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Comparative Analysis, Distribution, and Characterization of Microsatellites in Orf Virus Genome
www.nature.com/scientificreports OPEN Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome Basanta Pravas Sahu1, Prativa Majee 1, Ravi Raj Singh1, Anjan Sahoo2 & Debasis Nayak 1* Genome-wide in-silico identifcation of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036–1,181 microsatellites per strain. The further screening revealed the presence of 83–107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6–8.4 and 53.0–59.5 bp/ kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6–0.8 and 12.1–17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD signifcantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-signifcantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)- x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. -
ICD-9 Diagnosis Codes Effective 10/1/2011 (V29.0) Source: Centers for Medicare and Medicaid Services
ICD-9 Diagnosis Codes effective 10/1/2011 (v29.0) Source: Centers for Medicare and Medicaid Services 0010 Cholera d/t vib cholerae 00801 Int inf e coli entrpath 01086 Prim prg TB NEC-oth test 0011 Cholera d/t vib el tor 00802 Int inf e coli entrtoxgn 01090 Primary TB NOS-unspec 0019 Cholera NOS 00803 Int inf e coli entrnvsv 01091 Primary TB NOS-no exam 0020 Typhoid fever 00804 Int inf e coli entrhmrg 01092 Primary TB NOS-exam unkn 0021 Paratyphoid fever a 00809 Int inf e coli spcf NEC 01093 Primary TB NOS-micro dx 0022 Paratyphoid fever b 0081 Arizona enteritis 01094 Primary TB NOS-cult dx 0023 Paratyphoid fever c 0082 Aerobacter enteritis 01095 Primary TB NOS-histo dx 0029 Paratyphoid fever NOS 0083 Proteus enteritis 01096 Primary TB NOS-oth test 0030 Salmonella enteritis 00841 Staphylococc enteritis 01100 TB lung infiltr-unspec 0031 Salmonella septicemia 00842 Pseudomonas enteritis 01101 TB lung infiltr-no exam 00320 Local salmonella inf NOS 00843 Int infec campylobacter 01102 TB lung infiltr-exm unkn 00321 Salmonella meningitis 00844 Int inf yrsnia entrcltca 01103 TB lung infiltr-micro dx 00322 Salmonella pneumonia 00845 Int inf clstrdium dfcile 01104 TB lung infiltr-cult dx 00323 Salmonella arthritis 00846 Intes infec oth anerobes 01105 TB lung infiltr-histo dx 00324 Salmonella osteomyelitis 00847 Int inf oth grm neg bctr 01106 TB lung infiltr-oth test 00329 Local salmonella inf NEC 00849 Bacterial enteritis NEC 01110 TB lung nodular-unspec 0038 Salmonella infection NEC 0085 Bacterial enteritis NOS 01111 TB lung nodular-no exam 0039 -
Characterization of the Rubella Virus Nonstructural Protease Domain and Its Cleavage Site
JOURNAL OF VIROLOGY, July 1996, p. 4707–4713 Vol. 70, No. 7 0022-538X/96/$04.0010 Copyright q 1996, American Society for Microbiology Characterization of the Rubella Virus Nonstructural Protease Domain and Its Cleavage Site 1 2 2 1 JUN-PING CHEN, JAMES H. STRAUSS, ELLEN G. STRAUSS, AND TERYL K. FREY * Department of Biology, Georgia State University, Atlanta, Georgia 30303,1 and Division of Biology, California Institute of Technology, Pasadena, California 911252 Received 27 October 1995/Accepted 3 April 1996 The region of the rubella virus nonstructural open reading frame that contains the papain-like cysteine protease domain and its cleavage site was expressed with a Sindbis virus vector. Cys-1151 has previously been shown to be required for the activity of the protease (L. D. Marr, C.-Y. Wang, and T. K. Frey, Virology 198:586–592, 1994). Here we show that His-1272 is also necessary for protease activity, consistent with the active site of the enzyme being composed of a catalytic dyad consisting of Cys-1151 and His-1272. By means of radiochemical amino acid sequencing, the site in the polyprotein cleaved by the nonstructural protease was found to follow Gly-1300 in the sequence Gly-1299–Gly-1300–Gly-1301. Mutagenesis studies demonstrated that change of Gly-1300 to alanine or valine abrogated cleavage. In contrast, Gly-1299 and Gly-1301 could be changed to alanine with retention of cleavage, but a change to valine abrogated cleavage. Coexpression of a construct that contains a cleavage site mutation (to serve as a protease) together with a construct that contains a protease mutation (to serve as a substrate) failed to reveal trans cleavage. -
Measles and Rubella Initiative Outbreak Response Fund Application Standard Operating Procedures
