# ent

id: cord-005508-6zlqny9m
type: ORG
entity:
  Geneva World Health Organization International Spinal Cord Injury Data Sets International Spinal Cord Injury Core Data


id: cord-005508-6zlqny9m
type: ORG
entity:
  Institute for Health Information Version 2 0 Adelaide Australian Institute of Health and Welfare s AIHW National Injury Surveillance Unit NISU Development


id: cord-265682-yac7kzaf
type: ORG
entity:
  Fast Fourier Transform Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus Implications for Virus Origins


id: cord-265682-yac7kzaf
type: ORG
entity:
  Receptor Binding Whole Genome Sequencing Implications for Infection Prevention and Outbreak Investigations GISAID Global Initiative


id: cord-248932-i1v2lyd2
type: ORG
entity:
  COVID 19 Types Sources And Claims Of Reuters Institute for the Study of Journalism A Brief History Of


id: cord-276583-j8bf0eme
type: PROTEIN
entity:
  PGSs 1 aa 29 to 31 2 aa 141 to 143 3 aa 218 to 220 4 aa 298 to 300 5 aa 305 to 307 6 aa 492 to 494 and 7 aa 551 to 553


id: cord-271679-94h6rcih
type: ORG
entity:
  The World Health Organization Performance Assessment Tool for Quality Improvement in Hospitals PATH An Analysis


id: cord-271679-94h6rcih
type: ORG
entity:
  Biosurveillance A Review and Update Mass Casualty Incidents Organizational and Triage Management Issues Koenig


id: cord-322796-ojfrvtuy
type: DISEASE
entity:
  postviral olfactory dysfunction Postviral olfactory loss Postviral olfactory loss Taste and smell disorders Behavioural deficits


id: cord-301720-majpfxqn
type: DNA
entity:
  Kurdistan Sulaymania 12 Egypt Beni Suef 01 Turkey 10RS 3161 2010 IS VAR2 06 variant_2 Eg CLEVB 2 IBV 012 IR Bu variant2 SH1229 5


id: cord-272828-13i2y9kc
type: DISEASE
entity:
  postviral olfactory dysfunction Postviral olfactory loss Postviral olfactory loss Behavioural deficits


id: cord-347353-ll2pnl81
type: ORG
entity:
  the Chinese Center for Disease Control and Prevention Centre for Mathematical Modelling of Infectious Disease London School of Hygiene Tropical Medicine


id: cord-331701-izkz1hz4
type: ORG
entity:
  World Health Organisation Coronavirus Situation Report 8 th Evolution of Human Respiratory Syncytial Virus


# bib

id: cord-004041-2b2h1xog
author: Rezaei, Fatemeh
date: 2019-06-27
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6910748/
doi: 10.1136/fmch-2019-000124
title:
  Preparedness of community-based organisations in biohazard: reliability and validity of an assessment tool

abstract:
  The purpose of this study was to develop a tool for community-based health organisations (CBHOs) to evaluate the preparedness in biohazards concerning epidemics or bioterrorism. We searched concepts on partnerships of CBHOs with health systems in guidelines of the Centers for Disease Control and Prevention and literature. Then, we validated the researcher-made tool by face validity, content validity, exploratory factor analysis (EFA), confirmatory factor analysis (CFA) and criterion validity. Data were collected by sending the tool to 620 CBHOs serving under supervision of Iran’s ministry of health. Opinions of health professionals and stakeholders in CBHOs were used to assess face and content validity. Factor loads in EFA were based on three-factor structure that verified by CFA. We used SPSS V.18 and Mplus7 software for statistical analysis. About 105 health-based CBHOs participated. After conducting face validity and calculating content validity ratio and content validity index, we reached 54 items in the field of planning, training and infrastructure. We conducted construct validity using 105 CBHOs. Three items exchanged between the fields according to factor loads in EFA, and CFA verified the model fit as Comparative Fit Index, Tucker-Lewis index and root mean square error of approximation were 0.921, 0918 and 0.052, respectively. The Cronbach’s of the whole tool was 0.944. Spearman correlation coefficient confirmed criterion validity as coefficient was 0.736. Planning, training and infrastructure fields are the most important aspects of preparedness in health-based CBHOs. Applying the new assessment tool in future studies will show the weaknesses and capabilities of health-based CBHOs in biohazard and clear necessary intervention actions for health authorities.


id: cord-004110-xc8vv9x8
author: Eslahi, Aida Vafae
date: 2020-01-07
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6947998/
doi: 10.1186/s12879-020-4759-8
title:
  Prevalence of Toxocara and Toxascaris infection among human and animals in Iran with meta-analysis approach

abstract:
  BACKGROUND: Toxocariasis is a worldwide zoonotic parasitic disease caused by species of Toxocara and Toxascaris, common in dogs and cats. Herein, a meta-analysis was contrived to assess the prevalence of Toxocara/Toxascaris in carnivore and human hosts in different regions of Iran from April 1969 to June 2019. METHODS: The available online articles of English (PubMed, Science Direct, Scopus, and Ovid) and Persian (SID, Iran Medex, Magiran, and Iran Doc) databases and also the articles that presented in held parasitology congresses of Iran were involved. RESULTS: The weighted prevalence of Toxocara/Toxascaris in dogs (Canis familiaris) and cats (Felis catus) was 24.2% (95% CI: 18.0–31.0%) and 32.6% (95% CI: 22.6–43.4%), respectively. Also, pooled prevalence in jackal (Canis aureus) and red fox (Vulpes vulpes) was 23.3% (95% CI: 7.7–43.2%) and 69.4% (95% CI: 60.3–77.8%), correspondingly. Weighted mean prevalence of human cases with overall 28 records was 9.3% (95% CI: 6.3–13.1%). The weighted prevalence of Toxocara canis, Toxocara cati, and Toxascaris leonina was represented as 13.8% (95% CI: 9.8–18.3%), 28.5% (95% CI: 20–37.7%) and 14.3% (95% CI: 8.1–22.0%), respectively. CONCLUSION: Our meta-analysis results illustrate a considerable prevalence rate of Toxocara/Toxascaris, particularly in cats and dogs of northern parts of Iran. The presence of suitable animal hosts, optimum climate and close contact of humans and animals would have been the reason for higher seroprevalence rates of human cases in our region. Given the significance clinical outcomes of human Toxocara/Toxascaris, necessary measures should be taken.


id: cord-005279-w69ao8ic
title: Prevalence of subclinical coccidiosis in river buffalo calves of southwest of Iran
author: Bahrami, Somayeh
date: 2013-12-13
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089378/
doi: 10.2478/s11686-013-0167-1
abstract:
  Despite the importance of buffalo farming in Iran, little is known in this country about the abundance and distribution of Eimeria spp. in the animal species. The present study was designed to investigate the prevalence and species characterization of Eimeria oocysts in river buffalo calves of Khuzestan province, southwest of Iran. Of the total 108 fecal samples examined for Eimeria, 108 (100%) were found infected with 11 species of the parasite. Among the identified species of Eimeria, E. bovis was found to be the predominant etiological agent (76.85%), followed in order by E. canadensis (62.96%), E. zuernii (47.2%), E. ellipsoidalis (26.85%), E. subspherica (25.92%), E. brasiliensis (19.4%), E. auburnensis (18.51%), E. alabamensis (14.81%), E. pellita (11.1%), E. illinoisensis (5.5%) and E. bukidnonensis (2.7%). In most calves multiple infections with three species were present. While, 20.7% of calves showed heavy infection, 50.4 and 24.8% of calves showed weak and moderate infection, respectively. There was no significant difference in the OPG values between the calves of different localities. There was also no significant difference between the prevalence rate of infection in males and females. A total of 16.6% of all faecal samples were found to be diarrheic. A highly significant relationship could be identified between the occurrence of diarrhea and the level of E. bovis and E. zuernii oocysts excretion. Considering the pervasive occurrence and negative effects of the infection on the health condition and the growth performance of buffalo calves, infections should receive increased attention by both farmers and veterinarians.


