scholarly journals Attenuated infection by a Pteropine orthoreovirus isolated from an Egyptian fruit bat in Zambia

2021 ◽  
Vol 15 (9) ◽  
pp. e0009768
Author(s):  
Hayato Harima ◽  
Michihito Sasaki ◽  
Yasuko Orba ◽  
Kosuke Okuya ◽  
Yongjin Qiu ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Phylogenetic Analyses ◽  
Respiratory Illness ◽  
Replication Capacity ◽  
Fruit Bats ◽  
Rt Pcr ◽  
Fruit Bat ◽  
Eidolon Helvum ◽  
Severe Respiratory Illness ◽  
Generation Sequencing

Background Pteropine orthoreovirus (PRV) is an emerging bat-borne zoonotic virus that causes severe respiratory illness in humans. Although PRVs have been identified in fruit bats and humans in Australia and Asia, little is known about the prevalence of PRV infection in Africa. Therefore, this study performed an PRV surveillance in fruit bats in Zambia. Methods Egyptian fruit bats (Rousettus aegyptiacus, n = 47) and straw-colored fruit bats (Eidolon helvum, n = 33) captured in Zambia in 2017–2018 were screened for PRV infection using RT-PCR and serum neutralization tests. The complete genome sequence of an isolated PRV strain was determined by next generation sequencing and subjected to BLAST and phylogenetic analyses. Replication capacity and pathogenicity of the strain were investigated using Vero E6 cell cultures and BALB/c mice, respectively. Results An PRV strain, tentatively named Nachunsulwe-57, was isolated from one Egyptian fruit bat. Serological assays demonstrated that 98% of sera (69/70) collected from Egyptian fruit bats (n = 37) and straw-colored fruit bats (n = 33) had neutralizing antibodies against PRV. Genetic analyses revealed that all 10 genome segments of Nachunsulwe-57 were closely related to a bat-derived Kasama strain found in Uganda. Nachunsulwe-57 showed less efficiency in viral growth and lower pathogenicity in mice than another PRV strain, Miyazaki-Bali/2007, isolated from a patient. Conclusions A high proportion of Egyptian fruit bats and straw-colored fruit bats were found to be seropositive to PRV in Zambia. Importantly, a new PRV strain (Nachunsulwe-57) was isolated from an Egyptian fruit bat in Zambia, which had relatively weak pathogenicity in mice. Taken together, our findings provide new epidemiological insights about PRV infection in bats and indicate the first isolation of an PRV strain that may have low pathogenicity to humans.

scholarly journals Explore study: Retrospective Cohort study to show the start of SARS-CoV-2 in patients with severe respiratory illness by real-time PCR

2020 ◽  
Author(s):  
Sara H.A.Agwa ◽  
Hesham Elghazaly ◽  
Sarah El-Nakeep ◽  
Ahmad Moustafa ◽  
Manal H El-Sayed ◽  
...  
Keyword(s):  
Cohort Study ◽  
Retrospective Cohort Study ◽  
Retrospective Cohort ◽  
Respiratory Illness ◽  
Sequencing Analysis ◽  
Rt Pcr ◽  
University Hospitals ◽  
Common Causes ◽  
Causes Of Mortality ◽  
Severe Respiratory Illness

Abstract Aim: to know the start of COVID-19 in Ain shams University hospitals (El-Demerdash) in Severe acute respiratory illness.Materials and methods: retrospective collection of data records and previously collected nasopharyngeal and oropharyngeal sample stored in our lab for determining the start of COVID-19 in our hospitals, using RT-PCR and postive samples we will conduct Sequencing analysis and photogenic analysis. Also epidemiological and data study of the negatively screened patients, to determine the most common causes of SARI and the causes of mortality in this category of patients

scholarly journals Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017

Viruses ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 548 ◽  
Author(s):  
Jennifer Lun ◽  
Joanne Hewitt ◽  
Grace Yan ◽  
Daniel Enosi Tuipulotu ◽  
William Rawlinson ◽  
...  
Keyword(s):  
New Zealand ◽  
Next Generation Sequencing ◽  
Virus Infection ◽  
Phylogenetic Analyses ◽  
Rt Pcr ◽  
Molecular Surveillance ◽  
Recombinant Viruses ◽  
The Past ◽  
Wastewater Samples ◽  
Generation Sequencing

