SARS COV-2 PANDEMIC: EXPERIENCE AT REFERENCE VIROLOGY LABORATORY SHORT RUNNING TITLE: SARS COV-2 PANDEMIC EXPERIENCE

Objective: To share our large scale SARS CoV-2 PCR test experience in Northern Pakistan. Study Design: Prospective observational study. Place and Duration of Study: Virology Department, Armed Forces Institute of Pathology, Rawalpindi, from Feb to Dec 2020. Methodology: All the patients reporting to COVID-19 desk both indoor and outdoor were included in study. Nasopharyngeal swab specimen was taken from the patients arriving at reception. For hospitalized patient’s samples were received at reception placed in viral transport medium maintaining cold chain. Results: Among 193656 samples tested for SARS CoV-2 RNA by RT-PCR, 24338 (12.6%) were found positive and 169318 (87.4%) were negative. Mean age of patients was 38.25 ± 16.73 (1-110 years). 138781 (71.7%) were males and 54875 (28.3%) were females. 109765 (56.7%) samples were received from in patient department and 83891 (43.3%) samples were received from outpatient department. Highest number of cases (n=6224) seen during month of June followed by 5813 cases during May and 4786 cases during November (p-value <0.001). Most of the positive cases were in age group 21-40 years; 11122 (6%), followed by age group 41-60 years; 8133 (4.2%). More positive samples 14890 (7.7%) were received from in patient department and males 17928 (9.3%) were affected more than females. Conclusion: The two peaks of COVID-19 pandemic in Pakistan were observed during the months of May to July and again during October to December. Most positive patients in our setup were males in age group 21-40 years as this age group is more exposed to external environment.

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Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings

10.1101/2021.02.18.21251999 ◽

2021 ◽

Cited By ~ 1

Author(s):

Meredith S. Muller ◽

Srijana Bhattarai Chhetri ◽

Christopher Basham ◽

Tyler Rapp ◽

Feng-Chang Lin ◽

...

Keyword(s):

Cold Chain ◽

Nasopharyngeal Swab ◽

Resource Constrained ◽

Viral Loads ◽

Acute Infections ◽

Viral Transport ◽

Self Testing ◽

Nasal Swabs ◽

3D Printed ◽

Rna Stabilization

ABSTRACTBackgrounStandard nasopharyngeal swab testing for SARS-CoV-2 detection by PCR is not always feasible due to limitations in trained personnel, personal protective equipment, swabs, PCR reagents, and access to cold chain and biosafety hoods.MethodWe piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including both standard polyester flocked swabs as well as 3D printed plastic lattice swabs, placed into either viral transport media or an RNA stabilization agent. Quantitative SARS-CoV-2 viral detection by RT-qPCR was compared to that obtained by nasopharyngeal sampling as the reference standard. Pooling specimens in the lab versus pooling swabs at the point of collection was also evaluated.ResultsAmong 275 participants, flocked nasal swabs identified 104/121 individuals who were PCR-positive for SARS-CoV-2 by nasopharyngeal sampling (sensitivity 87%, 95% CI 79-92%), mostly missing those with low viral load (<10^3 viral copies/uL). 3D-printed nasal swabs showed similar sensitivity. When nasal swabs were placed directly into an RNA stabilizer, the mean 1.4 log decrease in viral copies/uL compared to nasopharyngeal samples was reduced to <1 log, even when samples were left at room temperature for up to 7 days. Pooling sample specimens or swabs both successfully detected samples >102viral copies/uL.ConclusionsNasal swabs are likely adequate for clinical diagnosis of acute infections to help expand testing capacity in resource-constrained settings. When collected into an RNA preservative that also inactivates infectious virus, nasal swabs yielded quantitative viral loads approximating those obtained by nasopharyngeal sampling.

