Global germplasm collections: sure benefits without seedborne diseasesCIAT
The Genetic Resources Program is the germplasm bank of CIAT which conserves the collections of bean and tropical forage seeds, and the collection of cassava "in vitro" for a total of approximately 67,500 different accessions. The conservation of these collections allows the benefit of the distribution of germplasm of approximately 6,000 samples of genetic material per year, at national and international level. To minimize the risks associated with the movement of germplasm, especially the transport of pathogens of quarantine interest, it is required a process of laboratory tests certifying the plant quality. This process is carried out in the Germplasm Health Laboratory of the GRP, where also research is developed to improve the effectiveness of the detection, testing reliability and efficiency of operations.
Background
Influenza A viruses are medically significant pathogens responsible for higher mortality and morbidity throughout the world. Swine influenza is known to be caused by influenza A subtypes H1N1, H1N2, and H3N2, which are highly contagious, and belongs to the family Orthomyxoviridae. Efficient and accurate diagnosis of influenza A in individuals is critical for monitoring of a constantly evolving pandemic. A rapid result is important, because timely treatment can reduce disease severity and duration. Rapid antigen tests were among the first-line diagnostic tools for the detection of pandemic H1N1 (2009) virus infection during the initial outbreak. Current study focuses on the significant approach of the usage of molecular method utilizing real-time PCR for the detection of type A influenza virus (H1N1 subtype) in humans.
Methods
A total of 2000 mixed nasal/throat swab specimens collected in commercial viral transport from Apollo hospitals, Hyderabad were submitted to Institute of Preventive Medicine for molecular testing by reverse transcriptase polymerase chain reaction (RT-PCR) from 2009 to 2015 from its affiliated primary care clinics.
Results
Among the 2000 samples collected, 700 samples were positive for Human Inf A, swine Inf A, and Swine Inf H1 (fourth table in the article). One thousand two hundred samples were negative for Human Inf A, swine Inf A, and Swine Inf H1, and 100 samples were positive for Influenza A only.
Conclusion
The molecular testing of H1N1 patients helped the clinicians in timely diagnosis and treatment of these patients during the pandemic surveillance. The RT-PCR test has higher sensitivity and specificity; hence it is considered to be the best tool to use during the pandemic surveillance, as compared to the any other commercial antigen-based tests, which show a variable performance, with the sensitivities of tests from different manufacturers ranging from 9 to 77%.
Genomic surveillance of the Rift Valley fever: From sequencing to Lineage ass...ILRI
Poster prepared John Juma, Vagner Fonseca, Samson Limbaso, Peter van Heusden, Kristina Roesel, Bernard Bett, Rosemary Sang, Alan Christoffels, Tulio de Oliveira and Samuel Oyola for the Kenya One Health Online Conference, 6-8 December 2021
Perspectives of predictive epidemiology and early warning systems for Rift Va...ILRI
Presentation by MO Nanyingi, GM Muchemi, SG Kiama, SM Thumbi and B Bett at the 47th annual scientific conference of the Kenya Veterinary Association held at Mombasa, Kenya, 24-27 April 2013.
An integrated genomic surveillance platform reveals multiple introductions an...Data Con LA
Data Con LA 2020
Description
The Children's Hospital, Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) (https://covid19.cpmbiodev.net/) is a comprehensive genomic resource of SARS-CoV-2 viral genomes and associated meta-data of over 80,000 (as of August 13, 2020) isolates collected from global sequencing laboratories and the Center for Personalized Medicine (CPM) at CHLA. A Virus Genome Tracker accepts virus genome sequence and places the new viral isolate within the global or USA phylogenetic contexts based upon variant and haplotype comparisons to trace the transmission for genomic surveillance.
By haplotype analysis of 4,200 California isolates, 6,356 USA isolates, and over 80,000 global isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions. Phylogenetic analyses revealed the cryptic introduction of multiple SARS-CoV-2 lineages into California and Los Angeles, deriving from state-to-state transmission, and from international travel by air and ship. The majority of sequences Orange County isolates formed distinct outbreak clusters whose haplotypes were different from isolates of the neighboring Los Angeles. From the 50,000 global isolates, 22,171 (45.8%) isolates carried country-private haplotypes. The percentage were 28.2-29.6% in January to March, and rapidly increased to 46.4% and 59.6% in April and May, co-occurring with global travel restrictions.