For the past two decades, norovirus pandemic variants have emerged every 3–5 years, and dominate until they are replaced by alternate strains. However, this scenario changed in 2016 with the co-circulation of six prevalent viruses, three of which possessed the pandemic GII.4 Sydney 2012 capsid. An increased number of institutional gastroenteritis outbreaks were reported within the Oceania region in mid-2017. This study identified emerging noroviruses circulating in Australia and New Zealand in 2017 to assess the changing dynamics of the virus infection. RT-PCR-based methods, next generation sequencing, and phylogenetic analyses were used to genotype noroviruses from both clinical and wastewater samples. Antigenic changes were observed between the capsid of pandemic Sydney 2012 variant and the two new Sydney recombinant viruses. The combination of these antigenic changes and the acquisition of a new ORF1 through recombination could both facilitate their ongoing persistence in the population. Overall, an increased prevalence of GII.P16/GII.4 Sydney 2012 viruses was observed in 2017, replacing the GII.P16/GII.2 recombinant that dominated in the region at the end of 2016. This shift in strain dominance was also observed in wastewater samples, demonstrating the reliability of wastewater as a molecular surveillance tool.

scholarly journals Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters

2021 ◽  
Author(s):  
Rakesh Kulkarni ◽  
Wen-Ching Chen ◽  
Ying Lee ◽  
Chi-Fei Kao ◽  
Shiu-Lok Hu ◽  
...  
Keyword(s):  
Vaccinia Virus ◽  
Mammalian Cells ◽  
Neutralizing Antibodies ◽  
Protective Immunity ◽  
Respiratory Illness ◽  
Cold Chain ◽  
Infection Model ◽  
Recombinant Vaccines ◽  
Viral Spread ◽  
Severe Respiratory Illness

COVID-19 in humans is caused by Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that belongs to the beta family of coronaviruses. SARS-CoV-2 causes severe respiratory illness in 10-15% of infected individuals and mortality in 2-3%. Vaccines are urgently needed to prevent infection and to contain viral spread. Although several mRNA- and adenovirus-based vaccines are highly effective, their dependence on the cold chain transportation makes global vaccination a difficult task. In this context, a stable lyophilized vaccine may present certain advantages. Accordingly, establishing additional vaccine platforms remains vital to tackle SARS-CoV-2 and any future variants that may arise. Vaccinia virus (VACV) has been used to eradicate smallpox disease, and several attenuated viral strains with enhanced safety for human applications have been developed. We have generated two candidate SARS-CoV-2 vaccines based on two vaccinia viral strains, MVA and v-NY, that express full-length SARS-CoV-2 spike protein. Whereas MVA is growth-restricted in mammalian cells, the v-NY strain is replication-competent. We demonstrate that both candidate recombinant vaccines induce high titers of neutralizing antibodies in C57BL/6 mice vaccinated according to prime-boost regimens. Furthermore, our vaccination regimens generated TH1-biased immune responses in mice. Most importantly, prime-boost vaccination of a Syrian hamster infection model with MVA-S and v-NY-S protected the hamsters against SARS-CoV-2 infection, supporting that these two vaccines are promising candidates for future development. Finally, our vaccination regimens generated neutralizing antibodies that partially cross-neutralized SARS-CoV-2 variants of concern.

scholarly journals A comprehensive review on epidemiology, aetiopathogenesis, diagnosis and treatment of the novel coronavirus syndrome – COVID-19

2020 ◽  
Vol 2 (2) ◽  
pp. 110-123
Author(s):  
Kulvinder Kochar Kaur ◽  
◽  
Gautam Allahbadia ◽  
Mandeep Singh ◽  
◽  
...  
Keyword(s):  
Respiratory Illness ◽  
World Health ◽  
The Novel ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Rapid Spread ◽  
Polymerase Chain ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Severe Respiratory Illness