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The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses

10.1101/2020.06.09.142323 ◽

2020 ◽

Cited By ~ 2

Author(s):

P.D. Kirkland ◽

M.J. Frost

Keyword(s):

Nucleic Acid ◽

Bovine Serum ◽

Large Scale ◽

Transport Medium ◽

Viral Transport ◽

Animal Pathogens ◽

Intact Virus ◽

Viral Transport Medium ◽

The Impact ◽

Foetal Bovine Serum

AbstractDuring the 2020 SARS-Cov-2 pandemic, there has been an acute shortage of viral transport medium. Many different products have been used to meet the demands of large-scale diagnostic and surveillance testing. The stability of SARS-Cov-2 RNA was assessed in several commercially produced transport media and an in-house solution. Coronavirus RNA was rapidly destroyed in the commercial transport media though the deleterious effects on intact virus were limited. Similar results were obtained for a Type A influenza virus. There was reduced detection of both virus and nucleic acid when a herpesvirus sample and purified DNA were tested. Collectively these data showed that the commercial viral transport media contained nucleases or similar substances and may seriously compromise diagnostic and epidemiological investigations.Recommendations to include foetal bovine serum as a source of protein to enhance the stabilising properties of viral transport media are contraindicated. Almost all commercial batches of foetal bovine serum contain pestiviruses and at times other bovine viruses. In addition to the potential for there to be nucleases in the transport medium, the presence of these viruses and other extraneous nucleic acid in samples may compromise the interpretation of sequence data. The inclusion of foetal bovine serum presents a biosecurity risk for the movement of animal pathogens and renders these transport media unsuitable for animal disease diagnostic applications. While these transport media may be suitable for virus culture purposes, there could be misleading results if used for nucleic acid-based tests. Therefore, these products should be evaluated to ensure fitness for purpose.

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THE SOME QUESTIONS OF AUTONOMOUS MOTION AND MANAGEMENT OF LAND-MOBILE ROBOTIC COMPLEXES FOR UKRAINIAN GROUND FORCESE

Collection of scientific works of Odesa Military Academy ◽

10.37129/2313-7509.2019.11.53-58 ◽

2019 ◽

pp. 53-58

Author(s):

О. Кravchuk ◽

V. Symonenkov ◽

I. Symonenkova ◽

O. Hryhorev

Keyword(s):

Large Scale ◽

Armed Forces ◽

Distributed Information ◽

Wide Range ◽

Highly Effective ◽

Information Management Systems ◽

Robotic Devices ◽

Principles And Standards ◽

And Control ◽

The Eu

Today, more than forty countries of the world are engaged in the development of military-purpose robots. A number of unique mobile robots with a wide range of capabilities are already being used by combat and intelligence units of the Armed forces of the developed world countries to conduct battlefield intelligence and support tactical groups. At present, the issue of using the latest information technology in the field of military robotics is thoroughly investigated, and the creation of highly effective information management systems in the land-mobile robotic complexes has acquired a new phase associated with the use of distributed information and sensory systems and consists in the transition from application of separate sensors and devices to the construction of modular information subsystems, which provide the availability of various data sources and complex methods of information processing. The purpose of the article is to investigate the ways to increase the autonomy of the land-mobile robotic complexes using in a non-deterministic conditions of modern combat. Relevance of researches is connected with the necessity of creation of highly effective information and control systems in the perspective robotic means for the needs of Land Forces of Ukraine. The development of the Armed Forces of Ukraine management system based on the criteria adopted by the EU and NATO member states is one of the main directions of increasing the effectiveness of the use of forces (forces), which involves achieving the principles and standards necessary for Ukraine to become a member of the EU and NATO. The inherent features of achieving these criteria will be the transition to a reduction of tasks of the combined-arms units and the large-scale use of high-precision weapons and land remote-controlled robotic devices. According to the views of the leading specialists in the field of robotics, the automation of information subsystems and components of the land-mobile robotic complexes can increase safety, reliability, error-tolerance and the effectiveness of the use of robotic means by standardizing the necessary actions with minimal human intervention, that is, a significant increase in the autonomy of the land-mobile robotic complexes for the needs of Land Forces of Ukraine.

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Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints

Future Microbiology ◽

10.2217/fmb-2020-0094 ◽

2020 ◽

Vol 15 (15) ◽

pp. 1483-1487

Author(s):

Nikhil S Sahajpal ◽

Ashis K Mondal ◽

Allan Njau ◽

Sudha Ananth ◽

Kimya Jones ◽

...

