Novel Virus Research Articles

Prediction of the effects of environmental factors towards novel corona virus (COVID-19) outbreak using AI-based models

The need for elucidating the effects of environmental factors in the determination of the novel corona virus (COVID-19) is very vital. This study is a methodological study to compare three different test models (1. Artificial neural networks (ANN), 2. Adaptive neuro fuzzy inference system (ANFIS), 3. A linear classical model (MLR)) used to determine the relationship between COVID19 spread and environmental factors (temperature, humidity, wind etc.). Three different models were used including two artificial intelligence (AI) based models (artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS)) and a linear regression model (multilinear regression analysis (MLR). These data were obtained from the studies (Pirouz, Haghshenas, Haghshenas, & Piro, 2020) with confirmed COVID-19 patients in Wuhan, China, using temperature, humidity and wind as the independent variables. The measured and the predicted results were checked based on three different performance indices; Root mean square error (RMSE), determination coefficient (R 2 ) and correlation coefficient (R). The results showed that ANFIS and ANN are more promising over the classical MLR models having an average R-values of 0.90 in both calibration and verification stages. The findings indicated that ANFIS outperformed MLR and ANN. In addition, their performance skills boosted up to 25% and 9% respectively based on the determination coefficient for the prediction of confirmed COVID-19 cases in Wuhan city of China. Overall, the results depict the reliability and ability of AI-based models (ANFIS and ANN) for the simulation of COVID-19 using the effects of various environmental variables.

A non-redundant, reference virus database (RVDB) to facilitate high-throughput sequencing (HTS) bioinformatics analysis for detection of known and novel viruses

A non-redundant, reference virus database (RVDB) to facilitate high-throughput sequencing (HTS) bioinformatics analysis for detection of known and novel viruses

Clinical outcomes of Patients infected with Novel Corona virus COVID- 19 at Covid Center in Dehradun, Uttarakhand

Novel Corona virus, COVID – 19, virus is highly contagious, and has become pandemic globally in a very short period. This virus in human can cause illness ranging from common cold to severe respiratory tract symptoms as MERS, SARS. In the present study we report the clinical outcome of patients infected with COVID- 19, in Covid Center, GDMC, Dehradun, Uttarakhand. Material and Methods- All the patients infected with COVID- 19 in Garhwal region Uttarakhand, were admitted in Covid center, GDMC, Dehradun. We collected and analyzed the Data of laboratory confirmed COVID – 19 infection by RT- PCR. We also communicated with the patients and their family members regarding disease symptoms. Clinical outcome was compared and documented. The study protocol was approved by Ethical committee of GDMC, Dehradun, Uttarakhand. Results-About 4/5th patients were males, most of the patients were aged between 21-30 years. Most of the patients (84.1%) were residents of Dehradun and all patient were Indian. Mortality rate was 1% in this study. Females had more complaint of pain abdomen while males had more complaint of chills (p-value <0.05). Conclusion- An outbreak of novel Coronavirus, COVID–19 disease has affected worldwide and continue to represent a serious public health issue affecting all ages. Complications and mortality were higher in elderly and comorbid patients. Clinical presentation of the disease was less severe in Dehradun, Uttarakhand and mortality rate is much lower than the other parts of the world.

COVID-19 Diarrhea

In 2019, a novel virus emerged in Wuhan, China that caused a febrile respiratory illness, sometimes rapidly fatal and thought to be transmitted by droplet contact. It likely originated from another species (possibly the bat), but later, spread occurred from human-to-human. Over a period of months, this disease disseminated to more than 100 nations as a highly infectious pandemic, reminiscent of disease associated with other coronavirus agents in 2002 (SARS) and 2012 (MERS). This COVID-19 virus also caused other forms of clinical illness, albeit in the minority, and most infected patients (over 50%) had few symptoms or remained completely asymptomatic. Prominent in some patients was watery diarrhea, often lasting less than a week, but sometimes without any respiratory features, such as fever, cough or shortness of breath. It is believed that fecal-oral transmission may result. The virus attaches to the surface of human respiratory and intestinal cells, gains entry into these cells, ultimately leading to production of new virions intraluminally. Fecal shedding may occur for extended periods, even after respiratory secretions become negative. Apart from preventive measures, vaccine development remains the most important strategy.