Since the outbreak of the novel Coronavirus in December 2019 in Wuhan China, this novel Coronavirus disease(COVID-19) has spread worldwide taking not only epidemic proportions but with its rapid spread world health organization(WHO) was forced to declare it as a pandemic. The Severe Acute respiratory syndrome (SARS)-Coronavirus (CoV2) virus is responsible for clusters of severe respiratory illness that simulates acute respiratory syndrome that was what was initially. It is thought although that it is equivalent to the high altitude pulmonary oedema (HAPE), showing glass ground opacities in lungs. More experience is getting acquired with changes in treatment approaches from PEEP to avoid intubation and just ensure oxygen levels maintained. Human to human transmission through droplets, contaminated hands as well as surfaces, has been revealed with an incubation period varying from 2-14 days. Early diagnosis using reverse transcription polymerase chain reaction (RT-PCR) or computed tomography (CT) scan chest, quarantine, as well as supportive treatment are necessary for getting a cure. In this review we have tried to analyze the epidemiology, diagnosis, isolation, and treatment, including antiviral drugs like remdesivir, favipiravir, chloroquine and hydroxychloroquine, corticosteroids, antibiotics, and ivermectin. With 3 successful cases of convalescent plasma achieved in USA, trials going on in India along with vaccines are also detailed in this article.

scholarly journals Assessing roost disturbance of straw-coloured fruit bats (Eidolon helvum) through tri-axial acceleration

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242662
Author(s):  
Tânia Domingues Costa ◽  
Carlos D. Santos ◽  
Ana Rainho ◽  
Michael Abedi-Lartey ◽  
Jakob Fahr ◽  
...  
Keyword(s):  
Global Positioning System ◽  
Solar Irradiance ◽  
Positioning System ◽  
Fruit Bats ◽  
Fruit Bat ◽  
Large Numbers ◽  
Axial Acceleration ◽  
Global Positioning ◽  
Worldwide Phenomenon ◽  
Eidolon Helvum

The disturbance of wildlife by humans is a worldwide phenomenon that contributes to the loss of biodiversity. It can impact animals’ behaviour and physiology, and this can lead to changes in species distribution and richness. Wildlife disturbance has mostly been assessed through direct observation. However, advances in bio-logging provide a new range of sensors that may allow measuring disturbance of animals with high precision and remotely, and reducing the effects of human observers. We used tri-axial accelerometers to identify daytime flights of roosting straw-coloured fruit bats (Eidolon helvum), which were used as a proxy for roost disturbance. This bat species roosts on trees in large numbers (often reaching hundreds of thousands of animals), making them highly vulnerable to disturbance. We captured and tagged 46 straw-coloured fruit bats with dataloggers, containing a global positioning system (GPS) and an accelerometer, in five roosts in Ghana, Burkina Faso and Zambia. Daytime roost flights were identified from accelerometer signatures and modelled against our activity in the roosts during the days of trapping, as a predictor of roost disturbance, and natural stressors (solar irradiance, precipitation and wind speed). We found that daytime roost flight probability increased during days of trapping and with increasing solar irradiance (which may reflect the search for shade to prevent overheating). Our results validate the use of accelerometers to measure roost disturbance of straw-coloured fruit bats and suggest that these devices may be very useful in conservation monitoring programs for large fruit bat species.

scholarly journals Validation of Saliva and Self-Administered Nasal Swabs for COVID-19 Testing

2020 ◽  
Author(s):  
Alvin Kuo Jing Teo ◽  
Yukti Choudhury ◽  
Iain Beehuat Tan ◽  
Chae Yin Cher ◽  
Shi Hao Chew ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Migrant Workers ◽  
Phylogenetic Analyses ◽  
Kappa Statistic ◽  
Sample Type ◽  
Next Generation ◽  
Rt Pcr ◽  
Male Adult ◽  
Public Health Decision ◽  
Generation Sequencing