Keyword(s):

Supply Chain ◽

Rna Extraction ◽

Nasopharyngeal Swab ◽

Sample Collection ◽

Rt Pcr ◽

Pcr Assay ◽

Short Supply ◽

Viral Transport ◽

3D Printed ◽

Bridging Studies

RT-PCR-based assays for the detection of SARS-CoV-2 have played an essential role in the current COVID-19 pandemic. However, the sample collection and test reagents are in short supply, primarily due to supply chain issues. Thus, to eliminate testing constraints, we have optimized three key process variables: RNA extraction and RT-PCR reactions, different sample types and media to facilitate SARS-CoV-2 testing. By performing various validation and bridging studies, we have shown that various sample types such as nasopharyngeal swab, bronchioalveolar lavage and saliva, collected using conventional nasopharyngeal swabs, ESwab or 3D-printed swabs and, preserved in viral transport media, universal transport media, 0.9% sodium chloride or Amies media are compatible with RT-PCR assay for COVID-19. Besides, the reduction of PCR reagents by up to fourfold also produces reliable results.

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To Establish A Normal Range of Inter-Incisal Opening - A Study of 756 Subjects of Age Group 20-50 Years in Yamunanagar City, Haryana.

Dental Journal of Advance Studies ◽

10.1055/s-0038-1670583 ◽

2013 ◽

Vol 01 (01) ◽

pp. 001-003

Author(s):

Aruna Singh ◽

Nymphea Pandit ◽

Monica Sharma

Keyword(s):

Pearson Correlation ◽

Mouth Opening ◽

Clinical History ◽

P Value ◽

Age Group ◽

Male Population ◽

Female Population ◽

Odontogenic Infections ◽

Anterior Teeth ◽

Average Maximum

Abstract Aim- 1. The aim of this study was to investigate the average maximum range of inter-incisal mouth opening in a representative sample of the adult subjects of Haryana. 2. To see any correlation between maximal inter-incisal opening with age. Methods- Maximum mouth opening was studied in 756 adult subjects with age range of 20-50 years in Yamunanagar, Haryana. Age limit was further divided into three groups (20-30, 31-40, 41-50). Those with clinical history of TMJ involvement, OSMF, any trauma, odontogenic and non-odontogenic infections, dental prosthesis on the anterior teeth, congenital anomalies in the maxillofacial region were excluded from this study. The measurements were recorded twice and mean of the two values were taken. Statistical Analysis- Independent sample t-test was calculated to compare age and mouth opening in both male and females respectively. Bivariate pearson correlation was used to see any relationship between age and mouth opening. P-value ≤ 0.05 and CI (confidence interval) at 95% were considered statistically significant. The Results- The average mouth opening of males (45.36±6.70 mm) subjects was higher as compared to female (41.27 ± 6.75 mm) with significant, p-value 0.000. The mean mouth opening ± SD for both sexes combined was 43.39 ± 7.02 mm. The corresponding values for mean inter-incisal opening in male population aged 20-30, 31-40, 41-50 were 45.52 ± 7.15, 46.16 ± 5.47, 42.96 ± 6.82 mm and in female population aged 20-30, 31-40, 41-50 were 41.40 ± 7.08, 41.60 ± 6.29 and 40.03 ± 6.38 mm respectively. Conclusion- Maximal mouth opening differ significantly with gender. There is a decrease in MMO with older age group.

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Haematological profile of children with malaria in Sorong, West Papua, Indonesia

Malaria Journal ◽

10.1186/s12936-021-03638-w ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Syilvia Jiero ◽

Ayodhia Pitaloka Pasaribu

Keyword(s):