Speaker
Lishuang Shen, Children's Hospital Los Angeles, Sr. Bioinformatics Scientist
Global germplasm collections: sure benefits without seedborne diseasesCIAT
The Genetic Resources Program is the germplasm bank of CIAT which conserves the collections of bean and tropical forage seeds, and the collection of cassava "in vitro" for a total of approximately 67,500 different accessions. The conservation of these collections allows the benefit of the distribution of germplasm of approximately 6,000 samples of genetic material per year, at national and international level. To minimize the risks associated with the movement of germplasm, especially the transport of pathogens of quarantine interest, it is required a process of laboratory tests certifying the plant quality. This process is carried out in the Germplasm Health Laboratory of the GRP, where also research is developed to improve the effectiveness of the detection, testing reliability and efficiency of operations.
Background
Influenza A viruses are medically significant pathogens responsible for higher mortality and morbidity throughout the world. Swine influenza is known to be caused by influenza A subtypes H1N1, H1N2, and H3N2, which are highly contagious, and belongs to the family Orthomyxoviridae. Efficient and accurate diagnosis of influenza A in individuals is critical for monitoring of a constantly evolving pandemic. A rapid result is important, because timely treatment can reduce disease severity and duration. Rapid antigen tests were among the first-line diagnostic tools for the detection of pandemic H1N1 (2009) virus infection during the initial outbreak. Current study focuses on the significant approach of the usage of molecular method utilizing real-time PCR for the detection of type A influenza virus (H1N1 subtype) in humans.
Methods
A total of 2000 mixed nasal/throat swab specimens collected in commercial viral transport from Apollo hospitals, Hyderabad were submitted to Institute of Preventive Medicine for molecular testing by reverse transcriptase polymerase chain reaction (RT-PCR) from 2009 to 2015 from its affiliated primary care clinics.
Results
Among the 2000 samples collected, 700 samples were positive for Human Inf A, swine Inf A, and Swine Inf H1 (fourth table in the article). One thousand two hundred samples were negative for Human Inf A, swine Inf A, and Swine Inf H1, and 100 samples were positive for Influenza A only.
Conclusion
The molecular testing of H1N1 patients helped the clinicians in timely diagnosis and treatment of these patients during the pandemic surveillance. The RT-PCR test has higher sensitivity and specificity; hence it is considered to be the best tool to use during the pandemic surveillance, as compared to the any other commercial antigen-based tests, which show a variable performance, with the sensitivities of tests from different manufacturers ranging from 9 to 77%.
Genomic surveillance of the Rift Valley fever: From sequencing to Lineage ass...ILRI
Poster prepared John Juma, Vagner Fonseca, Samson Limbaso, Peter van Heusden, Kristina Roesel, Bernard Bett, Rosemary Sang, Alan Christoffels, Tulio de Oliveira and Samuel Oyola for the Kenya One Health Online Conference, 6-8 December 2021
Perspectives of predictive epidemiology and early warning systems for Rift Va...ILRI
Presentation by MO Nanyingi, GM Muchemi, SG Kiama, SM Thumbi and B Bett at the 47th annual scientific conference of the Kenya Veterinary Association held at Mombasa, Kenya, 24-27 April 2013.
An integrated genomic surveillance platform reveals multiple introductions an...Data Con LA
Data Con LA 2020
Description
The Children's Hospital, Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) (https://covid19.cpmbiodev.net/) is a comprehensive genomic resource of SARS-CoV-2 viral genomes and associated meta-data of over 80,000 (as of August 13, 2020) isolates collected from global sequencing laboratories and the Center for Personalized Medicine (CPM) at CHLA. A Virus Genome Tracker accepts virus genome sequence and places the new viral isolate within the global or USA phylogenetic contexts based upon variant and haplotype comparisons to trace the transmission for genomic surveillance.
By haplotype analysis of 4,200 California isolates, 6,356 USA isolates, and over 80,000 global isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions. Phylogenetic analyses revealed the cryptic introduction of multiple SARS-CoV-2 lineages into California and Los Angeles, deriving from state-to-state transmission, and from international travel by air and ship. The majority of sequences Orange County isolates formed distinct outbreak clusters whose haplotypes were different from isolates of the neighboring Los Angeles. From the 50,000 global isolates, 22,171 (45.8%) isolates carried country-private haplotypes. The percentage were 28.2-29.6% in January to March, and rapidly increased to 46.4% and 59.6% in April and May, co-occurring with global travel restrictions.