Background Active cases of COVID-19 has primarily been diagnosed via RT-PCR of nasopharyngeal (NP) swabs. Saliva and self-administered nasal (SN) swabs can be collected safely without trained staff. We aimed to test the sensitivity of naso-oropharyngeal saliva and SN swabs compared to NP swabs in a large cohort of migrant workers in Singapore. Methods We recruited 200 male adult subjects: 45 with acute respiratory infection, 104 asymptomatic close contacts, and 51 confirmed COVID-19 cases. Each subject underwent NP swab, SN swab and saliva collection for RT-PCR testing at 1 to 3 timepoints. We additionally used a direct-from-sample amplicon-based next-generation sequencing (NGS) workflow to establish phylogeny. Results Of 200 subjects, 91 and 46 completed second and third rounds of testing, respectively. Of 337 sets of tests, there were 150 (44.5%) positive NP swabs, 127 (37.7%) positive SN swabs, and 209 (62.0%) positive saliva. Test concordance between different sample sites was good, with a kappa statistic of 0.616 for NP and SN swabs, and 0.537 for NP and saliva. In confirmed symptomatic COVID-19 subjects, the likelihood of a positive test from any sample fell beyond 14 days of symptom onset. NGS was conducted on 18 SN and saliva samples, with phylogenetic analyses demonstrating lineages for all samples tested were Clade O (GISAID nomenclature) and lineage B.6 (PANGOLIN nomenclature). Conclusion This study supports saliva as a sensitive and less intrusive sample for COVID-19 diagnosis and further delineates the role of oropharyngeal secretions in increasing the sensitivity of testing. However, SN swabs were inferior as an alternate sample type. Our study also provides evidence that a straightforward next-generation sequencing workflow can provide direct-from-sample phylogenetic analysis for public health decision-making.

scholarly journals Are Megabats Flying Primates? Contrary Evidence from a Mitochondrial DNA Sequence

1988 ◽  
Vol 41 (3) ◽  
pp. 327 ◽  
Author(s):  
S Bennett ◽  
LJ Alexander ◽  
RH Crozier ◽  
AG Mackinlay
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Fruit Bats ◽  
Fruit Bat ◽  
Pteropus Poliocephalus ◽  
Connection System ◽  
Considerable Doubt ◽  
Contrary Evidence

Bats (Chiroptera) are divided into the suborders Megachiroptera (fruit bats, 'megabats') and Microchiroptera (predominantly insectivores, 'microbats'). It had been found that megabats and primates share a connection system between the retina and the midbrain not seen in microbats or other eutherian mammals, and challenging but plausible hypotheses were made that (a) bats are diphyletic and (b) megabats are flying primates. We obtained two DNA sequences from the mitochondrion of the fruit bat Pteropus poliocephalus, and performed phylogenetic analyses using the bat sequences in conjunction with homologous Drosophila, mouse, cow and human sequences. Two trees stand out as significantly more likely than any other; neither of these links the bat and human as the closest sequences. These results cast considerable doubt on the hypothesis that megabats are particularly close to primates.

scholarly journals Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alvin Kuo Jing Teo ◽  
Yukti Choudhury ◽  
Iain Beehuat Tan ◽  
Chae Yin Cher ◽  
Shi Hao Chew ◽  
...  
Keyword(s):  
Migrant Workers ◽  
Acute Respiratory Infection ◽  
Community Care ◽  
Phylogenetic Analyses ◽  
Care Facility ◽  
Rt Pcr ◽  
Nasal Swabs ◽  
Next Generation Sequencing Ngs ◽  
Positive Cycle ◽  
Generation Sequencing

AbstractWe aimed to test the sensitivity of naso-oropharyngeal saliva and self-administered nasal (SN) swab compared to nasopharyngeal (NP) swab for COVID-19 testing in a large cohort of migrant workers in Singapore. We also tested the utility of next-generation sequencing (NGS) for diagnosis of COVID-19. Saliva, NP and SN swabs were collected from subjects who presented with acute respiratory infection, their asymptomatic roommates, and prior confirmed cases who were undergoing isolation at a community care facility in June 2020. All samples were tested using RT-PCR. SARS-CoV-2 amplicon-based NGS with phylogenetic analysis was done for 30 samples. We recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively. In total, 62.0%, 44.5%, and 37.7% of saliva, NP and SN samples were positive. Cycle threshold (Ct) values were lower during the earlier period of infection across all sample types. The percentage of test-positive saliva was higher than NP and SN swabs. We found a strong correlation between viral genome coverage by NGS and Ct values for SARS-CoV-2. Phylogenetic analyses revealed Clade O and lineage B.6 known to be circulating in Singapore. We found saliva to be a sensitive and viable sample for COVID-19 diagnosis.