A Study of Covid -19 –Issues and Problems

This is a crucial time for all of us due to rapidly spreading coronavirus throughout the world from one person to another one through cough, sneezing and physical touch within one meter distance In this circumstances all of us have the most common emotions is fear It will makes anxious, emotional issues and mental health problems among the people Outbreaks of novel virus infections among people are always of public health concern The risk from these outbreaks depends on characteristics of the virus, including how well it spreads between people the severity of resulting illness and the medical or other measures available to control the impact of the virus This disease has become pandemic because it has caused illness also resulting in death in some cases As the novel coronavirus continues to spread some countries are patting their citizens on various forms lockdown, social distancing and also implementing the world's largest and most restrictive mass quarantines Lock down period that has made people live in fear of losing their business, jobs, earnings and savings or even basic resources Lockdown, social distancing, quarantines, isolation have had a massive impact on the life style of people They are staying indoors with limited resources so that they are now suffering from anxiety, panic attacks, and even alcohol withdrawal syndrome

An eye to the future

Novel virus: new problems and new lessons.

100-Year-Old Vaccine for a Novel Virus: Killing Two Birds with One Stone!

100-Year-Old Vaccine for a Novel Virus: Killing Two Birds with One Stone!

Distribution and significance of angiotensin-converting enzyme 2, a key receptor of 2019-nCoV, in ocular tissues

Corona virus disease-19 (COVID-19) outbroke in the end of 2019 in Wuhan and is spreading worldwide, and its pathogeny is 2019 novel corona virus (2019-nCoV). 2019-nCoV mainly causes human respiratory infection and pulmonary inflammation, however, some COVID-19 patients are found to present viral conjunctivitis. Bilateral viral conjunctivitis is an initial symptom in some other cases. It is vital for us to know whether the eye can be directly infected by the virus and the consequence of the viral infection in ocular tissue. 2019-nCoV invades human cells primarily through binding to the angiotensin-converting enzyme 2 (ACE2) receptors. ACE2 expresses not only in lung, kidney, and cardiovascular system, but also in human cornea, conjunctiva, aqueous humor and retina. Therefore, it is crucial to expand our understanding of the infection mechanism and pathogenesis of COVID-19 comprehensively by clarifying the distribution of ACE2 in the eye. ACE2 is not only the receptor of 2019-nCoV, but also a key enzyme in renin-angiotensin system (RAS). RAS, which appears relatively independent in the eye, plays a modulate role in the eye and is associated with many common eye diseases. This article reviews the distribution and clinical significance of ACE2 in ocular tissues. Key words: Angiotensin-converting enzyme 2; Eye; Novel corona virus; Infection; Renin-angiotensin system

Dynamics of transmission of severe acute respiratory syndrome coronavirus 2 and its control measures

Coronavirus disease 2019 (COVID-19) caused by the β coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a zoonotic disease that has spread beyond the site of outbreak in Wuhan, China, to become a pandemic of magnanimous proportions. As the whole world is reeling under the burden of its morbidity and mortality, researchers are busy tracing its origin, deciphering its transmission dynamics, devising new, rapid, inexpensive, accurate diagnostic modalities, testing potent vaccines, and exploring effective therapeutic measures. Although till date much is unknown about the novel virus, the present review attempts to provide an insight to the transmission dynamics of SARS CoV2 and cover the various control measures that has been adopted to control its transmission.

Cytokine storm in COVID-19 and the treatment simulacrum

Following the outbreak of the severe acute respiratory syndrome-coronavirus (SARS-CoV-2) in December 2019 at Wuhan, China, it spread through the world rapidly, and this disease was declared as a pandemic by the World Health Organization on March 11, 2020 A high mortality rate has been detected due to this respiratory involvement;this novel virus like the previous ones, SARS-CoV-1, from this family, can lead to lethal pneumonia, acute lung injury, and eventually acute respiratory distress syndrome (ARDS), which was reported in 20% of patients Surprisingly, this ARDS can have a mortality rate of 40%-50% As it is known that infection can manifest in a wide variety of symptoms, from a mild respiratory disease to life-threatening ARDS, multiorgan dysfunction, shock, and death, the exact mechanism of this ARDS in COVID-19 pneumonia is not known completely There are ongoing studies, but the term 'cytokine storm' can be a possible clue of the transformation of a mild disease to a lethal one, and also an explanation of this rapid and deadly inflammatory response which take a place in the lungs Our goal in this review is to express a better definition of molecular and cellular pathways of cytokine storms and also discuss some recent trials of the effect of different classes of drugs on this immunologic and inflammatory pathway of CoV infection In this study, we have addressed evidences for more efficient immunomodulatory drugs for this vivid storm © 2020 Medknow