Malaria Infection ◽

Clinical Symptoms ◽

Public Health Problem ◽

Malaria Diagnosis ◽

White Blood Count ◽

P Value ◽

Major Public Health Problem ◽

Age Group ◽

Haematological Profile ◽

West Papua

Abstract Background Malaria remains a major public health problem in Indonesian Papua, with children under five years of age being the most affected group. Haematological changes, such as cytopenia that occur during malaria infection have been suggested as potential predictors and can aid in the diagnosis of malaria. This study aimed to assess the haematological alterations associated with malaria infection in children presenting with signs and symptoms of malaria. Methods A retrospective study was performed by collecting data from the medical records of malaria patients at Sorong Regional General Hospital, Sorong, West Papua, Indonesia, both from outpatient and inpatient clinics, from January 2014 until December 2017. The laboratory profile of children suffering from malaria was evaluated. Results One hundred and eighty-two children aged 1 month to 18 years old were enrolled. The subjects were mostly male (112, 61.5%) with a mean age of 6.45 years (SD = 4.3 years). Children below 5 years of age suffered the most from malaria in this study (77, 42.3%). One hundred two subjects (56%) were infected with Plasmodium falciparum. Half of the enrolled subjects (50%) had haemoglobin level (Hb) between 5.1 and 10 gr/dL. A total of 41 children (53.2%) less than 5 years old suffered from P. falciparum infection. In the age group of 5–10 years, there were 34 children (57.6%) who suffered from P. falciparum, and in the age group > 10 years, 27 children (58.7%) suffered from P. falciparum infection. Only 4 subjects (5.2%) in the less than 5 years old age group had mixed malaria infection. Among eight predictors of the haematological profile, there were five predictors that were significantly associated with the diagnostic criteria, namely haemoglobin, haematocrit, leukocytes, platelets and monocytes (p < 0.05). Generally, clinical symptoms are not significantly associated with a malaria diagnosis, and only one variable showed a significant relationship, pale, with a P value of 0.001. Conclusions Children with malaria had changes in some haematological markers, with anaemia, low platelet count, white blood count, and lymphocyte count being the most important predictors of malaria infection in the study area. These markers could be used to raise suspicion of malaria in children living in high endemic areas, such as West Papua.

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Navigating gender in elite bargains: Women's movements and the quest for inclusive peace in Colombia

Review of International Studies ◽

10.1017/s0260210521000334 ◽

2021 ◽

pp. 1-24

Author(s):

Alexandra Phelan ◽

Jacqui True

Keyword(s):

Large Scale ◽

Armed Forces ◽

Women's Movements ◽

Power Structures ◽

Peace Agreement ◽

Bargaining Process ◽

Political Bargaining ◽

Significant Case ◽

Gender Based ◽

And Gender

Abstract A growing body of scholarship connects the participation of women and the inclusion of gender provisions to the sustainability of peace settlements. But how do women's groups navigate gender power structures and gendered forms of violence within complex and fragile political bargaining processes aimed at ending large-scale conflict? The 2016 Colombian peace agreement, internationally applauded for its inclusion of strong gender provisions and women's participation as negotiators and peace advocates, is a significant case for examining these questions. Drawing on original case material, including interviews of key actors on different sides of the conflict – this article analyses the political bargaining dynamics within and among women's movements, the Santos government and the Revolutionary Armed Forces of Colombia (Fuerzas Armadas Revolucionarias de Colombia, FARC). We argue that the inclusion of women was pivotal in transforming the elite bargaining process and power structures of Colombian society enabling a gender-based approach to the substantive peace agenda addressing transitional gender justice for sexual violence survivors and gender-equal redistribution through land and rural reform programmes. The study suggests that deeply situated political bargaining analysis is essential to navigating gender in elite bargains rather than a one-size-fits-all approach to inclusive peace.

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Trends of Stomach Cancer in Central Serbia

Medicina ◽

10.3390/medicina57070665 ◽

2021 ◽

Vol 57 (7) ◽

pp. 665

Author(s):

Miodrag M. Stojanovic ◽

Natasa K. Rancic ◽

Marija R. Andjelkovic Apostolovic ◽

Aleksandra M. Ignjatovic ◽

Mirko V. Ilic

Keyword(s):