scholarly journals Serum Neutralization Profiles of Straw-Colored Fruit Bats (Eidolon helvum) in Makurdi (Nigeria), against Four Lineages of Lagos Bat Lyssavirus

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2378
Author(s):  
Veronica Odinya Ameh ◽  
Guanghui Wu ◽  
Hooman Goharriz ◽  
Rebecca Shipley ◽  
Anthony R. Fooks ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Fluorescent Antibody ◽  
Virus Neutralization ◽  
Human Consumption ◽  
Fruit Bats ◽  
Serum Samples ◽  
Fatal Disease ◽  
Serum Neutralization ◽  
First Time ◽  
Eidolon Helvum

Lagos bat lyssavirus (LBV) comprising four lineages (A, B, C and D) can potentially cause the fatal disease rabies. Although LBV-B was initially isolated in Nigeria in 1956, there is no information on LBV lineages circulating in Nigeria. This study was undertaken for the first time to measure the neutralizing antibodies against four lineages of LBVs in straw-colored fruit bats (Eidolon helvum) in Makurdi, Nigeria. Serum samples (n = 180) collected during two periods (November 2017–March 2018 and November 2018–March 2019) from terminally bled bats captured for human consumption were tested using a modified fluorescent antibody virus neutralization (mFAVN) assay. A high proportion of bat sera (74%) neutralized at least one lineage of LBV (with reciprocal titers from 9 to >420.89) and most of them neutralized LBV-A (63%), followed by LBV-D (49%), LBV-C (45%) and LBV-B (24%). The majority of positive sera (75%, n = 100) neutralized multiple LBV lineages while the remaining 25% (n = 33) neutralized only a single lineage, i.e., LBV-A (n = 23), LBV-D (n = 8) and LBV-C (n = 2). None exclusively neutralized LBV-B. The results suggest that exposure to LBV is common in E. helvum and that LBV-A (but not LBV-B) is likely to be circulating in this region of Nigeria.

scholarly journals Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257191
Author(s):  
Rakesh Kulkarni ◽  
Wen-Ching Chen ◽  
Ying Lee ◽  
Chi-Fei Kao ◽  
Shiu-Lok Hu ◽  
...  
Keyword(s):  
Vaccinia Virus ◽  
Mammalian Cells ◽  
Neutralizing Antibodies ◽  
Protective Immunity ◽  
Respiratory Illness ◽  
Cold Chain ◽  
Infection Model ◽  
Recombinant Vaccines ◽  
Viral Spread ◽  
Severe Respiratory Illness

COVID-19 in humans is caused by Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that belongs to the beta family of coronaviruses. SARS-CoV-2 causes severe respiratory illness in 10–15% of infected individuals and mortality in 2–3%. Vaccines are urgently needed to prevent infection and to contain viral spread. Although several mRNA- and adenovirus-based vaccines are highly effective, their dependence on the “cold chain” transportation makes global vaccination a difficult task. In this context, a stable lyophilized vaccine may present certain advantages. Accordingly, establishing additional vaccine platforms remains vital to tackle SARS-CoV-2 and any future variants that may arise. Vaccinia virus (VACV) has been used to eradicate smallpox disease, and several attenuated viral strains with enhanced safety for human applications have been developed. We have generated two candidate SARS-CoV-2 vaccines based on two vaccinia viral strains, MVA and v-NY, that express full-length SARS-CoV-2 spike protein. Whereas MVA is growth-restricted in mammalian cells, the v-NY strain is replication-competent. We demonstrate that both candidate recombinant vaccines induce high titers of neutralizing antibodies in C57BL/6 mice vaccinated according to prime-boost regimens. Furthermore, our vaccination regimens generated TH1-biased immune responses in mice. Most importantly, prime-boost vaccination of a Syrian hamster infection model with MVA-S and v-NY-S protected the hamsters against SARS-CoV-2 infection, supporting that these two vaccines are promising candidates for future development. Finally, our vaccination regimens generated neutralizing antibodies that partially cross-neutralized SARS-CoV-2 variants of concern.

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