strains formed divergent branches within different lineages of marseillevirus. Notably, to our knowledge, futianmevirus was the first reported marseillevirus lacking translation elongation factor EF-1alpha (EF1A). Our in silico analysis of marseillevirus coded translation-associated homolgs suggested their conserved functions. Additionally, we predicted at least four novel proteins that were structurally similar to components of the protozoan ribosome. Overall, not only our data comprehensively described the diversity of marseillevirus biological properties, but also proposed a new perspective on the giant virus translation system. ImportanceThe family Marseilleviridae was the second reported family of giant viruses and distributed globally. In this work, we reported the four novel marseilleviruses isolated from saltwater samples of mangrove. Difference of biological properties between giant vesicles and viral particles revealed the environment fitness of marseillevirus. On the other hand, sensitivity to chloroform indicated the importance of lipid components for viral infection. Additionally, our comparative genomics, phylogenetic analysis, and protein structure comparison revealed the diverse translation-associated gene sets of marseilleviruses. The prediction of ribosome components expands the knowledge about the giant viral translation-associated proteins, and will be helpful in future to reveal how giant viruses hijack the amoeba translation system.

ABSTRACTPlant viral infections pose a significant threat to global crop productivity. Despite their profound impact on agriculture, plant viruses have been relatively understudied, primarily due to technological limitations associated with classical molecular methods. However, the advent of NGS RNA-seq analysis has revolutionized virus characterization in environmental settings, overcoming previous limitations and providing a powerful tool for studying plant viruses. In an RNA-seq experiment conducted on a diseased Colombian Cannabis sativa hemp plant, we identified a linear single-stranded RNA (ssRNA) genome belonging to Tobacco Necrosis Virus A (TNVA), a common cause of necrotic lesions in plants such as tobacco and tulipa. The affected Cannabis sativa hemp plant exhibited severe symptoms, including alterations in pigmentation, leaf morphology such as chlorosis, necrotic tissue formation, and surface wear on the leaves. The complete genome sequence of the Cannabis sativa TNVA was 3,656 nucleotides long, containing five putative ORFs, and was classified in the family Tombusviridae, genus Alphanecrovirus, and belonging to the Necro-like clade based on RdRp protein phylogenetic analysis. Our analysis revealed a well-conserved RdRp protein among the Alphanecroviruses, with 89% of the amino acid residues in the peptide being entirely conserved. In contrast, the coat protein exhibited significantly higher variability, with only 49.3% of the residues being 100% conserved. Regarding the viral genome expression of Cannabis sativa TNVA, we observed that the virus was highly abundant in the leaves of the diseased plant, ranking among the topmost abundant transcripts, occupying the percentile position of 3.06%. Overall, our study generated the first reference genome of TNVA virus in the tropical region and reported the first case of this virus infecting a Cannabis sativa plant.

Recent advances in sequencing technology and transcriptome mining have revealed highly divergent hepaciviruses in birds. However, only a limited number of avian hepaciviruses have been identified to date, leaving their diversity and evolutionary history poorly understood. Moreover, deep phylogenetic gaps among known avian hepaciviruses suggest that additional lineages remain undiscovered. Here, we screened publicly available RNA-seq data and identified three previously undescribed hepaciviruses from rock pigeon (Columba livia), rusty-margined flycatcher (Myiozetetes cayanensis), and Hispaniolan amazon (Amazona ventralis), named rock pigeon hepacivirus (RpHV), rusty-margined flycatcher hepacivirus (RfHV), and Hispaniolan amazon hepacivirus (HaHV). Although these three viruses meet the ICTV species demarcation criteria relative to their closest known relatives, the NS5B-based criterion was not satisfied between RfHV and HaHV. Notably, however, their genome sequence identity is low at 43.2%, and their hosts differ at the order level, suggesting that their classification warrants further consideration. Our phylogenetic analysis showed that avian hepaciviruses, including those found in this study, are monophyletic, but phylogenetic incongruence was observed between avian hepaciviruses and their hosts, suggesting past cross-species transmission among avian hepaciviruses. Overall, this study provides novel insights into the diversity and evolution of hepaciviruses.