id: cord-005508-6zlqny9m
author: Azadmanjir, Zahra
date: 2020-03-24
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093542/
doi: 10.1038/s41394-020-0265-x
title:
  The data set development for the National Spinal Cord Injury Registry of Iran (NSCIR-IR): progress toward improving the quality of care

abstract:
  STUDY DESIGN: Descriptive study. OBJECTIVES: The aim of this manuscript is to describe the development process of the data set for the National Spinal Cord Injury Registry of Iran (NSCIR-IR). SETTING: SCI community in Iran. METHODS: The NSCIR-IR data set was developed in 8 months, from March 2015 to October 2015. An expert panel of 14 members was formed. After a review of data sets of similar registries in developed countries, the selection and modification of the basic framework were performed over 16 meetings, based on the objectives and feasibility of the registry. RESULTS: The final version of the data set was composed of 376 data elements including sociodemographic, hospital admission, injury incidence, prehospital procedures, emergency department visit, medical history, vertebral injury, spinal cord injury details, interventions, complications, and discharge data. It also includes 163 components of the International Standards for the Neurologic Classification of Spinal Cord Injury (ISNCSCI) and 65 data elements related to quality of life, pressure ulcers, pain, and spasticity. CONCLUSION: The NSCIR-IR data set was developed in order to meet the quality improvement objectives of the registry. The process was centered around choosing the data elements assessing care provided to individuals in the acute and chronic phases of SCI in hospital settings. The International Spinal Cord Injury Data Set was selected as a basic framework, helped by comparison with data from other countries. Expert panel modifications facilitated the implementation of the registry process with the current clinical workflow in hospitals.


id: cord-103711-tnw82hbm
title: Modeling of COVID-19 Pandemic and Scenarios for Containment
author: Einian, Majid
date: 2020-03-30
url: https://doi.org/10.1101/2020.03.27.20045849
doi: 10.1101/2020.03.27.20045849
abstract:
  The impact of COVID-19 pandemic on the global health and world's economy have been profound and unseen since the Spanish flu of 1918-19. As of now, many countries have been severely affected, partly because of slow responses to the crisis, ill-preparedness of their health system, and the fragile health infrastructure and the shortage of protective equipment. This note evaluates various scenarios, based on an estimation of number of identified and unidentified infected cases, and examines the effectiveness of different policy responses to contain this pandemic. Our result, based on an estimation of the model for Iran, show that in many instances the number of unidentified cases, including asymptomatic individuals, could be much bigger than the reported numbers. The results confirm that in such circumstances, social distancing alone cannot be an effective policy unless a large portion of the population confine themselves for an extended period of time, which is not only difficult to implement, but it could also prove extremely costly and damaging to the economy. An alternative policy, this note argues, is to couple effective social distancing with extensive testing, even to those who are asymptomatic, and isolate the identified cases actively. Otherwise, many lives will be lost, and the health system will collapse, adding to the ongoing economic troubles that many countries have started to encounter.


id: cord-248932-i1v2lyd2
title: Characterizing and Comparing COVID-19 Misinformation Across Languages, Countries and Platforms
author: Madraki, Golshan
date: 2020-10-13
url: https://arxiv.org/pdf/2010.06455v2.pdf
doi: nan
abstract:
  Misinformation/disinformation about COVID-19 has been rampant on social media around the world. In this study, we investigate COVID-19 misinformation/ disinformation on social media in multiple languages - Farsi (Persian), Chinese, and English, about multiple countries - Iran, China, and the United States (US), and on multiple platforms such as Twitter, Facebook, Instagram, Weibo, and WhatsApp. Misinformation, especially about a global pandemic, is a global problem yet it is common for studies of COVID-19 misinformation on social media to focus on a single language, like English, a single country, like the US, or a single platform, like Twitter. We utilized opportunistic sampling to compile 200 specific items of viral and yet debunked misinformation across these languages, countries and platforms emerged between January 1 and August 31. We then categorized this collection based both on the topics of the misinformation and the underlying roots of that misinformation. Our multi-cultural and multilingual team observed that the nature of COVID-19 misinformation on social media varied in substantial ways across different languages/countries depending on the cultures, beliefs/religions, popularity of social media, types of platforms, freedom of speech and the power of people versus governments. We observe that politics is at the root of most of the collected misinformation across all three languages in this dataset. We further observe the different impact of government restrictions on platforms and platform restrictions on content in Iran, China, and the US and their impact on a key question of our age: how do we control misinformation without silencing the voices we need to hold governments accountable?


id: cord-257099-8k28vkgf
title: The epidemiology of reverse transmission of COVID-19 in Gansu Province, China
author: Fan, Jingchun
date: 2020-05-12
url: https://api.elsevier.com/content/article/pii/S1477893920302209
doi: 10.1016/j.tmaid.2020.101741
abstract:
  BACKGROUND: The transmission of COVID-19 is about to come under control within China, however, an emerging challenge to the Chinese authorities is reverse transmission due to COVID-19 patients/carriers evacuating from overseas to China. METHODS: We analysed the epidemiological characteristics of 311 Chinese citizens evacuated from Iran. All confirmed COVID-19 cases amongst the returnees were displayed by the spatial distribution pattern of the extent of COVID-19 infection. RESULTS: Characteristics that differed significantly amongst these returnees compared to the original infected cohorts in Gansu were mean age, occupation and sex. Differences observed between infected patients and non-patients amongst returnees were age, sex, race, occupation, the use of facemasks, and residential situation in Iran. The clinical features that were significantly related to infection were chill, shortness of breath, chest pain and nausea. Spatial distribution pattern analysis indicated that infected returnees had resided within Iranian provinces that had experienced high levels of COVID-19. The spatial distribution of the original homes of these returnees before departure for Iran demonstrated that returnees will largely return to northwest China, to regions that have only experienced low levels of infection within China. CONCLUSION: Blocking the reverse transmission of COVID-19 is critical in preventing a secondary outbreak of COVID-19.


