scholarly journals Ecological surveillance of bat coronaviruses in Sarawak, Malaysian Borneo

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Cheng-Siang Tan ◽  
Vaenessa Noni ◽  
Jaya Seelan Sathiya Seelan ◽  
Azroie Denel ◽  
Faisal Ali Anwarali Khan
Keyword(s):  
Posterior Probability ◽  
Pcr Primers ◽  
Bayesian Posterior Probability ◽  
The Past ◽  
Viral Transport ◽  
Column Method ◽  
Viral Transport Medium ◽  
Human Coronaviruses ◽  
Sanger Method ◽  
Malaysian Borneo

Abstract Objective Coronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at − 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidirectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed. Results CoV-RNA was detected in ten specimens (47.6%, n  = 21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses.

scholarly journals Genetic Analysis of Two Sympatric Sea Urchins from Genus Diadema (Echinodermata: Echinoidea: Diadematidae) from Malaysian Borneo

1970 ◽  
Vol 5 (1) ◽  
pp. 16-25
Author(s):  
Nursyuhaida Md Shahid ◽  
Raymie Nurhassan ◽  
Siti Akmar Khadijah Ab Rahim ◽  
Ruhana Hassan
Keyword(s):  
Posterior Probability ◽  
Sea Urchins ◽  
Strong Support ◽  
Sympatric Species ◽  
Bayesian Posterior Probability ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Morphological Variations ◽  
Tropical Sea ◽  
Malaysian Borneo

Genus Diadema (Echinoidea: Diadematidae) has been reported to be the most widespread and ecologically important shallow water tropical sea urchins. Morphological variations and species distributions are complicated to elucidate due to complexity in making reliable identifications. Genus Diadema had involved in many debates, particularly on the mode of speciation and the specific status of Diadema setosum and Diadema savignyi. Therefore, relationships among Diadema species found in Malaysian Borneo have been examined using 16S rRNA gene analysis. Monophyletic clade of genus Diadema with respect to the outgroup was obtained with high bootstrap values of 100% (MP), 100% (NJ), 100% (ML) and Bayesian Posterior Probability is equal to 1.00. Two monophyletic clades were apparent separating D. setosum (Clade I) and D. savignyi (Clade II), with strong support of 100% (MP), 100% (NJ), 80% (ML) and Bayesian Posterior Probability is equal to 1.00. In addition, high genetic variation among species had been recorded (9.85%), suggesting that D. setosum and D. savignyi are two distinct entities. Furthermore, D. setosum and D. savignyi are sympatric species based on their distribution and overlapping ranges in Malaysian Borneo.

scholarly journals An Impact Location Algorithm for Spacecraft Stiffened Structure Based on Posterior Possibility Correlation

Sensors ◽  
2020 ◽  
Vol 20 (2) ◽  
pp. 368 ◽  
Author(s):  
Lei Qi ◽  
Zhoumo Zeng ◽  
Lichen Sun ◽  
Xiaobo Rui ◽  
Fan Fan ◽  
...  
Keyword(s):  
Posterior Probability ◽  
Cross Correlation ◽  
Bayesian Posterior Probability ◽  
Probability Method ◽  
Stiffened Plate ◽  
Plate Structures ◽  
Impact Location ◽  
Weight Method ◽  
Location Algorithm ◽  
The Impact

In order to ensure the safety of spacecrafts in orbit, impact location is an important part of structural health monitoring systems. In this paper, an impact location algorithm based on posterior probability correlation is proposed to solve the problem, that is, the impact point in the stiffened structure of a spacecraft is difficult to locate. The algorithm combines the Gaussian cross-correlation possibility weight method and the Bayesian posterior probability method. The cross-correlation possibility weight superposition based on grids was used to reduce the dependence of the accuracy of time difference extraction. Gaussian and normalized fitting were used to compensate the reflection, modal transformation, and amplitude attenuation of a stiffened plate. The location result was further optimized by the posterior probability. The proposed algorithm can be applied to the impact source localization of complex stiffened plate structures. The experiment results showed that the average location error can be 2.57 cm with proper sensor network schemes.

scholarly journals QuickVue Influenza Test for Rapid Detection of Influenza A and B Viruses in a Pediatric Population

2002 ◽  
Vol 9 (4) ◽  
pp. 925-926 ◽  
Author(s):  
Caroline Quach ◽  
Diane Newby ◽  
Ghislaine Daoust ◽  
Earl Rubin ◽  
Jane McDonald
Keyword(s):  
Cell Culture ◽  
Respiratory Tract ◽  
Rapid Detection ◽  
Influenza A ◽  
Respiratory Tract Infections ◽  
Pediatric Population ◽  
Lateral Flow Immunoassay ◽  
Viral Transport ◽  
Viral Transport Medium ◽  
Tract Infections

ABSTRACT The performance of a lateral-flow immunoassay, the QuickVue Influenza Test, for detection of influenza A and B viruses in comparison with that of cell culture was evaluated by using nasopharyngeal aspirates, in viral transport medium, from children with respiratory tract infections. The sensitivity and specificity were 79.2 and 82.6%, respectively.