Rationality and applicability of Jeevaneeya mahakashaya (Rejuvenating and vitality boosting herbs) in prevention and management of COVID-19

Introduction: COVID-19, caused by SARS-CoV-2 or novel corona virus is declared as a global emergency. Researchers are working hard to develop effective remedy and vaccine, but still the challenge to manage the spread and disease progression is existing. In Ayurveda, a good number of herbs are ascribed for health promotion and longevity; many of them are scientifically proven to boost immunity. Jeevaneeya mahakashaya of Charaka Samhita is such group of ten herbs enumerated for longevity and rejuvenation. However, few of the herbs of Jeevaneeya mahakashaya are endangered and not available easily. Thus, in the present article, the herbs of Jeevaneeya mahakashaya having Pratinidhi (substitutes) suggested in Bhavaprakasha Nighantu were reviewed. Objective: The objective of this study is to analyze the rationality and applicability of Jeevaneeya mahakashaya in the prevention and management of COVID-19. Data Source: The data was collected from Charaka Samhita and Bhavaprakasha Nighantu and PubMed database. Review Methods: Jeevaneeya mahakashaya and its Pratinidhi herbs were reviewed from Charaka Samhita and Bhavaprakasha Nighantu, respectively. Herbs of Jeevaneeya mahakashaya were also reviewed from PubMed data base for reported pharmacological activities beneficial in the management of COVID-19 by their botanical name. Results: The literature search revealed that the herbs enumerated in the Jeevaneeya mahakashaya were scientifically evaluated in various preclinical and clinical studies and showed anti-viral, anti-bacterial, immunomodulatory, anti-inflammatory, anti-oxidant, anti-tussive, cardio-protective, neuroprotective, nephroprotective, and hepatoprotective activity. These potential of herbs may help in CD4+ and CD8+ cell proliferation, interleukin 6, tumour necrosis factor alpha, inflammatory markers inhibition. It also protects various organs from damage, and improves respiration. Conclusion: The rational use of plants of Jeevaneeya mahakashaya may help in the prevention and management of SARS-CoV 2.

Identification and characterization of novel human papillomaviruses in oral rinse samples from oral cavity and oropharyngeal cancer patients

ObjectivesThe objectives of this study were to: I) discover novel human papillomaviruses (HPVs) using next generation sequencing (NGS) technology in oral rinse samples collected from oral cavity cancer (OCC) and oropharyngeal cancer (OPC) patients; II) determine the prevalence of novel HPVs in archived OCC and OPC tissue samples; and III) examine the frequency of novel oncogenic HPVs in cancer and non-cancer oral rinse samples using real-time PCR. MethodsOral rinse samples were collected from 100 head and neck cancer patients, and 110 healthy individuals. NGS techniques were used to detect novel HPVs. ResultsThree potentially new types of HPV were discovered. Novel virus (NV) 14.4 was closely related to HPV76 with an 89% homology and is a member of the genus Beta-papillomavirus (β-PV); NV69.1 was distantly related to the genus Alpha-papillomavirus (α-PV), and NV95 was closely related to HPV147 with a 65–77% homology and is part of the genus Gamma-papillomavirus (γ-PV). In archived oral tissue samples, NV14.4 was detected in a single patient with OCC. Of the oral rinse samples, NV69.1 was more prevalent than the other two NVs. ConclusionsOur results demonstrated that there are novel HPVs present in oral rinse samples that may be associated with OCC and OPC. These novel HPVs can be identified and characterized using NGS techniques.

New guidelines for identifying novel viruses

New guidelines for identifying novel viruses

Genetic origin of avian influenza A H7N4 virus causing a case of human infection in China, 2018