id: cord-263518-6puccigu
title: Coronavirus Outbreak and Stress in Iranians
author: Maarefvand, Masoomeh
date: 2020-06-20
url: https://www.ncbi.nlm.nih.gov/pubmed/32575763/
doi: 10.3390/ijerph17124441
abstract:
  Iran has faced one of the worst COVID-19 outbreaks in the world, and no studies to date have examined COVID-19-related stress in the general Iranian population. In this first population-based study, a web-based survey was conducted during the peak of the outbreak to assess stress and its correlates in the Iranian population. A 54-item, valid, and reliable questionnaire, including items on demographic characteristics and past medical history, stress levels, awareness about signs and symptoms of COVID-19, knowledge about at-risk groups and prevention methods, knowledge about transmission methods, trust in sources of information, and availability of facemasks and sanitizers, was deployed via social and mass media networks. A total of 3787 Iranians participated in the study where the majority of the participants were females (67.4%), employed (56.1%), from developed provinces (81.6%), without chronic diseases (66.6%), and with ≥13 years of formal education (87.9%). The mean age of study participants was 34.9 years (range = 12–73), and the average stress score was 3.33 (SD = ±1.02). Stress score was significantly higher for females, those who were 30–39 years old, housewives, those with chronic diseases, individuals who were aware that there is no vaccine to prevent COVID-19, those who could not get facemasks or sanitizers, and individuals with higher knowledge about at-risk groups (p < 0.05). There was a significant correlation of stress scores with knowledge about prevention methods for COVID-19 (r = 0.21, p = 0.01) and trust in sources of information about COVID-19 (r = −0.18, p = 0.01). All of the predictors, except knowledge of two important at-risk groups and education, had a significant effect on stress scores based on a multivariate regression model. The COVID-19 outbreak could increase stress among all population groups, with certain groups at higher risk. In the high-risk groups and based on experience with previous pandemics, interventions are needed to prevent long-term psychological effects. Professional support and family-centered programs should be a part of pandemic mitigation-related policymaking and public health practices.


id: cord-265682-yac7kzaf
title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
author: Eden, John-Sebastian
date: 2020-04-10
url: https://www.ncbi.nlm.nih.gov/pubmed/32296544/
doi: 10.1093/ve/veaa027
abstract:
  The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.


id: cord-269679-dfma5kqc
title: Spread of Novel Coronavirus by Returning Pilgrims from Iran to Pakistan
author: Badshah, Syed Lal
date: 2020-04-09
txt: ./txt/cord-269679-dfma5kqc.txt
cache: ./cache/cord-269679-dfma5kqc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32268358/
doi: 10.1093/jtm/taaa044
abstract: nan
summary:
  key: cord-269679-dfma5kqc authors: Badshah, Syed Lal; Ullah, Asad; Badshah, Syed Hilal; Ahmad, Irshad cord_uid: dfma5kqc Iran was initially reluctant to close its borders with its neighbors as religious tourism is a big part of its revenue generation and the international community has already imposed economic sanctions over it due to its nuclear program. 3 Every year approximately 0.7 million Shia sect Muslims from Pakistan visit for a pilgrimage to various shrines in the cities of Iran that include Qom, Tehran, Tabriz, and Mashhad. It has been estimated that there are over eight thousand sacred sites in Iran alone and every year around eight million foreigners visit these shrines ( Figure 1 ). The pilgrimage mostly includes visits to cities like Karbala, Najaf, Kufa, Samara, and Baghdad in Iraq and several places in Damascus in Syria. Estimation of Coronavirus Disease 2019 (COVID-19) Burden and Potential for International Dissemination of Infection From Iran COVID-19 battle during the toughest sanctions against Iran The authors declared no conflict of interest.


id: cord-270614-4q7itegc
author: Bisaillon, Laura
date: 2020-08-25
txt: ./txt/cord-270614-4q7itegc.txt
cache: ./cache/cord-270614-4q7itegc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32840857/
doi: 10.1007/s11673-020-10032-9
summary:
  We argue that reflexive comparative analysis bridging social and visual analysis, anchored in embodied conditions of such people, offers a way to learn from responses to COVID-19 while also being an exercise in ethical research practice. We argue that reflexive comparative analysis bridging social and visual analysis, anchored in embodied conditions of such people, offers a way to learn from responses to COVID-19 while also being an exercise in ethical research practice. Such rituals have been repeated for millennia, and there are local and regional variations in the way people in Iran and its bordering countries and their diasporas enact Nowruz and the haft seen. This is a new Fig. 1 Separate, but together: Changing haft seen and Nowruz practices to care for each other within conditions imposed by COVID-19 experience for us, who have shared a roof for more than a decade.

title:
  Clever COVID-19, Clever Citizens-98: Critical and Creative Reflections from Tehran, Toronto, and Sydney

abstract:
  Our world suffers. Some people suffer more than others. Since the first part of 2020, ours is justly described as a time of uncertainty, threat, and upheaval. In this article, we offer reflections threaded narratively, told from the specificity of our societal contexts in Iran, Canada, and Australia. What might we learn in the present and anticipated future from people living chronically within conditions of uncertainty and immobility and also those experiencing uncertainty and immobility for the first time? We argue that reflexive comparative analysis bridging social and visual analysis, anchored in embodied conditions of such people, offers a way to learn from responses to COVID-19 while also being an exercise in ethical research practice. This reflection builds on and extends from our scholarly collaborations that have been ongoing since 2015. Our title recognizes this specific virus as stealthy. Importantly, our choice of words identifies resident Iranians—whose experiences were the original impetuses for this paper, and whose lives provide its empirical basis (98 is Iran’s country code)—as equally steely.


id: cord-271679-94h6rcih
title: Factors affecting hospital response in biological disasters: A qualitative study
author: Sharififar, Simintaj
date: 2020-03-16
url: https://doi.org/10.34171/mjiri.34.21
doi: 10.34171/mjiri.34.21
abstract:
  Background: The fatal pandemics of infectious diseases and the possibility of using microorganisms as biological weapons are both rising worldwide. Hospitals are vital organizations in response to biological disasters and have a crucial role in the treatment of patients. Despite the advances in studies about hospital planning and performance during crises, there are no internationally accepted standards for hospital preparedness and disaster response. Thus, this study was designed to explain the effective factors in hospital performance during biological disasters. Methods: Qualitative content analysis with conventional approach was used in the present study. The setting was Ministry of Health and related hospitals, and other relevant ministries responsible at the time of biologic events in Islamic Republic of Iran (IR of Iran) in 2018. Participants were experts, experienced individuals providing service in the field of biological disaster planning and response, policymakers in the Ministry of Health, and other related organizations and authorities responsible for the accreditation of hospitals in IR of Iran. Data were collected using 12 semi-structured interviews in Persian language. Analysis was performed according to Graneheim method. Results: After analyzing 12 interviews, extraction resulted in 76 common codes, 28 subcategories, and 8 categories, which are as follow: detection; treatment and infection control; coordination, Resources; training and exercises; communication and information system; construction; and planning and assessment. Conclusion: Hospital management in outbreaks of infectious diseases (intentional or unintentional) is complex and requires different actions than during natural disasters. In such disasters, readiness to respond and appropriate action is a multifaceted operation. In IR of Iran, there have been few researches in the field of hospital preparation in biologic events, and the possibility of standardized assessment has be reduced due to lack of key skills in confronting biological events. It is hoped that the aggregated factors in the 8 groups of this study can evaluate hospital performance more coherently.