Paurodontella gilanica n. sp. (Nematoda: Sphaerularioidea) from Iran

Nematology ◽  
2018 ◽  
Vol 20 (5) ◽  
pp. 471-482 ◽  
Author(s):  
Ali Yaghoubi ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Posterior Probability ◽  
Small Body ◽  
Bootstrap Support ◽  
Bayesian Posterior Probability ◽  
Female Reproductive System ◽  
Lateral Field ◽  
Morphological Differences ◽  
Tail Tip ◽  
18S Rdna Sequence

Summary Paurodontella gilanica n. sp. is described and illustrated based on morphological, morphometric and molecular characters. The new species is characterised by its small body size, four lines in the lateral field, weak stylet with minute asymmetrical knobs, female reproductive system lacking a diverticulum but with small post-vulval uterine sac, elongate conoid tail with pointed, sometimes filiform, tip, males common with small spicules and cloacal bursa not reaching tail tip. Morphological differences between the new species and seven known species of the genus, namely P. asymmetrica, P. auriculata, P. balochistanica, P. minuta, P. myceliophaga, P. parapitica and P. persica, are discussed. The new species is also compared with four known species of Paurodontus having four lines in the lateral field. Using a 1123 nt long partial 18S rDNA sequence of the new species to reconstruct the phylogenetic relationships revealed that it formed a clade with members of the Sphaerulariidae and Paurodontidae. Using a 746 nt long partial sequence of the 28S rDNA D2-D3 segment revealed that P. gilanica n. sp. formed a clade with Abursanema iranicum in both Bayesian inference (BI) and maximum likelihood (ML) analyses with 0.99 Bayesian posterior probability (BPP) and 89% bootstrap support value (BS). The morphological affinities of Paurodontella and Paurodontus are discussed.

Molecular and morphological characterization of Austrodiplostomum ostrowskiae Dronen, 2009 (Digenea: Diplostomatidae), a parasite of cormorants in the Americas

2015 ◽  
Vol 90 (2) ◽  
pp. 174-185 ◽  
Author(s):  
M. García-Varela ◽  
A.L. Sereno-Uribe ◽  
C.D. Pinacho-Pinacho ◽  
O. Domínguez-Domínguez ◽  
G. Pérez-Ponce de León
Keyword(s):  
Posterior Probability ◽  
Mitochondrial Gene ◽  
Single Species ◽  
Morphological Characterization ◽  
Bayesian Posterior Probability ◽  
Consensus Trees ◽  
Monophyletic Lineage ◽  
The Usa ◽  
Posterior Probability Support

AbstractThe diplostomid genus Austrodiplostomum currently contains two species, i.e. A. mordax and A. ostrowskiae. Adults of these species inhabit the intestine of cormorants of the genus Nannopterum, whereas larval forms (metacercariae) are found in the eyes (vitreous humor) of freshwater fishes. Records of both species have been established across a wide geographic range in the Americas. Diplostomid adults and metacercariae were collected from a wide geographical range that spans from south-eastern Mexico, southwards to Central and South America. Even though the diplostomid has been largely reported in Mexico as Diplostomum (Austrodiplostomum) compactum, our specimens were identified morphologically as A. ostrowskiae. Sequences of the mitochondrial gene cytochrome c oxidase (cox 1) were obtained for 86 individuals, including 15 adults recovered from the intestine of Nannopterum brasilianus, in five localities, and 71 metacercariae from the eyes of ten fish species, in 13 localities. Sequences were used to evaluate the genetic diversity, and to test conspecificity of these specimens with the available sequence of A. ostrowskiae. Sequences were aligned with another 12 taxa representing five genera of Diplostomatidae, forming a dataset of 104 taxa with 478 nucleotides. The genetic divergence estimated among the 86 sequenced individuals, and that of A. ostrowskiae from the double-crested cormorant, Nannopterum auritus, in the USA, was very low, ranging from 0 to 0.8%. The maximum likelihood (ML) and Bayesian consensus trees showed that all sequences nested within a monophyletic lineage, with strong bootstrap and Bayesian posterior probability support values (100/1.0). In conclusion, a link between the metacercariae in fish and the adults in cormorants was established, indicating also that a single species is found in the distribution range comprising southern USA, southwards to Venezuela. Previous records of this species, particularly from Mexico, need to be corrected.

scholarly journals Optimal Preparation of COVID-19 Viral Transport Medium for Culture

2020 ◽  
Author(s):  
Julie McAuley ◽  
Claire Fraser ◽  
Elena Paraskeva ◽  
Elizabeth Trajcevska ◽  
Michelle Sait ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Vero Cells ◽  
Nucleic Acid Detection ◽  
Transport Medium ◽  
Viral Culture ◽  
Viral Transport ◽  
Viral Transport Medium ◽  
Escape Mutants ◽  
Diagnostic Approaches ◽  
Manual Handling