M&RI SOP Feb 24, 2020 Final Measles and Rubella Initiative Outbreak Response Fund Application Standard Operating Procedures This update of the M&RI ORF Standard Operating Procedures (SOPs) includes the following modifications: 1. To encourage countries to submit applications for ORF support early in the evolution of the outbreak in order to effectively stop measles virus transmission before it becomes more widespread, M&RI will monitor indicators of timeliness of outbreak response immunization in accordance with Immunization Agenda 2030 guidelines; 2. To accelerate the process to receive support, M&RI has removed requirements for advance notification when requesting ORF support and has established a limited timeframe to evaluate the application for ORF support and to provide feedback or issue a decision letter; 3. To more comprehensively address outbreak response linked to timely and efficient use of vaccine, M&RI will allow for greater flexibility in areas of support on an exceptional basis and with adequate justification; 4. To reduce the likelihood of requested additional information or clarifications from M&RI, the SOPs provide greater detail regarding the key data elements and analysis recommended when investigating measles outbreaks and preparing reports, plans and budgets; 5. To maximize use of outbreak investigations and their follow up to strengthen immunization systems, M&RI requests countries to include findings from root cause analyses and, based on these, plans to improve routine immunization, surveillance and outbreak preparedness in the required post-outbreak report. A. Background The Measles and Rubella Initiative (M&RI) has provided funding through an outbreak response fund (ORF) since 2012 to support bundled vaccine and operational costs for measles and rubella outbreak response immunization (ORI), with Gavi supporting up to a total of US$10 million per year for Gavi-eligible countries. -
List of Codes Used to Identify Measures Reported in the QDFC
List of Codes Used to Identify Measures Reported in the Quarterly Dialysis Facility Compare Reports July 2018 List of Codes Used to Identify Measures Reported in the Quarterly Dialysis Facility Compare Reports Table of Contents Table 1a: Transfusion Summary for Medicare Dialysis Patients, Codes Used for Exclusions 3 CARCINOMA 3 COAGULATION 5 HEAD/NECK CANCER 5 HEMOLYTIC OR APLASTIC ANEMIA 9 LEUKEMIA 11 LYMPHOMA 15 METASTATIC 27 MYELOMA, ETC. 29 OTHER CANCER 30 SICKLE CELL 34 SOLID ORGAN CANCER 34 Table 1b: Transfusion Summary for Medicare Dialysis Patients, Codes Used to Identify Transfusion Events .................................................................................................................. 45 REVENUE CENTER CODES 45 PROCEDURE CODES 45 VALUE CODES 46 HCPCS CODE 46 Table 2a: Vascular Access Measures (SFR and Long-Term Catheter) for Medicare Dialysis Patients Based on Medicare Claims, Codes Used for Exclusions ........................................... 46 Produced by The University of Michigan Kidney Epidemiology and Cost Center Page 1 of 135 List of Codes Used to Identify Measures Reported in the Quarterly Dialysis Facility Compare Reports July 2018 COMA 46 END STAGE LIVER DISEASE 48 METASTATIC CANCER 48 Table 2b: Standardized Fistulae Rate (SFR) for Medicare Dialysis Patients Based on Medicare Claims, Codes Used for Prevalent Comorbidities Adjusted in Model .................................... 50 ANEMIA 50 CORONARY ARTERY DISEASE 52 CONGESTIVE HEART FAILURE 55 CEREBROVASCULAR DISEASE 56 CHRONIC OBSTRUCTIVE PULMONARY DISEASE 68 DIABETES 69 DRUG DEPENDENCE 79 INFECTIONS (NON-VASCULAR ACCESS-RELATED): 93 PERIPHERAL VASCULAR DISEASE (INCLUDES ARTERIAL, VENOUS AND NONSPECIFIC DISEASES) 124 Table 3: Dialysis Adequacy ................................................................................................... -
Client Services Manual Public Health Laboratory
CLIENT SERVICES MANUAL PUBLIC HEALTH LABORATORY COUNTY OF SANTA CLARA 2220 MOORPARK AVE, 2ND FLOOR SAN JOSE, CA 95128 (P) 408.885.4272 | (F) 408.885.4275 http://www.sccgov.org/sites /sccphd/en-us/HealthProviders/Lab Patricia Dadone, Public Health Laboratory Director Sara H. Cody, MD, Health Officer and Public Health Director Table of Contents 1 GENERAL INFORMATION ............................................................................................... 1.1 ROLE .............................................................................................................................................................. 1.1 MISSION STATEMENT ..................................................................................................................................... 1.1 ABBREVIATIONS.............................................................................................................................................. 1.2 LABORATORY CERTIFICATIONS ........................................................................................................................ 1.4 CLIENT SERVICES ............................................................................................................................................ 1.5 Hours of Operation: .............................................................................................................................. 1.5 Supplies .................................................................................................................................................. -
Specimen Type, Collection Methods, and Diagnostic Assays Available For