id: cord-272828-13i2y9kc
title: Coincidence of COVID-19 epidemic and olfactory dysfunction outbreak in Iran
author: Bagheri, Seyed Hamidreza
date: 2020-06-15
url: https://doi.org/10.34171/mjiri.34.62
doi: 10.34171/mjiri.34.62
abstract:
  Background: The occurrence of anosmia/hyposmia during novel Coronavirus disease 2019 (COVID-19) may indicate a relationship between coincidence of olfactory dysfunction and coronavirus disease 2019 (COVID-19). This study aimed to assess the frequency of self-reported anosmia/hyposmia during COVID-19 epidemic in Iran. Methods: This population-based cross sectional study was performed through an online questionnaire from March 12 to 17, 2020. Cases from all provinces of Iran voluntarily participated in this study. Patients completed a 33-item patient-reported online questionnaire, including smell and taste dysfunction and their comorbidities, along with their basic characteristics and past medical histories. The inclusion criteria were self-reported anosmia/hyposmia during the past 4 weeks, from the start of COVID-19 epidemic in Iran. Results: A total of 10 069 participants aged 32.5±8.6 (7-78) years took part in this study, of them 71.13% women and 81.68% nonsmokers completed the online questionnaire. The correlation between the number of olfactory disorders and reported COVID-19 patients in all provinces up to March 17, 2020 was highly significant (Spearman correlation coefficient = 0.87, P< 0.001). A sudden onset of olfactory dysfunction was reported in 76.24% of the participations and persistent anosmia in 60.90% from the start of COVID19 epidemic. In addition, 80.38% of participants reported concomitant olfactory and gustatory dysfunctions. Conclusion: An outbreak of olfactory dysfunction occurred in Iran during the COVID-19 epidemic. The exact mechanisms by which anosmia/hyposmia occurred in patients with COVID-19 call for further investigations.


id: cord-276583-j8bf0eme
author: Ghalyanchi Langeroudi, Arash
date: 2012-01-21
url: https://www.ncbi.nlm.nih.gov/pubmed/32214973/
doi: 10.1007/s00580-012-1405-x
title:
  Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998–2007

abstract:
  H9N2 avian influenza A viruses (AIV) have become panzootic in Eurasia over the last decade and are endemic in Iran since 1998, and inactivated vaccine has been used in chickens to control the disease. The hemagglutinin (HA), one of eight protein-coding genes, plays an important role during the early stage of infection. To study their evolution and zoonotic potential, we conducted an in silico analysis of H9N2 viruses that have infected broiler in Tehran Province, Iran between 1998 and 2007. The complete coding region of HA genes from nine H9N2 subtypes isolated from chicken flocks in Tehran Province during 1998–2007 was amplified and sequenced. Sequence analysis and phylogenetic studies of H9N2 subtype viruses on the basis of data of 9 viruses in this study and 30 selected strains are available in the GenBank. Sequence and phylogenetic analyses revealed a large number of similar substitution mutations and close evolutionary relation among sequences of HA. The isolates possessed two types of amino acid motif –R–S-S-R/G-L- and -R-S-N-R/G-L- at the cleavage site of HA. The results showed that all nine representative H9N2 isolates belong to low pathogenic AIVs since none of the amino acid sequences at the cleavage site of the HA of the isolates possessed the basic motif required for highly pathogenic viruses (R-X-R/K-R). Six out of these nine isolates possessed leucine at position 226, which prevails in the sequences found in human strains. Phylogenetic analysis showed that all our isolates belonged to the G1-like sublineage. Also, these isolates showed some degree of homology with other H9N2 isolates, e.g., 89.46–93.93.39% with qu/HK/G1/97 and 93.39–98.39% with pa/Narita/92A/98. The available evidence indicates that HA genes of H9 influenza virus circulating in Iran during the past years were not well conserved. Our finding emphasizes the importance of reinforcing AIV surveillance, especially after the emergence of high pathogenicity in poultry in Iran.


id: cord-283133-jspfwuqu
author: Farangi, Mostafa
date: 2020-07-01
url: https://www.ncbi.nlm.nih.gov/pubmed/32367905/
doi: 10.1016/j.energy.2020.117771
title:
  The environmental and economic analysis of grid-connected photovoltaic power systems with silicon solar panels, in accord with the new energy policy in Iran

abstract:
  In recent years, authorities in Iran have introduced supporting policies for renewable energy resources but there is no comprehensive and updated survey from this perspective. This work aims to give a comprehensive survey on the country’s background from energy outlook and its prominent policies for renewable energy resources. Due to the high CO(2) emissions alongside with the high solar energy harvesting potential in Iran, We have presented a clear simulation on 20 kW and 1 MW grid-connected photovoltaic (PV) power plants using RETScreen software to determine the environmental and economic aspects based on the net greenhouse gases (GHG) emissions reduction, the annual electricity exported to the grid, the cumulative cash flows, and the payback period for the initial investment. According to this simulation, the annual GHG emissions reduction and the annual electricity exported to the grid for 20 kW and 1 MW PV power plants are 22.06 tCO(2), 1103 tCO(2), 39 MWh, and 1953 MWh, respectively. From the economic outlook, based on the new feed-in tariff for power plants and the supposed initial costs, the payback period for the initial investments are between 3 and 4, and 5 years for 20 kW and 1 MW PV power plants, respectively.


id: cord-294690-fpjhkb4g
author: Sharifi, Hamid
date: 2020-04-25
url: http://medrxiv.org/cgi/content/short/2020.04.22.20075440v1?rss=1
doi: 10.1101/2020.04.22.20075440
title:
  Estimating the number of COVID-19-related infections, deaths and hospitalizations in Iran under different physical distancing and isolation scenarios: A compartmental mathematical modeling

abstract:
  Background: Iran is one of the countries that has been overwhelmed with COVID-19. We aimed to estimate the total number of COVID-19 related infections, deaths, and hospitalizations in Iran under different physical distancing and isolation scenarios. Methods: We developed a Susceptible-Exposed-Infected-Removed (SEIR) model, parameterized to the COVID-19 pandemic in Iran. We used the model to quantify the magnitude of the outbreak in Iran and assess the effectiveness of isolation and physical distancing under five different scenarios (A: 0% isolation, through E: 40% isolation of all infected cases). We used Monte-Carlo simulation to calculate the 95% uncertainty intervals (UI). Findings: Under scenario A, we estimated 5,196,000 (UI 1,753,000 - 10,220,000) infections to happen till mid-June with 966,000 (UI 467,800 - 1,702,000) hospitalizations and 111,000 (UI 53,400 - 200,000) deaths. Successful implantation of scenario E would reduce the number of infections by 90% (i.e. 550,000) and change the epidemic peak from 66,000 on June 9th to 9,400 on March 1st. Scenario E also reduces the hospitalizations by 92% (i.e. 74,500), and deaths by 93% (i.e. 7,800). Interpretation: With no approved vaccination or therapy, we found physical distancing and isolation that includes public awareness and case-finding/isolation of 40% of infected people can reduce the burden of COVID-19 in Iran by 90% by mid-June.