Abstract IntroductionThe sudden arrival of the COVID-19 pandemic placed significant stresses on supply chains including viral transport medium (VTM). The VTM that was urgently required needed to support viral replication, as well as other routine diagnostic approaches. We describe the preparation and validation testing of VTM for rapidly expanding diagnostic testing, where the capacity of the VTM to preserve viral integrity, for culture, isolation and full sequence analysis, was maintained.MethodsVTM was prepared using different methods of sterilization then ‘spiked’ with virus. The VTM was investigated using viral culture in Vero cells, and for nucleic acid detection by quantitative PCR (qPCR).ResultsThe best results were obtained by filter and autoclave-based sterilization. The VTM proved robust for culture-based analyses provided the inoculated VTM was stored at 4oC, and tested within 48 hours. The filtered VTM also supported PCR-based diagnosis for at least 5 days when the mock inoculated VTM was held at room temperature (RT).DiscussionThe manual handling of VTM production, including filling and sterilization, was optimized. SARS-CoV-2 was spiked into VTM to assess different sterilization methods and measure the effects of storage time and temperature upon VTM performance. While most diagnostic protocols will not require replication competent virus, the use of high quality VTM will allow for the next phase of laboratory analysis in the COVID-19 pandemic, including drug and antibody susceptibility analysis of re-isolated SARS--CoV-2, and for the testing of vaccine escape mutants.

scholarly journals Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin-Yan Li ◽  
Zhi-Jian Zhou ◽  
Qiong Wang ◽  
Qing-Nan He ◽  
Ming-Yi Zhao ◽  
...  
Keyword(s):  
Immune Response ◽  
Pattern Recognition ◽  
Current Knowledge ◽  
Viral Pathogenesis ◽  
Host Cells ◽  
Highly Pathogenic ◽  
Cellular Processes ◽  
Antiviral Therapies ◽  
The Past ◽  
Human Coronaviruses

In the past two decades, coronavirus (CoV) has emerged frequently in the population. Three CoVs (SARS-CoV, MERS-CoV, SARS-CoV-2) have been identified as highly pathogenic human coronaviruses (HP-hCoVs). Particularly, the ongoing COVID-19 pandemic caused by SARS-CoV-2 warns that HP-hCoVs present a high risk to human health. Like other viruses, HP-hCoVs interact with their host cells in sophisticated manners for infection and pathogenesis. Here, we reviewed the current knowledge about the interference of HP-hCoVs in multiple cellular processes and their impacts on viral infection. HP-hCoVs employed various strategies to suppress and evade from immune response, including shielding viral RNA from recognition by pattern recognition receptors (PRRs), impairing IFN-I production, blocking the downstream pathways of IFN-I, and other evasion strategies. This summary provides a comprehensive view of the interplay between HP-hCoVs and the host cells, which is helpful to understand the mechanism of viral pathogenesis and develop antiviral therapies.

scholarly journals Studi Awal Analisis Molekuler Human Papillomavirus dari Apusan Glans dan Batang Penis

2021 ◽  
Vol 9 (4) ◽  
pp. 433
Author(s):  
Maya Savira ◽  
Resty Yuwandari ◽  
Yossi Maryanti ◽  
Rahmat Azhari Kemal ◽  
Donel S
Keyword(s):  
Human Papillomavirus ◽  
Rna Extraction ◽  
Viral Rna ◽  
Transport Medium ◽  
Viral Transport ◽  
Viral Transport Medium

Pria juga dapat mengalami keganasan akibat infeksi Human Papillomavirus (HPV) serta bertindak sebagai reservoir virus. Metode skrining HPV pada wanita telah terstandardisasi, namun belum ada standar metode skrining pada pria di Indonesia. Beberapa studi pada populasi pria di luar negeri menunjukkan potensi sampling pada daerah genitalia eksterna untuk skrining HPV. Tujuan: mengoptimasi metode skrining HPV secara molekuler pada pria. Metode: Responden adalah partner seksual wanita pansien kanker serviks di RSUD Arifin Achmad Provinsi Riau. Apusan dari glans dan batang penis diambil menggunakan nylon-flocked swab yang kemudian dimasukkan ke dalam 350µl viral transport medium terpisah. DNA diisolasi dari sampel yang kemudian dianalisis untuk mendeteksi gen human β-globin dan HPV. Hasil: Optimasi awal menunjukkan gen β-globin dapat terdeteksi dari hasil ekstraksi dengan kit Zeesan Viral RNA Extraction. Pita HPV hasil PCR dengan primer MY09 dan MY11 dapat muncul namun masih tipis. Simpulan: Studi awal ini menunjukkan bahwa apusan glans dan batang penis dapat digunakan untuk deteksi HPV secara molekuler pada pria, namun proses pengambilan sampel, ekstraksi DNA, dan PCR masih perlu dioptimasi.Kata kunci: apusan, glans, HPV, penis

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