Specimen type, collection methods, and diagnostic assays available for the detection of poxviruses from human specimens by the Poxvirus and Rabies Branch, Centers for Disease Control and Prevention1. Specimen Orthopoxvirus Parapoxvirus Yatapoxvirus Molluscipoxvirus Specimen type collection method PCR6 Culture EM8 IHC9,10 Serology11 PCR12 EM8 IHC9,10 PCR13 EM8 PCR EM8 Lesion material Fresh or frozen Swab 5 Lesion material [dry or in media ] [vesicle / pustule Formalin fixed skin, scab / crust, etc.] Paraffin block Fixed slide(s) Container Lesion fluid Swab [vesicle / pustule [dry or in media5] fluid, etc.] Touch prep slide Blood EDTA2 EDTA tube 7 Spun or aliquoted Serum before shipment Spun or aliquoted Plasma before shipment CSF3,4 Sterile 1. The detection of poxviruses by electron microscopy (EM) and immunohistochemical staining (IHC) is performed by the Infectious Disease Pathology Branch of the CDC. 2. EDTA — Ethylenediaminetetraacetic acid. 3. CSF — Cerebrospinal fluid. 4. In order to accurately interpret test results generated from CSF specimens, paired serum must also be submitted. 5. If media is used to store and transport specimens a minimal amount should be used to ensure as little dilution of DNA as possible. 6. Orthopoxvirus generic real-time polymerase chain reaction (PCR) assays will amplify DNA from numerous species of virus within the Orthopoxvirus genus. Species-specific real-time PCR assays are available for selective detection of DNA from variola virus, vaccinia virus, monkeypox virus, and cowpox virus. 7. Blood is not ideal for the detection of orthopoxviruses by PCR as the period of viremia has often passed before sampling occurs. 8. EM can reveal the presence of a poxvirus in clinical specimens or from virus culture, but this technique cannot differentiate between virus species within the same genus. -
Diagnosis and Treatment of Orf
Vet Times The website for the veterinary profession https://www.vettimes.co.uk Diagnosis and treatment of orf Author : Graham Duncanson Categories : Farm animal, Vets Date : March 3, 2008 When I used to do a meat inspection for an hour each week, I came across a case of orf in one of the slaughtermen. The lesion was on the back of his hand. The GP thought it was an abscess and lanced the pustule. I was certain it was orf and got some pus into a viral transport medium. The Veterinary Investigation Centre in Norwich confirmed the case as orf and it took weeks to heal. I have always taken the zoonotic aspects of this disease very seriously ever since. When I got a pustule on my finger from my own sheep, I took potentiated sulphonamides by mouth and it healed within three weeks. I always advise clients to wear rubber gloves when dealing with the disease. I also advise any affected people to go to their GP, but not to let the doctor lance the lesion. Virus Orf, which should be called contagious pustular dermatitis, is not a pox virus but a Parapoxvirus. It is allied to viral diseases in cattle, pseudocowpox (caused by the most common virus found on the bovine udder) and bovine papular stomatitis (the oral form of pseudocowpox occurring in young cattle). Both these cattle viruses are self-limiting, rarely causing problems. Sheeppox, which is a Capripoxvirus, is not found in the UK or western Europe. However, it seems to have spread from the Middle East to Hungary. -
Orf, Also Known As Sheep Pox, Is a Common Disease
ORF http://www.aocd.org Orf, also known as sheep pox, is a common disease in sheep-farming regions of the world. Human infection with the orf virus is typically acquired by direct contact with open lesions of an infected animal. However, infection from fomites can also occur due to the virus being resistant to heat and dryness. An infected person will usually have a single nodular lesion at the point of contact, on the hand or forearm. The cause of orf is attributed to the orf virus. This virus is a member of the parapoxvirus genus which also contains milker’s nodule virus. The parapoxvirus genus is a member of the poxviridae family which also includes small pox and cowpox viruses. Orf is considered a zoonotic disease, meaning it affects animals; yet humans can contract the disease from infected sheep and goats. However, the orf virus is not transmitted human-to-human. Occupational acquisition of the disease is the most common means of contraction of the virus. Once a human is infected with the parapoxvirus a nodular lesion will appear. This lesion evolves through several stages. It begins as a papule but then progresses into a lesion with a red center surrounded by a white ring. The lesion then becomes red and weeping. If the lesion is located in an area with hair, temporary alopecia (hair loss) occurs. With further progression, the lesion becomes dry with black spots on the surface. It then flattens and forms a dry crust. The lesion then heals with minimal scarring. The progression of this disease occurs in about 6 weeks. -
Supporting Information