id: cord-301720-majpfxqn
author: Saadat, Yousef
date: 2017-09-15
url: https://www.ncbi.nlm.nih.gov/pubmed/29085606/
doi: nan
title:
  Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015

abstract:
  The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. Samples were collected from broiler flocks in Bushehr province during 2014 - 2015. These flocks had respiratory problems such as gasping, sneezing and bronchial rales. A number of 135 tracheal swabs were taken from fifteen flocks (nine swabs per flock). Each three swabs collected from each flock were pooled in one tube (finally, we had three tubes for each flock). The samples were subjected to reverse transcription polymerase chain reaction (RT-PCR). The PCR products of positive samples were analyzed by sequencing of a (392 bp) segment of the spike gene and the related results were compared with the other IBV sequences in GenBank database. Samples from twelve farms (80.0%) were found to be positive. The viruses from seven farms (46.6%) were identified as field viruses closely related to variant 2. The viruses from three farms (20.0%) were characterized as Mass type and were related to vaccine strains. Two different IB viruses (variant 2 and Mass) were detected in samples from two farms (13.3%). The variant 2 genotype detected in Bushehr had high similarity to variant 2 reported from the Middle East. These variants displayed homologies ranging from 72.9% to 76.5%, and 78.8% to 80.0% with H120 and 4/91, respectively. It is necessary to design vaccination program of poultry farms using IBV strains circulating in the region.


id: cord-303331-xolksoy3
author: Pourghasemi, Hamid Reza
date: 2020-07-28
url: https://www.ncbi.nlm.nih.gov/pubmed/32722716/
doi: 10.1371/journal.pone.0236238
title:
  Assessment of the outbreak risk, mapping and infection behavior of COVID-19: Application of the autoregressive integrated-moving average (ARIMA) and polynomial models

abstract:
  Infectious disease outbreaks pose a significant threat to human health worldwide. The outbreak of pandemic coronavirus disease 2019 (COVID-19) has caused a global health emergency. Thus, identification of regions with high risk for COVID-19 outbreak and analyzing the behaviour of the infection is a major priority of the governmental organizations and epidemiologists worldwide. The aims of the present study were to analyze the risk factors of coronavirus outbreak for identifying the areas having high risk of infection and to evaluate the behaviour of infection in Fars Province, Iran. A geographic information system (GIS)-based machine learning algorithm (MLA), support vector machine (SVM), was used for the assessment of the outbreak risk of COVID-19 in Fars Province, Iran whereas the daily observations of infected cases were tested in the—polynomial and the autoregressive integrated moving average (ARIMA) models to examine the patterns of virus infestation in the province and in Iran. The results of the disease outbreak in Iran were compared with the data for Iran and the world. Sixteen effective factors were selected for spatial modelling of outbreak risk. The validation outcome reveals that SVM achieved an AUC value of 0.786 (March 20), 0.799 (March 29), and 86.6 (April 10) that displays a good prediction of outbreak risk change detection. The results of the third-degree polynomial and ARIMA models in the province revealed an increasing trend with an evidence of turning, demonstrating extensive quarantines has been effective. The general trends of virus infestation in Iran and Fars Province were similar, although a more volatile growth of the infected cases is expected in the province. The results of this study might assist better programming COVID-19 disease prevention and control and gaining sorts of predictive capability would have wide-ranging benefits.


id: cord-306925-yt5cscf1
author: Haji-Abdolvahab, Habibbolah
date: 2018-10-30
url: https://www.ncbi.nlm.nih.gov/pubmed/30377950/
doi: 10.1007/s11250-018-1743-z
title:
  Prevalence of avian influenza, Newcastle disease, and infectious bronchitis viruses in broiler flocks infected with multifactorial respiratory diseases in Iran, 2015–2016

abstract:
  In this study, the prevalence and spatial distribution of Newcastle disease, infectious bronchitis, and avian influenza have been evaluated in commercial broiler farms in 31 provinces in Iran. In this survey, a total of 233 affected broiler chicken farms were sampled. The infectious bronchitis virus (alone) was detected with highest frequency in 60 farms, and separately or combined with other agents, in 110 farms; Newcastle disease virus, separately, was detected in 28 farms, and in 63 farms separately or combined with other infectious agents; and avian influenza H9N2 was detected in 22 farms separately and in 51 farms separately or concomitant with other infectious agents. The sample tested negative for all H5 serotypes. The results of the present study show that the most prevalent avian viral infectious disease contributing to respiratory syndromes in broiler farms in Iran was infectious bronchitis due to infectious bronchitis virus serotypes variant 2 and 793/B. On the other hand, combined with the alternation of dominant viruses and circulating strains, flocks are exposed to unremitting anamorphic viral infections. Thus, the permanent monitoring of cases that have occurred and the review of vaccination plans of affected flocks every year are some of the necessary measures needed for strategic control of respiratory syndrome in broilers. It is noteworthy that execution of epidemiologic examinations on the cogent factors of prevalence of this syndrome and defeat of vaccination strategy in the flocks is urgent and has to be fulfilled on the definite causes of time.


id: cord-309762-p266f3el
author: Ahmady, Soleiman
date: 2020-05-07
url: https://doi.org/10.1017/dmp.2020.142
doi: 10.1017/dmp.2020.142
title:
  Transition to Virtual Learning During the Coronavirus Disease–2019 Crisis in Iran: Opportunity Or Challenge?

abstract:
  COVID-19 is a respiratory disease that can spread from one person to person. This virus is a novel coronavirus that was first identified during an investigation into an outbreak in Wuhan, China. Iran’s novel coronavirus cases reached 17,361 on 17 March, while death toll reached approximately 1,135. Its first death was officially announced on 20 February 2020 in Qom. The 2019 coronavirus pandemic has affected educational systems around the world, Also in Iran, and led to the closure of face to face courses in schools and universities. Therefore, virtual education can be seen as a turning point in education of these days in Iran.


id: cord-311495-svgw59ic
title: Short and long term impacts of COVID-19 on the pharmaceutical sector
author: Ayati, Nayyereh
date: 2020-07-03
url: https://www.ncbi.nlm.nih.gov/pubmed/32617864/
doi: 10.1007/s40199-020-00358-5
abstract:
  BACKGROUND: The novel coronavirus disease 2019 (COVID-19) was characterized as a global pandemic by the WHO on March 11th, 2020. This pandemic had major effects on the health market, the pharmaceutical sector, and was associated with considerable impacts; which may appear in short and long-term time-horizon and need identification and appropriate planning to reduce their socio-economic burden. OBJECTIVES: Current short communication study assessed pharmaceutical market crisis during the COVID-19 era; discussing short- and long-term impacts of the pandemic on the pharmaceutical sector. RESULTS: Short-term impacts of COVID-19 pandemic includes demand changes, regulation revisions, research and development process changes and the shift towards tele-communication and tele-medicine. In addition, industry growth slow-down, approval delays, moving towards self-sufficiency in pharm-production supply chain and trend changes in consumption of health-market products along with ethical dilemma could be anticipated as long-term impacts of COVID-19 pandemic on pharmaceutical sector in both global and local levels. CONCLUSION: The pandemic of COVID-19 poses considerable crisis on the health markets, including the pharmaceutical sector; and identification of these effects, may guide policy-makers towards more evidence-informed planning to overcome accompanying challenges. [Figure: see text]


id: cord-313286-nqvuas3p
author: Afshar Jahanshahi, A.
date: 2020-04-07
url: http://medrxiv.org/cgi/content/short/2020.04.03.20052571v1?rss=1
doi: 10.1101/2020.04.03.20052571
title:
  The distress of Iranian adults during the Covid-19 pandemic - More distressed than the Chinese and with different predictors