Stomach Cancer ◽

Preventive Measures ◽

Age Groups ◽

Optimal Number ◽

P Value ◽

Age Group ◽

Joinpoint Regression ◽

Mortality Trends ◽

Incidence Trend ◽

Incidence And Mortality

Somach cancer is the third most common cause of cancer-related deaths worldwide. The objective of the paper was to analyze the incidence and mortality trends of stomach cancer in Central Serbia in the period between 1999–2017. Materials and Methods: trends and annual percentage change (APC) of the incidence and mortality rate with corresponding 95% confidence intervals (CI) were calculated by joinpoint regression analyses. The optimal number of Joinpoints was identified using the Monte Carlo permutation method. The trend was considered to be significantly increasing (positive change) or decreasing (negative change) when the p-value was below 0.05 (p < 0.05). Results: the total number of new cases was 16,914 (10,873 males and 6041 females) and the total number of mortality cases was 14,790 (9348 in and 5442 in females). Almost one third (30.8%) of new cases were registered in the 60–69-year age group, and new cases were significantly more frequent in males than in females (30.8% vs. 29.02%, p < 0.001). Joinpoint regression analysis showed a significant decrease of incidence trend in females during the 2000–2015 period with APC of −2.13% (95% CI: −3.8 to −0.5, p < 0.001). An insignificant decrease in incidence trend was in males with APC of −0.72% (95% CI: −2.3 to 0.9, p = 0.30). According to the joinpoint analysis, a significant decrease of mortality trends both in males during 2000–2015 with APC of −2.21% (95% CI: −1.6 to −7.5, p ≤ 0.001 and in females, during the same period, with APC of −1.75% (95% CI: −2.9 to −0.6, p < 0.001) was registered. From 2015 to 2017, a significant increase of mortality was registered with APC of 44.5% (95% CI: from 24.2 to −68.1, p ≤ 0.001) in females and in males with APC of 53.15% (95% CI: 13.5 to −106.6, p ≤ 0.001). Conclusion: a significant decrease of stomach cancer incidence trend in females and insignificant decrease of incidence trend in males were determined in Central Serbia. Based on presented results, the mortality trend decreased significantly both in males and in females during 2000–2015, and from 2015 to 2017 we recorded a significant increase in mortality in both sexes. We found significantly more new cases in women than in men in the age group of 40–49, and the mortality of stomach cancer was significantly more frequent among females compared to males in the age groups 30–39, as well as in the 50–59 age group. There is a need for improving recording and registration of new cases of stomach cancer, especially in females. Urgent primary and secondary preventive measures are needed—introducing stomach cancer screening and early detection of premalignant changes. Urgent primary and secondary preventive measures are needed.

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Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

Scientific Reports ◽

10.1038/s41598-021-81487-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shan Wei ◽

Esther Kohl ◽

Alexandre Djandji ◽

Stephanie Morgan ◽

Susan Whittier ◽

...

Keyword(s):

Limit Of Detection ◽

Point Of Care ◽

Diagnostic Testing ◽

Rna Extraction ◽

Cost Effective ◽

Clinical Samples ◽

Nasopharyngeal Swab ◽

Percentage Agreement ◽

Testing Method ◽

Viral Transport

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.

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Condom Use During Last Sexual Contact and Last 30 Days in Two Samples of Caribbean Military Personnel

American Journal of Men s Health ◽

10.1177/1557988311418218 ◽

2011 ◽

Vol 6 (2) ◽

pp. 132-135 ◽

Cited By ~ 2

Author(s):

Rachel Hallum-Montes ◽

Rohan D’Souza ◽

Maria Isabel Tavarez ◽

Russell Manzanero ◽

Grace E. Dann ◽

...

Keyword(s):

Condom Use ◽

Large Scale ◽

Monitoring And Evaluation ◽

Armed Forces ◽

Sexual Contact ◽

Unprotected Sex ◽

Sexually Transmitted ◽

Populations At Risk ◽

Two Samples ◽

Biological And Behavioral Surveillance

Condom use during last sexual contact is a survey measure that may be used to inform monitoring and evaluation indicators of recent condom use in populations at risk for HIV infection and other sexually transmitted infections, such as the uniformed services. The authors tested for differences in condom use measures that were fielded within separate Biological and Behavioral Surveillance Surveys conducted in the armed forces of two separate nations: the Dominican Republic and Belize. Both surveys included measures of condom use during last sexual contact with specified partners and both surveys included the Risk Behavior Assessment (RBA), which measures specific sexual acts and condom use frequency during a specified time period. In both samples, more than 40% of respondents who reported condom use during last sexual contact with a regular partner also reported engaging in unprotected sex when screened with the RBA. Furthermore, more than 60% of respondents who reported condom use during last sexual encounter with a commercial sex worker also reported engaging in unprotected sex when screened with the RBA. The results carry implications for monitoring and evaluation indicators of large-scale HIV prevention programs. The authors recommend that, when feasible, more in-depth instruments such as the RBA be considered to measure recent condom use in populations of uniformed services personnel.

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