Speaker
Lishuang Shen, Children's Hospital Los Angeles, Sr. Bioinformatics Scientist
Sensitivity and Specificity of an In-house Sandwich ELISA Kit for Newcastle D...Dr. Md. Ehsanul Haque
Of all serological tests enzyme-linked immunosorbent assay (ELISA) is still considered the gold standard for the detection of antigens and antibodies of either macro or micro-organisms worldwide. The ELISA kits for serum antibody detection against many viruses and other micro-organisms of both man and animals are available in the market. Whereas, antigen detection ELISA kits for Newcastle disease virus
(NDV) is not yet available in Bangladesh. The Present study was designed for the development of an economically feasible In-house Sandwich ELISA and to test its sensitivity and specificity for the detection of NDV antigens from clinically suspected field samples. 96-well flat bottom polystyrene plates coated with hyperimmune polyclonal serum against NDV raised in rabbits was used to capture NDV
antigens. The anti-rabbit IgG and DAB with 30% H2O2 were used as conjugate and substrate respectively for standardization of the test method. The plate coated with serum diluted 10-3 was found suitable for capturing maximum antigen of NDV by the In-house Sandwich ELISA. The cut-off value of the present ELISA test was calculated as 0.855 and was able to capture the viral antigen present in the 10-4 fold
dilution of allantoic fluid (AF) which is equivalent to 1HA unit, indicating the highest degree of sensitivity of the newly developed ELISA. In case of field samples, the newly developed ELISA kit was able to detect 100% viral antigens of NDV present in the feces, 95.50% of the brain tissue and oro-nasal swab and 94.12% of colon swab samples of either naturally and experimentally infected birds in this study. The
ND virus specific polyclonal antibody used in the kit bind only with ND virus without any cross reactive antigens of other viruses of chicken like Avian influenza virus (AIV) and Infectious bursal disease viruses (IBDV). Therefore, findings of the present study clearly indicates that the newly developed In-house Sandwich ELISA kit can be used for rapid confirmatory diagnosis of Newcastle disease (ND) with minimum cost, using any kind of field samples from either sick or dead birds.
One of the main challenges for a versatile application of monitoring technologies in the
veterinary and food industry is to develop fast, quantitative and low cost devices that
can be used with minimal expertise. Most of the diagnostic technologies in use today
require laboratory facilities, expensive equipments and trained personnel. During the
last decade, a few technologies have been proposed and developed that fulfill most
requirements of versatility mentioned above. One of the most promising approaches is
the lateral flow immunoassay technique.
Genome Sequencing: FAO's relevant activities in Animal HealthFAO
http://tiny.cc/faowgsworkshop
FAO's activities relevant to genome sequencing- Animal Health. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Nucleic Acid-its structural and functional complexity.
OS18 - 10.a.4 Results of the 2016 AND 2017 proficiency testing schemes for FMD diagnostic methods - A. Ludi
1. Proficiency Testing
Schemes;
Results from 2016 & 2017
Anna Lüdi, Ginette Wilsden, Clare Browning, Hannah Baker, Valerie Mioulet,
Britta Wood, Ashley Gray, Lissie Henry, Jemma Wadsworth, Julie Maryan, Sarah
Belgrave, Donald King
FMD and SVD
Reference Laboratories
2. To assist National FMD Laboratories to develop/improve
accurate and reproducible FMD diagnostic tests
Achieved by feedback, training and consultation
Quality Assurance requirements to support ISO/IEC 17025
Harmonisation amongst laboratories
Achieved by presenting results on how reference laboratories
compare, distribution of reagents and protocols
Purpose of Proficiency Testing Scheme (PTS)
3. 3 panels for FMDV
Panel 1 – outbreak scenario
Panel 2 – can your diagnostic assay detect the latest strains?
Panel 3 – serology
Panel 3a - outbreak scenario
Panel 3b - QA
Quality Assurance
Virology - all strains are isolated from field strains and
sequenced
Serology - all sera are from experimental studies
10x testing has occurred for all diagnostic test types
The Scheme
NOTE – Swine Vesicular Disease Virus samples/panels will not be discussed
5. Supplied as infectious and non-infectious specimens
Based on the scenarios provided (Panel 1a-b), use your national
contingency plan or similar document to identify the appropriate tests
and testing sequence. Please provide a flow chart in English to show the
testing and decision tree adopted for evaluating these samples (the original
contingency plan is not necessary). This panel is primarily intended to
evaluate your overall diagnostic procedure and interpretation of these
suspect cases, rather than focussing on the performance of individual test
methods. Therefore, it may not be necessary to use all of your assays
to test these samples. If downstream characterisation methods, (such as
viral sequencing) are part of your contingency plan, please use and report
the results of these assays.