abstract:
  Background Early papers on the mental health of the public during the Covid-19 pandemic surveyed participants from China. Outside of China, Iran has emerged as one of the most affected countries with a high death count and rate. The paper presents the first empirical evidence from Iranian adults during the Covid-19 pandemic on their level of distress and its predictors. Methods On March 25-28, 2020, a dire time for Covid-19 in Iran, we surveyed 1058 adults from all 30 provinces in Iran using the Covid-19 Peritraumatic Distress Index (CPDI). Findings The distress level of Iranian adults (mean: 34.54; s.d.: 14.92) was significantly higher (mean difference: 10.9; t=22.7; p<0.0001; 95% CI: 10.0 to 11.8) than that of Chinese adults (mean: 23.65; s.d.: 5.45) as reported in a prior study with the same measure of Covid-19 Peritraumatic Distress Index (CPDI). We also found the predictors of distress in Iran vary from those in China. Interpretation Our findings that the predictors of distress in Iran vary from those in China suggest the need to study the predictors of mental health in individual countries during the Covid-19 pandemic to effectively identify and screen for those more susceptible to mental health issues. Keywords: Coronavirus; 2019-nCoV; Distress; Mental health; Psychiatric screening; Identifiers of mental issues in Covid-19 pandemic; Iran; Early evidence


id: cord-315925-hnvf634e
author: Bandarian, Fatemeh
date: 2020-10-03
url: https://doi.org/10.1007/s40200-020-00645-7
doi: 10.1007/s40200-020-00645-7
title:
  Endocrinology and Metabolism Research Institute from inception to maturity: an overview of 25-year activity

abstract:
  Endocrinology and Metabolism Research Institute (EMRI) was founded in 1993. EMRI progressed step by step from inception and reached to its maturation during the past 25 years. EMRI has expanded and progressed in different aspects including human resources and infrastructures (laboratories and new technologies) and has obtained the first rank in the country in endocrinology research. It has also collaborated with regional and international organizations such as World Health Organization (WHO), International Osteoporosis Foundation (IOF), and American Association of Clinical Endocrinologists (AACE). This article provides an overview of EMRI activities during a quarter of a century.


id: cord-318043-1x3dp1vv
title: Investigation of effective climatology parameters on COVID-19 outbreak in Iran
author: Ahmadi, Mohsen
date: 2020-04-17
url: https://doi.org/10.1016/j.scitotenv.2020.138705
doi: 10.1016/j.scitotenv.2020.138705
abstract:
  Abstract SARS CoV-2 (COVID-19) Coronavirus cases are confirmed throughout the world and millions of people are being put into quarantine. A better understanding of the effective parameters in infection spreading can bring about a logical measurement toward COVID-19. The effect of climatic factors on spreading of COVID-19 can play an important role in the new Coronavirus outbreak. In this study, the main parameters, including the number of infected people with COVID-19, population density, intra-provincial movement, and infection days to end of the study period, average temperature, average precipitation, humidity, wind speed, and average solar radiation investigated to understand how can these parameters effects on COVID-19 spreading in Iran? The Partial correlation coefficient (PCC) and Sobol’-Jansen methods are used for analyzing the effect and correlation of variables with the COVID-19 spreading rate. The result of sensitivity analysis shows that the population density, intra-provincial movement have a direct relationship with the infection outbreak. Conversely, areas with low values of wind speed, humidity, and solar radiation exposure to a high rate of infection that support the virus's survival. The provinces such as Tehran, Mazandaran, Alborz, Gilan, and Qom are more susceptible to infection because of high population density, intra-provincial movements and high humidity rate in comparison with Southern provinces.


id: cord-320895-y6pzrbdi
author: Arab-Zozani, Morteza
date: 2020-09-27
url: https://www.ncbi.nlm.nih.gov/pubmed/32713382/
doi: 10.1017/dmp.2020.261
title:
  COVID-19 in Iran: the Good, the Bad, and the Ugly Strategies for Preparedness – A Report From the Field

abstract:
  The emergence of coronavirus disease 2019 (COVID-19), a novel unknown virus that is challenging whole countries all over the world, has prompted different strategies from various governments. Iran, as one of the first countries to experience the onset of the virus outbreak, made and implemented some policies that should be assessed, so that lessons may be learned for the future. Although some negative actions and policies, such as delays in cancellation of international flights especially from China, not taking the disease seriously and comparing it with seasonal influenza, and the like, are hard to ignore, some impressive actions are also vividly clear. Policies, such as social distancing, dramatically increasing social awareness about preventive actions in terms of public health, and using masks and hand washing, were cost-effective policies that resulted in successful control of the virus in the first onset. While some quite clearly ineffective decisions were made by Iranian authorities, the huge catastrophic effect of sanctions cannot be forgotten. Possibly in level situations with similar countries, Iran will have far better results regarding preparedness for future pandemics like COVID-19.


id: cord-322796-ojfrvtuy
title: Coincidence of COVID-19 epidemic and olfactory dysfunction outbreak
author: Bagheri, S. H. R.
date: 2020-03-27
url: https://doi.org/10.1101/2020.03.23.20041889
doi: 10.1101/2020.03.23.20041889
abstract:
  Background Recent surge of olfactory dysfunction in patients who were referred to ENT clinics and concurrent COVID-19epidemic in Iran motivated us to evaluate anosmic/hyposmic patients to find any relation between these two events. Methods This is a cross-sectional study with an online checklist on voluntary cases in all provinces of Iran between the 12th and 17th March, 2020. Cases was defined as self-reported anosmia/hyposmia in responders fewer than 4 weeks later (from start the of COVID-19 epidemic in Iran). Variables consist of clinical presentations, related past medical history, family history of recent respiratory tract infection and hospitalization. Results In this study 10069 participants aged 32.5 +/- 8.6 (7-78) years, 71.13% female and 81.68% non-smoker completed online checklist. They reported 10.55% a history of a trip out of home town and 1.1% hospitalization due to respiratory problems recently. From family members 12.17% had a history of severe respiratory disease in recent days and 48.23% had anosmia/hyposmia. Correlation between the number of olfactory disorder and reported COVID-19 patients in all 31 provinces till 16th March 2020 was highly significant (Spearman correlation coefficient=0.87, p-Value<0.001). The onset of anosmia was sudden in 76.24% and till the time of filling the questionnaire in 60.90% of patients decreased sense of smell was constant. Also 83.38 of this patients had decreased taste sensation in association with anosmia. Conclusions It seems that we have a surge in outbreak of olfactory dysfunction happened in Iran during the COVID-19 epidemic. The exact mechanism of anosmia/hyposmia in COVID-19 patients needs further investigations.