Supporting Information Rosenberg et al. 10.1073/pnas.1307243110 SI Results and Discussion domestic ungulates (horses, cows, sheep, goats, camels, and pigs) Of the 83 arboviruses, nonhuman vertebrate hosts have been and rodents in both groups might be a consequence of spatial identified for 70 (84%); the remaining 13 are presumed to be proximity to humans. Sentinel monkeys were often used in pro- zoonoses because there is no indication they can be transmitted cedures to isolate arboviruses, which might account for their directly between humans by vectors (Table S1). Animal hosts have higher representation among arboviruses. In contrast, there are been identified for at least 57 (44%) of the 130 nonarboviruses; an few published records of bats being routinely sampled during additional 5 (8%) are presumed on epidemiological evidence to arbovirus studies, and only two arboviruses (3%) have been iso- have nonhuman reservoirs (Table S1). A number of viruses infect lated from bats. The reason a much larger number of arbovirus more than one nonhuman vertebrate host species and it is likely species (n = 16) have been isolated from birds than have that the variety of hosts is wider than has been recorded. The nonarbovirus species (n = 1) might, however, be characteristic of predominant host groups for arboviruses (n = 70) are nonhuman the pathogenicity of the togaviruses and flaviviruses, which are primates (31%), rodents (29%), ungulates (26%), and birds (23%); much more common among the arboviruses. The most prominent for the nonarboviruses (n = 57), they are rodents (30%), ungu- vectors of arboviruses were mosquitoes (67%), ticks (19%), and lates (26%), bats (23%), and primates (16%). -
Human Papillomavirus and HPV Vaccines: a Review
Human papillomavirus and HPV vaccines: a review FT Cutts,a S Franceschi,b S Goldie,c X Castellsague,d S de Sanjose,d G Garnett,e WJ Edmunds,f P Claeys,g KL Goldenthal,h DM Harper i & L Markowitz j Abstract Cervical cancer, the most common cancer affecting women in developing countries, is caused by persistent infection with “high-risk” genotypes of human papillomaviruses (HPV). The most common oncogenic HPV genotypes are 16 and 18, causing approximately 70% of all cervical cancers. Types 6 and 11 do not contribute to the incidence of high-grade dysplasias (precancerous lesions) or cervical cancer, but do cause laryngeal papillomas and most genital warts. HPV is highly transmissible, with peak incidence soon after the onset of sexual activity. A quadrivalent (types 6, 11, 16 and 18) HPV vaccine has recently been licensed in several countries following the determination that it has an acceptable benefit/risk profile. In large phase III trials, the vaccine prevented 100% of moderate and severe precancerous cervical lesions associated with types 16 or 18 among women with no previous infection with these types. A bivalent (types 16 and 18) vaccine has also undergone extensive evaluation and been licensed in at least one country. Both vaccines are prepared from non-infectious, DNA-free virus-like particles produced by recombinant technology and combined with an adjuvant. With three doses administered, they induce high levels of serum antibodies in virtually all vaccinated individuals. In women who have no evidence of past or current infection with the HPV genotypes in the vaccine, both vaccines show > 90% protection against persistent HPV infection for up to 5 years after vaccination, which is the longest reported follow-up so far. -
Standardization of the Nomenclature for Genetic Characteristics of Wild-Type Rubella Viruses
Standardization of the nomenclature for genetic characteristics of wild-type rubella viruses. A number of genetically distinct groups of rubella viruses currently circulate in the world. The molecular epidemiology of rubella viruses will be primarily useful in rubella control activities for tracking transmission pathways, for documenting changes in the viruses present in particular regions over time, and for documenting interruption of transmission of rubella viruses. Use of molecular epidemiology in control activities is now more relevant since the W HO European Region and the Region of the Americas have adopted congenital rubella infection prevention and elimination goals respectively, targeted for 2010. However, a systematic nomenclature for wild-type rubella viruses has been lacking, which has limited the usefulness of rubella virus genetic data in supporting rubella control activities. A meeting was organized at W HO headquarters on 2-3 September, 2004 to discuss standardization of a nomenclature for describing the genetic characteristics of wild-type rubella viruses. This report is a summary of the outcomes of that meeting. The main goals of the meeting were to provide guidelines for describing the major genetic groups of rubella virus and to establish uniform genetic analysis protocols. In addition, development of a uniform virus naming system, rubella virus strain banks and a sequence database were discussed. Standardization of a nomenclature should allow more efficient communication between the various laboratories conducting molecular characterization of wild-type strains and will provide public health officials with a consistent method for describing viruses associated with cases, outbreaks and epidemics. Epidemiology and logistics Rubella viral surveillance is an important part of rubella surveillance at each phase of rubella control/elimination; the goal should be to obtain a virus sequence from each chain of transmission during the elimination phase or from representative samples from each outbreak during the control phase.