Objective To analyze the molecular characteristics and genetic origin of a novel avian influenza A H7N4 virus casuing a case of human infection in China. Methods Specimens were collected from the patient and chickens and ducks kept by the patient and neighbours and then detected by real-time quantitative PCR. The original specimens and virus isolates were analyzed by next-generation sequencing technology to obtain viral whole-genome sequences. Pairwise sequence alignments and phylogenetic analysis were performed by BLASTs, ClustalX and MEGA 6.1 softwares. Results In January 2018, a human case infected with avian influenza A H7N4 virus was confirmed. Seven H7N4 viruses were isolated from specimens collected from chicken and ducks kept in the patient`s backyard. H7N4 virus was a novel reassortant virus with all eight gene fragments derived from wild waterfowl in Eurasia. HA protein contained a single basic amino acid residue R in cleavage site, suggesting that H7N4 virus was low pathogenic. The receptor-binding sites of HA had QSG at 226-228 residues, which indicated that the virus retained avian-type receptor specificity (SAα2-3Gal). Different from H7N4 viruses in avian, the virus isolated from the patient had substitution at position 627 (E→K) in PB2 protein, which might increase its adaptation in human host. Conclusion This study reported a case of human infection with a novel reassortant avian influenza A H7N4 virus, which revealed that the traditional backyard breeding models might facilitate cross-species transmission of avian influenza viruses in southern China. Key words: Avian influenza A virus; H7N4 subtype; Cross-species transmission

Next generation sequencing technologies in clinical virological detection

Next generation sequencing technologies, providing high speed and throughput that contribute greatly to DNA sequencing, have many applications in clinical virology, including identification of novel or unsuspected viruses, evaluation of human viromes, investigation of viral genetic diversity and evolution, monitoring of antiviral drug resistance, and analysis of virus-host interaction. Meanwhile, due to the complexity in bioinformatics data processing and lack of quality management standards, further efforts and explorations need to be put in the application and quality management of NGS in clinical laboratory.(Chin J Lab Med, 2017, 40: 338-340) Key words: Virology; High-throughput nucleotide sequencing; Genome, viral; Quality control

Effect of a novel oncolytic herpes simplex virus type II on lung adenocarcinoma

Objective To establish the subcutaneous transplantation tumor models with Lewis lung adenocarcinoma in C57BL/6 mice, and to observe the influence of oHSV2, DDP and drug combination on tumor volume, median survival time and weight of tumor-burdened mice. Methods Subcutaneous transplantation tumor models were established with Lewis lung adenocarcinoma in tumor-burdened mice. Tumor-burdened mice were randomly divided into the control group, oHSV2 group, DDP group, oHSV2/DDP sequential group, DDP/oHSV2 sequential group and oHSV2+ DDP combination group with 12 rats in each group using the random number table method. The tumor size and weight of mice were measured every 3 days. Results On the 21st day, the tumor size of tumor-burdened mice in every group was as follows: control group (1.82±0.06)cm3, oHSV2 group (0.63±0.05)cm3, DDP group (0.58±0.03)cm3, oHSV2/DDP sequential group (0.49±0.05)cm3, DDP/oHSV2 sequential group (0.42±0.04)cm3, and the difference was statistically significant (F=1 359.01, P=0.000). The data in oHSV2+ DDP group were put away because of premature death in mice. The differences were statistically significant between control group and oHSV2 group (P=0.000), control group and DDP group (P=0.000), control group and oHSV2/DDP sequential group (P=0.000), control group and DDP/oHSV2 sequential group (P=0.000), oHSV2 group and DDP group (P=0.017), DDP group and DDP/oHSV2 sequential group (P=0.000), oHSV2/DDP sequential group and DDP/oHSV2 sequential group (P=0.001). The weight of tumor-burdened mice in every group was listed as follows: control group (21.64±0.40)g, oHSV2 group (21.34±0.37)g, DDP group (15.96±0.43)g, oHSV2/DDP sequential group (19.04±0.31)g, DDP/oHSV2 sequential group (16.34±0.30)g, and the difference was statistically significant (F=588.67, P=0.000). The difference was not statistically significant between control group and oHSV2 group (P=0.076). However, the differences were statistically significant between control group and DDP group (P=0.000), control group and oHSV2/DDP sequential group (P=0.000), control group and DDP/oHSV2 sequential group (P=0.000), oHSV2 group and DDP group (P=0.000), oHSV2 group and oHSV2/DDP sequential group (P=0.000), DDP group and DDP/oHSV2 group (P=0.013), oHSV2/DDP sequential group and DDP/oHSV2 sequential group (P=0.000). The median survival time of tumor-burdened mice in every group was displayed as follows: control group 23 d , oHSV2 group 32 d, DDP group 30 d, oHSV2/DDP sequential group 37 d, DDP/oHSV2 sequential group 39 d, oHSV2+ DDP combination group 16 d, and the difference was statistically significant (χ2=120.81, P=0.000). The differences were statistically significant between control group and oHSV2 group (χ2=10.88, P=0.001), control group and DDP group (χ2=10.69, P=0.001), oHSV2 group and DDP/oHSV2 sequential group (χ2=10.09, P=0.001), DDP group and DDP/oHSV2 sequential group (χ2=9.67, P=0.002). However, the differences were not statistically significant between oHSV2 group and DDP group (χ2=0.00, P=0.996), oHSV2/DDP sequential group and DDP/oHSV2 sequential group (χ2=2.70, P=0.100). Conclusion On the premise of that the weight of mice is no affected, oHSV2 can inhibit the tumor size and prolong the median survival time of tumor-burdened mice effectively, and the effect of DDP/oHSV2 sequential group is the most significant. This article provides an experimental basis for exploring therapeutic methods of lung adenocarcinoma. Key words: Oncolytic virus; Cisplatin; Lung neoplasms