id: cord-328930-5a0z1ryz
author: Karatayev, Marat
date: 2020-10-31
url: https://www.sciencedirect.com/science/article/pii/S0301420720300532
doi: 10.1016/j.resourpol.2020.101746
title:
  Establishing and comparing energy security trends in resource-rich exporting nations (Russia and the Caspian Sea region)

abstract:
  Abstract In the international arena, it is often the case that in countries which largely depend on foreign resources, energy security, and its key components i.e. security of energy supply, environment, technology, geopolitical and economic factors, is a subject of concern. However, due to the abundance of fossil fuel resources in resource-rich exporting nations, there is a lack of understanding of the risks around energy security and accordingly often a policy vacuum. Conceptualising energy security from different geopolitical vantage points will allow future concerns around energy supply security, climate change, and regional economic crises to be evaluated. By using policy documents and developing a time series approach and normalized z-scores for a range of comparable metrics this article compares the energy security performance in six Caspian Sea countries individually and collectively. The article results show that Azerbaijan, Iran, Kazakhstan made significant progress in energy security since 1990, while energy security indicators in Russia, Uzbekistan, and Turkmenistan regressed. Iran has a leading position in energy security performance, while Uzbekistan and Turkmenistan have the lowest level of the energy security indicators compare to other region countries. This article both contributes a replicable definition of energy security that can be undertaken for other global regions, and begins to incorporate diversification and renewables development to enhance domestic energy security assessment.


id: cord-331701-izkz1hz4
title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
author: Eden, John-Sebastian
date: 2020-03-17
url: https://doi.org/10.1101/2020.03.15.992818
doi: 10.1101/2020.03.15.992818
abstract:
  The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.


id: cord-336192-5uxq5xrs
author: Alavi, Maryam
date: 2020-08-17
url: https://doi.org/10.1016/j.drugpo.2020.102908
doi: 10.1016/j.drugpo.2020.102908
title:
  Coordination, cooperation, and creativity within harm reduction networks in Iran: COVID-19 prevention and control among people who use drugs

abstract:
  An unprecedented public health crisis confronts the world. Iran is among the hardest-hit countries, where effects of the COVID-19 pandemic are stretched across society and felt by the most marginalised people. Among people who use drugs, a comprehensive response to the crisis calls for broad collaboration, coordination, and creativity involving multiple government and non-government organisations. This commentary provides early insights into an unfolding experience, demonstrating the operational and policy impact of an initiative, bringing together a diverse array of harm reduction stakeholders to address the pandemic. In the context of lived experiences of social and economic marginalization, this initiative intends to lead efforts in developing an equitable response to the COVID-19 pandemic.


id: cord-337000-k1qq4qgg
title: Epidemic curve and reproduction number of COVID-19 in Iran
author: Sahafizadeh, Ebrahim
date: 2020-05-18
url: https://www.ncbi.nlm.nih.gov/pubmed/32419024/
doi: 10.1093/jtm/taaa077
abstract:
  COVID-19 was first reported in Iran on 19 February, 2020. We estimated the initial basic reproduction number to be 4.86. With increasingly stringent public health measures, the effective reproduction number declined to below 1 after 2 months.


id: cord-339235-8xslz4bs
author: Boroomand, Zahra
date: 2018-09-15
url: https://doi.org/10.30466/vrf.2018.32089
doi: 10.30466/vrf.2018.32089
title:
  Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene

abstract:
  Infectious bronchitis (IB) is a highly contagious disease involving mostly upper respiratory tract in chickens, leading to significant economic losses in the poultry industry worldwide. One of the major concerns regarding to IB is the emergence of new types of infectious bronchitis viruses (IBVs). The purpose of this study was to identify the IBVs isolated from Iranian broiler chickens with respiratory symptoms. Twenty-five broiler flocks around Ahwaz (southwest of Iran) were examined for IBV. The specimens including trachea, lung, liver, kidney, and ceacal tonsil, were collected from diseased birds and inoculated into chicken embryonated eggs. Harvested allantoic fluids were subjected to reverse transcription polymerase chain reaction (RT-PCR) using primers in order to amplify spike 1 (S1) gene of IBV. The RT-PCR products of four IBV isolates were sequenced. The results showed that from 25 examined flocks with respiratory disease, 12 flocks (48.00%) were positive for IBV. In phylogenetic analysis, our isolates were closely related to the QX-like viruses such as PCRLab/06/2012 (Iran), QX, HC9, HC10, CK/CH/GX/NN11-1, CK/CH/JS/YC11-1, CK/CH/JS/2010/13, CK/CH/JS/2011/2 (China), QX/SGK-21, QX/SGK-11 (Iraq) with nucleotide homology up to 99.00%. This study indicates the role of IBVs in the respiratory disorders of broiler flocks located in southwest Iran, and also the existence of a variant of IBV, which is distinguishable from the other Iranian variants.


id: cord-342517-bzmhjvr5
author: Rassouli, Maryam
date: 2020-09-15
url: https://www.ncbi.nlm.nih.gov/pubmed/33072688/
doi: 10.3389/fpubh.2020.00510
title:
  COVID-19 Management in Iran as One of the Most Affected Countries in the World: Advantages and Weaknesses

abstract:
  COVID-19 management is a hot topic due to its extensive spread across the world and the declaration of pandemic status. How a crisis is managed in each country is influenced by several factors, and various strategies are applied in accordance with these factors in order to manage the crisis. Due to the rapid spread and increasing trend of the crisis and the fact that almost more than half of the countries are engaged in this pandemic, it is impossible to apply trial-and-error based strategies. One of the best strategies is to use the experiences of other countries in dealing with COVID-19. This report explores the advantages and weaknesses of the Islamic Republic of Iran in the management of this crisis in regard with political economic and cultural issues, health service coverage, and the transparency of information that can be used as a model for other countries around the world.


id: cord-347353-ll2pnl81
author: Saberi, M.
date: 2020-05-06
url: https://doi.org/10.1101/2020.05.02.20087270
doi: 10.1101/2020.05.02.20087270
title:
  Accounting for underreporting in mathematical modelling of transmission and control of COVID-19 in Iran

abstract:
  BACKGROUND: Iran has been the hardest hit country by the outbreak of SARS-CoV-2 in the Middle East with 74,877 confirmed cases and 4,683 deaths as of 15 April 2020. With a relatively high case fatality ratio and limited testing capacity, the number of confirmed cases reported is suspected to suffer from significant under-reporting. Therefore, understanding the transmission dynamics of COVID-19 and assessing the effectiveness of the interventions that have taken place in Iran while accounting for the uncertain level of underreporting is of critical importance. We use a mathematical epidemic model utilizing official confirmed data and estimates of underreporting to understand how transmission in Iran has been changing between February and April 2020. METHODS: We developed a compartmental transmission model to estimate the effective reproduction number and its fluctuations since the beginning of the outbreak in Iran. We associate the variations in the effective reproduction number with a timeline of interventions and national events. The estimation method also accounts for the underreporting due to low case ascertainment by estimating the percentage of symptomatic cases using delay adjusted case fatality ratio based on the distribution of the delay from hospitalization to death. FINDINGS: Our estimates of the effective reproduction number ranged from 0.66 to 1.73 between February and April 2020, with a median of 1.16. We estimate a reduction in the effective reproduction number during this period, from 1.73 (95% CI 1.60-1.87) on 1 March 2020 to 0.69 (95% CI 0.68-0.70) on 15 April 2020, due to various non-pharmaceutical interventions including school closures, a ban on public gatherings including sports and religious events, and full or partial closure of non-essential businesses. Based on these estimates and given that a near complete containment is no longer feasible, it is likely that the outbreak may continue until the end of the 2020 if the current level of physical distancing and interventions continue and no effective vaccination or therapeutic are developed and made widely available. INTERPRETATION: The series of non-pharmaceutical interventions and the public compliance that took place in Iran are found to be effective in slowing down the speed of the spread of COVID-19 within the studied time period. However, we argue that if the impact of underreporting is overlooked, the estimated transmission and control dynamics could mislead the public health decisions, policy makers, and general public especially in the earlier stages of the outbreak. FUNDING: Nil.