Panel 1
Outbreak scenarios of vesicular diseases
Tests used – Virus Isolation, Antigen ELISA, rRT-PCR and sequence
6. Continued improvement – 2017 PTS all correct
results for virus isolation, rRT-PCR and antigen
ELISA
Panel 1
Take home messages
7. Supplied as non-infectious
This panel of viruses represents recent FMDV isolates that pose a current
threat to the EU and elsewhere. The aim of the evaluation is to make sure
these latest strains can be detected. Please use appropriate methods to
test these virological samples. Note that some of these samples may not
contain viruses.
Panel 2
Quality assurance to ensure
recent FMDV strains are detected
Tests used – Antigen ELISA and rRT-PCR
8. FMD-free (without vaccination)
Sporadic
Endemic
Pool 1
Pool 2
Pool 3
Pool 5
Panel 2
Strains Selected
Strain Lineage
O/MOR/1/2015 O/ME-SA/Ind-2001d
A/PAK/12/2015 A/ASIA/Iran-05FAR-11
Asia 1/TUR/12/2015 Asia 1/ASIA/Sindh-08
O/EGY/18/2016 O/EA-3
A/IRN/8/2016 A/ASIA/G-VII
SAT 2/OMN/4/2015 SAT 2/VIIAlx-12
20162017
9. To Consider
What strains and lineages are endemic in your area?
What is the risk from surrounding pools?
FMD-free (without vaccination)
Sporadic
Endemic
Pool 1
Pool 2
Pool 3
Pool 5
10. To Consider
What strains and lineages are endemic in your area?
What is the risk from surrounding pools?
FMD-free (without vaccination)
Sporadic
Endemic
Pool 1
Pool 2
Pool 3
Pool 5
11. Continued Improvements
The antigen ELISA shows less cross-reactivity than in
the past
More laboratories are determining serotypes as
PanFMD rather than negative
For 2017 all laboratories correctly identified FMDV
samples as FMDV
However, four laboratories incorrectly identified a negative
sample as inconclusive/positive
Overall Conclusions
13. Panel 3 – FMDV serology
Non-structural protein ELISAs being used
0
10
20
30
40
50
42
20
8
6
3 2
14. Panel 3a
Continuation of outbreak scenarios
During the outbreak described in scenario 1 (Panels 1a and b), some animals were
vaccinated with a high potency, purified monovalent vaccine. Three sera have been
collected after vaccination from farms within the 10km surveillance zone surrounding
the outbreaks. Please test them and define whether the samples are from infected
animals, and if not, whether or not there is any evidence of vaccine-induced
immunity. Note you should use information from Panels 1a and b to limit the range of
testing that you need to carry out.
15. Continued improvement – compared to 2016, more
laboratories correctly chose the ELISA for serological
testing
Although individual serotypes were correctly identified
for each assay, some laboratories included multiple
serotypes in overall conclusions.
Panel 3a
Take home messages
16. Panel 3b
QA Panel
You have been asked to carry out post-vaccination monitoring for a country where
FMD is endemic. Cattle have been vaccinated with serotype Asia 1 (Asia-1 Shamir)
vaccine or A (A22) vaccine; however, there is concern that there may have been an
outbreak in the area and the vaccination history is not clear. Please test the samples
and comment as to whether the samples are from infected animals, and if not,
whether or not there is any evidence of vaccine-induced immunity.
17. Continued improvement – for 2017 all laboratories
correctly identified NSP-specific antibodies
However, four laboratories incorrectly identified a negative
sample as inconclusive/positive
Although individual serotypes were correctly identified
for each assay, some laboratories included multiple
serotypes in overall conclusions
Question of cross reactivity?
Panel 3b
Take home messages
18. O
A
C
More on cross-reactivity
See poster by Alison Morris
O
A
C
O
A
C
050100
050100
050100
050100
050100
050100
Partners:
SAT1
SAT2
SAT3
Asia1
SAT1
SAT2
Asia1
SAT1
SAT2
SAT3
Asia1
SAT3
19. Acknowledgement
World Reference Laboratory
Central Service Unit
Proficiency Testing Scheme Advisory Board
for participating
FMD and SVD
Reference Laboratories
Contact for PTS – Anna.Ludi@pirbright.ac.uk
20. 2019 PTS and beyond
From January 1st 2019 the European Union PTS will
be carried out by by anses and sciensano
There is currently no budget for the FAO/self-funded
PTS for 2019
However, final decisions have not yet been made
Your feedback as participants would be useful to
determine a way forward…