Coronavirus 2019 infection (COVID-19) outbroke in Wuhan, Hubei and spread to all provinces in China and other countries. Shenzhen ranked the top cities outside Wuhan with reported 416 confirmed cases by February 20, 2020. Here, we analyzed the epidemiological characteristics of COVID-19 in Shenzhen and potential link to the preventive strategies for the whole city and inside hospitals. Based on the daily new cases, the epidemic of COVID-19 in Shenzhen can be classified into three phases: the slow increase phase from January 19 to January 28, the rapid increase and plateau phase from January 29 to February 5 and the decline phase since February 6. In the three phases, the number of patients from Hubei decreased, and the number of familial clustering cases increased. The newly diagnosed COVID-19 cases reached its peak around January 31, which was 7 days after the peak date of cases arrival at Shenzhen. A series of early preventive strategies were implemented since January 19, which included detection of body temperature at all entrances of main traffic and buildings, outpatients service specially for patients with fever in all main hospitals in Shenzhen. All the patients with fever were screened with nasal or throat swab PCR detection of coronavirus 2019, Chest CT and blood lymphocyte counting in order to find out early case of COVID-19. Observation wards were established in every main hospital and a designated hospital was responsible for admission and medical care of all confirmed cases. Protection procedure was established for all medical staff involved in the screening and care of suspected and confirmed cases. 14 days isolated observation of all subjects arrived at Shenzhen from Hubei was implemented in February 2. After the implementation of all these strategies and measures, the COVID-19 cases started to decline since February 6. There were almost no community transmission and nosocomial infection occurred in Shenzhen. In conclusion, in situation of major outbreak of respiratory infectious disease, such as COVID-19, in nearby province of Hubei, Shenzhen, a high population density, high proportion of external population and high mobility city, has to face the imported cases and risk of spreading the outbreak into Shenzhen city. The implementation of early preventive strategies and measures in Shenzhen were successful in early identification of COVID-19 cases and prevented major outbreak occurred in Shenzhen. Early identification of imported cases, prevention of family clustering transmission, preventive measures in the public area and very strict infection control procedure in hospital setting are crucial for the successful control of outbreak in Shenzhen.

PurposeCoronavirus disease (COVID-19) pandemic is now a global health concern. However, there is no detailed analysis of the factors related to patients improvement. Patients and methodsWe compared the clinical characteristics, laboratory findings, CT images, and treatment of COVID-19 patients from two different cities in China. One hundred and sixty-nine patients were recruited from January 27 to March 17, 2020 at five hospitals in Hubei and Guangxi. They were divided into four groups according to age and into two groups according to presence of comorbidities. Multivariate statistical analyses were performed for the prognosis of the disease. ResultsFifty-two patients (30.8%) had comorbidities, and the percentage of critical COVID-19was higher in the comorbidities group (11.6%vs.0.9%, p<0.05). Older patients had higher proportion of severe or critical disease. The results showed that lymphocyte count was significantly associated with the number of days from positive COVID-19 nucleic acid test to negative test; number of days from onset of symptoms to confirmation of diagnosis was significantly associated with the time it took for symptoms to improve; and number of days from onset of symptoms to confirmation of diagnosis and disease severity were significantly associated with chest computed tomography improvement. ConclusionsAge, comorbidities, lymphocyte count, and SpO2 may predict the risk of severity of COVID-19. Early isolation, early diagnosis, and early initiation of management can slow down the progression and spread of COVID-19. Key PointsAge and comorbidities can predict the risk of severity of COVID-19, Lymphocyte count and SpO2 may predict the risk of severity of COVID-19. Early isolation, Early diagnosis can slow down the progression of COVID-19

Seasonal influenza (flu) is an underappreciated source of disease morbidity and mortality worldwide. While vaccination remains the cornerstone of influenza prevention, common measures practiced during the COVID-19 pandemic such as social distancing, the use of protective face masks, and frequent hand washing are rarely utilized during flu season. In this investigation, we examined the effect of these preventative measures in decreasing influenza burden this year. We examined three countries with major COVID-19 outbreaks i.e. China, Italy and the United States, and compared the flu activity this year to the average of the last 4 years (2015-2019). We found that this year in China and Italy, there was a significantly steeper decline of flu cases than average, which correlated with an increase in positive COVID-19 case reports in those countries. These "averted" cases can be translated into a substantial decrease in morbidity and mortality. As such, we conclude that the current COVID-19 pandemic is a reminder that behavioral measures can decrease the burden of communicable respiratory infections, and these measures should be adopted to an extent during normal influenza season.