id: cord-348111-fkjmzpuw
author: Pishgar, Elahe
date: 2020-10-07
txt: ./txt/cord-348111-fkjmzpuw.txt
cache: ./cache/cord-348111-fkjmzpuw.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s13104-020-05319-4
doi: 10.1186/s13104-020-05319-4
summary:
  title: A spatio-temporal geodatabase of mortalities due to respiratory tract diseases in Tehran, Iran between 2008 and 2018: a data note Mortality rates due to respiratory tract diseases (MRRTDs) follow a spatial pattern and this may suggest a potential link between environmental risk factors and MRRTDs. Spatial analysis of RTDs mortality data in an urban setting can provide new knowledge on spatial variation of potential risk factors for RTDs. This will enable health professionals and urban planners to design tailored interventions. Spatio-temporal analyses of mortality data can provide new knowledge on spatial variation of MRRTDs and potential Open Access BMC Research Notes *Correspondence: kiani.behzad@gmail.com drivers of this variation. Data on 43,176 death events due to RTDs from September 2008 to September 2018 were obtained from the Behesht-e Zahra Organization, a local health department under the supervision of the Tehran Municipality [15] . Data for: mortality due to respiratory tract diseases in Tehran Iran between

title:
  A spatio-temporal geodatabase of mortalities due to respiratory tract diseases in Tehran, Iran between 2008 and 2018: a data note

abstract:
  OBJECTIVES: Respiratory tract diseases (RTDs) are among the top five leading causes of death worldwide. Mortality rates due to respiratory tract diseases (MRRTDs) follow a spatial pattern and this may suggest a potential link between environmental risk factors and MRRTDs. Spatial analysis of RTDs mortality data in an urban setting can provide new knowledge on spatial variation of potential risk factors for RTDs. This will enable health professionals and urban planners to design tailored interventions. We aim to release the datasets of MRRTDs in the city of Tehran, Iran, between 2008 and 2018. DATA DESCRIPTION: The Research data include four datasets; (a) mortality dataset which includes records of deaths and their attributes (age, gender, date of death and district name where death occurred), (b) population data for 22 districts (age groups with 5 years interval and gender by each district). Furthermore, two spatial datasets about the city are introduced; (c) the digital boundaries of districts and (d) urban suburbs of Tehran.


id: cord-351941-fgtatt40
title: Simulation‐based estimation of the early spread of COVID‐19 in Iran: actual versus confirmed cases
author: Ghaffarzadegan, Navid
date: 2020-07-06
txt: ./txt/cord-351941-fgtatt40.txt
cache: ./cache/cord-351941-fgtatt40.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32834468/
doi: 10.1002/sdr.1655
summary:
  Estimates using data up to March 20th, 2020, point to 916,000 (90% UI: 508 K, 1.5 M) cumulative cases and 15,485 (90% UI: 8.4 K, 25.8 K) total deaths, numbers an order of magnitude higher than official statistics. The current paper focuses on using a standard dynamic epidemiological model as a tool for incorporating various sources of data into a unified estimation of the actual trajectory of disease, applying the method to COVID-19 outbreak in Iran. We also use unofficial data points including four observations about the number of Iranian passengers diagnosed with COVID-19 upon arrival in international airports, and three estimates aggregated by healthcare providers in Iran and reported by BBC and Iran International news agencies about total cases of death from COVID-19. We define a likelihood function for change over time (net-inflow) of official reports on cumulative death, recovered and infection assuming they are count events drawn from model-predicted rates (Poisson distribution).

abstract:
  Understanding the state of the COVID‐19 pandemic relies on infection and mortality data. Yet official data may underestimate the actual cases due to limited symptoms and testing capacity. We offer a simulation‐based approach which combines various sources of data to estimate the magnitude of outbreak. Early in the epidemic we applied the method to Iran's case, an epicenter of the pandemic in winter 2020. Estimates using data up to March 20th, 2020, point to 916,000 (90% UI: 508 K, 1.5 M) cumulative cases and 15,485 (90% UI: 8.4 K, 25.8 K) total deaths, numbers an order of magnitude higher than official statistics. Our projections suggest that absent strong sustaining of contact reductions the epidemic may resurface. We also use data and studies from the succeeding months to reflect on the quality of original estimates. Our proposed approach can be used for similar cases elsewhere to provide a more accurate, early, estimate of outbreak state. © 2020 System Dynamics Society


id: cord-353976-gns5omyb
title: COVID-19 in Iran: A Deeper Look Into The Future
author: Kafieh, Rahele
date: 2020-04-27
url: https://doi.org/10.1101/2020.04.24.20078477
doi: 10.1101/2020.04.24.20078477
abstract:
  The novel corona-virus (COVID-19) has led to a pandemic, affecting almost all countries and regions in a few weeks, and therefore a global plan is needed to overcome this battle. Iran has been among the first few countries that has been affected severely, after China, which forced the government to put some restriction and enforce social distancing in majority of the country. In less than 2 months, Iran has more than 80,000 confirmed cases, and more than 5,000 death. Based on the official statistics from Iran's government, the number of daily cases has started to go down recently, but many people believe if the lockdown is lifted without proper social distancing enforcement, there is a possibility for a second wave of COVID-19 cases. In this work, we analyze at the data for the number cases in Iran in the past few weeks, and train a predictive model to estimate the possible future trends for the number of cases in Iran, depending on the government policy in the coming weeks and months. Our analysis may help political leaders and health officials to take proper action toward handling COVID-19 in the coming months.


id: cord-356117-ksfcc8x8
title: Impacts of the COVID‐19 pandemic on Iranian patients with epilepsy
author: Asadi‐Pooya, Ali A.
date: 2020-07-06
url: https://doi.org/10.1111/ane.13310
doi: 10.1111/ane.13310
abstract:
  OBJECTIVE: To investigate the effects of COVID‐19 pandemic on patients’ perceptions of hardship in obtaining their drugs and if this pandemic and the social restrictions in response to that has resulted in any changes in their seizure control status. We also investigated factors potentially associated with the perceptions of difficulty in obtaining their drugs (e.g., polytherapy vs. monotherapy, taking imported drugs, and seizure status worsening). METHODS: 1. What has been your experience on obtaining your antiseizure medications in the past four weeks (compared to before)? 2. Have you experienced any changes in your seizure control status in the past four weeks? RESULTS: We included 100 patients (53 male and 47 female patients). In response to the question “Have you had any difficulties in the past 4 weeks to obtain your drugs?”, 31 people (31%) expressed hardship obtaining their drugs. In response to the question “How has been your seizure control status compared with before?”, six people (6%) expressed worsening of their seizure control status in the past 4 weeks. None of the patients reported symptoms of coronavirus infection. CONCLUSION: About one‐third of patients with epilepsy expressed significant hardship obtaining their drugs after the intensification of the COVID‐19 outbreak in Iran. The current COVID‐19 pandemic could be considered as a major shock to a nation that has already been under significant pressure (i.e., Iran).