Avian Influenza Infections Increasing in China

There have now been five annual epidemics in China caused by the novel avian influenza virus A(H7N9) since 2013 involving a total of 1258 people.

New Tools to Research Novel Virus

New Tools to Research Novel Virus

Epidemic pattern and molecular variation of respiratory syncytial virus strains isolated in Shenzhen from year 2012 to 2013

Objective To study the epidemic pattern and molecular variation of respiratory syncy-tial virus （ RSV） strains isolated in Shenzhen from year 2012 to 2013.Methods The clinical samples iso-lated from patients with influenza-like illness were analyzed by fluorescent RT-PCR to screen RSV positive strains.The C-terminal variable regions of genes encoding G proteins were amplified by nested RT-PCR. Molecular variation was analyzed by using Clustal W and MEGA softwares.Results RSV strains were wide-ly prevalent in Shenzhen from 2012 to 2013.Two epidemic peaks usually occurred in spring and summer/au-tumn of each year.The RSV isolates were subtyped into group A belonging to genotype NA1 and group B be-longing to genotype BAⅨ.Most of the mutations scattered at the C-terminal region of G protein.A few mu-tations caused the disappearance of certain glycosylation sites.A novel recombinant virus strain containing 24 inserted amino acids was identified in 2013, which was likely to be introduced into our country from abroad. Conclusion RSV strains were widely and continuously prevalent in Shenzhen, characterized by constant evolution and variation. Key words: Respiratory syncytial virus; Epidemic pattern; Molecular variation

VIRUSES OF KIWIFRUIT (ACTINIDIA SPECIES)

Kiwifruit (Actinidia deliciosa) was introduced to New Zealand more than one hundred years ago and the New Zealand-raised cv. Hayward is now the dominant cultivar grown worldwide. Further accessions of kiwifruit seed and scionwood have been sourced from China for research and breeding. In one importation consignment, the first virus naturally infecting kiwifruit, Apple stem grooving virus (ASGV), was identified following symptoms observed in quarantined plants (2003). Since that time a further 12 viruses have been identified in kiwifruit. We classify these 13 viruses into three groups. The first group comprises the non-specialist viruses and includes Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV) both members of the family Bromoviridae. The group also includes a further five viruses that appear to have limited effect on kiwifruit: two tobamoviruses, Ribgrass mosaic virus (RMV) and Turnip vein clearing virus (TVCV); a tombusvirus, Cucumber necrosis virus (CNV); a novel potexvirus; and Apple stem gooving virus (ASGV, genus Capillovirus). Most of the viruses classified in this first group are cosmopolitan and sometimes orchard weeds provide reservoirs for infection. The second group comprises the kiwifruit-adapted viruses. This group includes three novel viruses. i.e. two vitiviruses, Actinidia virus A (AcVA) and Actinidia virus B (AcVB), and a citrivirus closely related to Citrus leaf blotch virus (CLBV). In addition, preliminary evidence of a novel virus belonging to the Closteroviridae family has been obtained. The third group of viruses induces disease in kiwifruit. To date only two viruses have caused significant damage to kiwifruit within commercial orchards. In New Zealand, Cherry leaf roll virus (CLRV) has been detected on kiwifruit associated with symptoms including leaf spots, fruit malformation, reduction in yield, bark cracking and cane wilting. Pelargonium zonate spot virus (PZSV) has been detected in Italy associated with severe symptoms on leaves and fruit.