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The NY Times variant tracker is perhaps the most accessible and relevant publication for non-molecular biologists and the general public
Each coronavirus contains nearly 30,000 letters of RNA. This genetic information allows the virus to infect ce
...
lls and hijack them to make new viruses.
more
Our awareness necessity of cystic fibrosis (CF) significantly predates our ability to comprehend the molecular factors that underpin its cause and affect prognosis. The dire warning “Woe to that child which when kissed on the forehead tastes salty
...
. He is bewitched and soon must die” has been circulating since the 1800s. CF patients taste salty when kissed because an elevated level of sweat chloride is a hallmark of the disease. If untreated, they rarely make it past their first birthday. Typical presentation also includes failure to thrive caused by pancreatic insufficiency and chronic recurrent chest infections.
more
The Institut Pasteur has created a MOOC entirely focused on Malaria, providing a glimpse of the wide range of disciplines involved and questions addressed in malaria research. It goes from basic cell and molecular bi
...
ology of malaria parasites to field and hospital based clinical research on malaria pathology. It covers the application of the latest genomic-based to investigate parasite biology to translational research on development of new control tools, including drugs and vaccines. It also deals with malaria epidemiology and clinical research, to better under-stand malaria as a public health
problem.
more
Interim Guidance 31 march 2020
WHO has established a shipment mechanism to expedite and cover the costs of the shipment of clinical samples from patients with suspected COVID-19 from the country of collection to one of the WHO reference laboratories providing confirmatory
...
molecular testing for COVID-19. This document explains the process and documentation required for shipment of specimens.
more
Many in-house and commercial assays that detect the COVID-19 virus have been developed or are currently under development. Many of these molecular assays are currently being validated in partner laboratories. An overview of assays that have applied
...
to FIND for participation in their assay assessment work can be found here
more
Accessed 2017
Please Download all Documents directly from the website: https://www.finddx.org/tb-laboratory-standard-operating-procedures-sops/
Laboratory Quality (TB01), General Procedures (TB02), Specimen Handling (TB03), Microscopy Procedures (TB04), Culture and drugs susceptibility testing (T
...
B05), Molecular methods (TB06), Equipment use and maintenance (TB07).
more
This document outlines minimum requirements of laboratory testing for COVID-19 and link laboratory testing with surveillance and contact tracing to guide the outbreak response by national health authorities using a reduced number of tests performed. The strategies are organized according to stages o
...
f transmission: (1) No cases reported or observed (Stage 0); (2) Imported cases (Stage 1); (3) Localized community transmission (Stage 2); (4) Large-scale community transmission (Stage 3). For each stage, the recommended approaches indicate which testing strategy to prioritize when there are severe limitations on laboratory testing. The document is based on the current epidemiology of COVID-19 and available molecular testing methods.
more
Standard operating procedures (SOP) for the management of tuberculosis in children
National Tuberculosis, Leprosy and Lung Disease Program (NTLD-Program), Kenya
Ministry of Health, Kenya
(2017)
C1
2nd edition. Children with TB comprise about 10-12% of the total TB cases diagnosed in the country. This burden is likely to be higher given the challenges in diagnosing TB in children. The symptoms of TB in children mimic those of other childhood diseases. Children do not readily expectorate and th
...
ey have pauci-bacillary TB hence some will be missed using bacteriological tests. The government has however introduced GeneXpert molecular testing that is more sensitive than microscopy in detecting TB. Health care workers therefore need a reference guide to obtaining sputum from children for testing. Treatment of TB in children has been reviewed and now includes Ethambutol. There are now improved paediatric friendly TB medicines for treatment of TB in children and health care workers need a reference guide to enable them accurately dispense the TB medicine to children. Malnutrition is a common predisposing factor for TB in children. On the other hand, TB predisposes children to malnutrition or worsens an existing state of malnutrition. Nutrition care and support forms an integral part of treatment for a child with TB disease.
more
Sequencing SARS-CoV-2 in the Americas
The COVID-19 Genomic Surveillance Regional Network was created in 2020 not only to strengthen the sequencing capacity in the participating laboratories, but also for them to establish a routine SARS-CoV-2 genomic sequencing, as a strategy to increase the amoun
...
t of genetic sequence data available to the global community, which is critical to support the development of diagnostic protocols, the information for vaccine development and to better understand the evolution and molecular epidemiology of the SARS-CoV-2.
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This document summarizes current WHO guidance for public health surveillance of coronavirus disease 2019 (COVID-19) in humans caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
New elements include:
update of contact definitions, in line with latest cont
...
act tracing guidance
update of detection strategies in line with updated version of WHO SARS-CoV-2 testing guidance
reinfection evidence standardization and surveillance: molecular, genomic and immunological evidence of reinfection
inclusion of clinical case definition of Post COVID-19 condition as defined by WHO
definition of breakthrough infection
more
Leishmaniasis is a vector-borne disease that is transmitted by sandflies and caused by obligate intracellular protozoa of the genus Leishmania. Human infection is caused by about 21 of 30 species that infect mammals. These include the L. donovani complex with 3 species (L. donovani, L. infantum, and
...
L. chagasi); the L. mexicana complex with 3 main species (L. mexicana, L. amazonensis, and L. venezuelensis); L. tropica; L. major; L. aethiopica; and the subgenus Viannia with 4 main species (L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) panamensis, and L. (V.) peruviana). The different species are morphologically indistinguishable, but they can be differentiated by isoenzyme analysis, molecular methods, or monoclonal antibodies.
more
Dengue is a significant public health problem. There are four dengue virus serotypes identified; however, its diagnosis is difficult due to the existence of many viruses, bacteria, and parasites producing the same clinical presentation, being present in the same geographical area and even producing
...
coinfections. Therefore, determining whether a person has, had, or is infected with dengue virus is of great importance. In order to do so, direct and indirect laboratory tests have been developed to identify the virus or part of its structure that generally detects the antibody response. These techniques are used for diagnosis, epidemiological studies, monitoring, assessment and production of vaccines and antivirals, etc. They range from the use of cell cultures, animal models, inoculation by insects, and serology tests to the use of detection molecular tests and quantification of genetic material that are described in this chapter herein, a brief explanation of this methodology, its strengths and weaknesses, and its application in the dengue research.
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Background: The human helminth infections include ascariasis, trichuriasis, hookworm infections, schistosomiasis, lymphatic filariasis (LF) and onchocerciasis. It is estimated that almost 2 billion people worldwide are infected with helminths. Whilst the WHO treatment guidelines for helminth infecti
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ons are mostly aimed at controlling morbidity, there has been a recent shift with some countries moving towards goals of disease elimination through mass drug administration, especially for LF and onchocerciasis. However, as prevalence is driven lower, treating entire populations may no longer be the most efficient or cost-effective strategy. Instead, it may be beneficial to identify individuals or demographic groups who are persistently infected, often termed as being “predisposed” to infection, and target treatment at them.
Methods: The authors searched Embase, MEDLINE, Global Health, and Web of Science for all English language, humanbased papers investigating predisposition to helminth infections published up to October 31st, 2017. The varying definitions used to describe predisposition, and the statistical tests used to determine its presence, are summarised. Evidence for predisposition is presented, stratified by helminth species, and risk factors for predisposition to infection are identified and discussed.
Results: In total, 43 papers were identified, summarising results from 34 different studies in 23 countries. Consistent evidence of predisposition to infection with certain species of human helminth was identified. Children were regularly found to experience greater predisposition to Ascaris lumbricoides, Schistosoma mansoni and S. haematobium than adults. Females were found to be more predisposed to A. lumbricoides infection than were males. Household clustering of infection was identified for A. lumbricoides, T. trichiura and S. japonicum. Ascaris lumbricoides and T. trichiura also showed evidence of familial predisposition. Whilst strong evidence for predisposition to hookworm infection was identified, findings with regards to which groups were affected were considerably more varied than for other helminth species.
Conclusion: This review has found consistent evidence of predisposition to heavy (and light) infection for certain human helminth species. However, further research is needed to identify reasons for the reported differences between demographic groups. Molecular epidemiological methods associated with whole genome sequencing to determine ‘who infects whom’ may shed more light on the factors generating predisposition.
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Severe and difficult asthma in a low- and middle-income country (LMIC) can relate to lack of availability of basic medications; potentially reversible factors such as poor adherence or comorbidities such as obesity inhibiting a good response to treatment; and (rarely) true severe, therapy-resistant
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asthma. However, definitions of severity should encompass not merely doses of prescribed medication, but also underlying risk. The nature of asthmatic airway disease shows geographical variation, and LMIC asthma should not be assumed to be phenotypically the same as that in high-income countries (HICs). The first assessment step is to ensure another diagnosis is not being missed. Largely, political action is needed if children with asthma are to get access to basic medications. If a child is apparently not responding to low dose, simple medications, the next step is not to increase the dose but perform a detailed assessment of what factors (for example co-morbidities such as obesity, or social factors like poor adherence) are inhibiting a treatment response; in most cases, an underlying reason can be found. An assessment of risk of future severe asthma attacks, side-effects of medication and impaired lung development is also important. True severe, therapy-resistant asthma is rare and there are multiple underlying molecular pathologies. In HICs, steroid-resistant eosinophilia would be treated with omalizumab or mepolizumab, but the cost of these is prohibitive in LMICs, the biomarkers of successful therapy are likely only relevant to HICs. In LMICs, a raised blood eosinophil count may be due to parasites, so treating asthma based on the blood eosinophil count may not be appropriate in these settings.
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Advice on the use of point-of-care immunodiagnostic tests for COVID-19
OCHA; Reliefweb; World Health Organization (WHO)
OCHA; Reliefweb; World Health Organization (WHO); Health Cluster
(2020)
C2
Scientific brief
8 April 2020
J Infect Dis. (2012) 206 (suppl. 1): S61-S67
Influenza data gaps in sub-Saharan Africa include incidence, case fatality, seasonal patterns, and associations with prevalent disorders. The authors found that the burden of influenza was small during 2007–2010 in this paediatric hospital in Kenya. In
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fluenza A virus subtype H3N2 predominated, and 2009 pandemic influenza A virus subtype H1N1 had little impact
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Many features of the environment have been found to exert an important influence on cardiovascular disease (CVD) risk, progression, and severity. Changes in the environment due to migration to different geographic locations, modifications in lifestyle choices, and shifts in social policies and cultu
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ral practices alter CVD risk, even in the absence of genetic changes. Nevertheless, the cumulative impact of the environment on CVD risk has been difficult to assess
and the mechanisms by which some environment factors influence CVD remain obscure. Human environments are complex; and their natural, social and personal domains are highly variable due to diversity in human ecosystems, evolutionary histories, social structures, and individual choices. Accumulating evidence supports the notion that ecological features such as the diurnal cycles of
light and day, sunlight exposure, seasons, and geographic characteristics of the natural environment such altitude, latitude and greenspaces are important determinants of cardiovascular health and CVD risk. In highly developed societies, the influence of the natural environment is moderated by the physical characteristics of the social environments such as the built environment
and pollution, as well as by socioeconomic status and social networks. These attributes of the
social environment shape lifestyle choices that significantly modify CVD risk. An understanding
of how different domains of the environment, individually and collectively, affect CVD risk could
lead to a better appraisal of CVD, and aid in the development of new preventive and therapeutic
strategies to limit the increasingly high global burden of heart disease and stroke.
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