scholarly journals Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries

2021 ◽  
Vol 22 (5) ◽  
pp. 2630
Author(s):  
Chunguang Liang ◽  
Elena Bencurova ◽  
Eric Psota ◽  
Priya Neurgaonkar ◽  
Martina Prelog ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Class Ii ◽  
Viral Envelope ◽  
Structural Proteins ◽  
P Value ◽  
Fatality Rate ◽  
Different Populations ◽  
Infection Spread

We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.

scholarly journals Pemberantasan Sarang Nyamuk 3M Plus terhadap Kejadian Demam Berdarah Dengue di Puskesmas Payung Sekaki Kota Pekanbaru; Studi Kasus Kontrol

2020 ◽  
Vol 3 (2) ◽  
Author(s):  
Tyagita Widya Sari ◽  
Retno Putri
Keyword(s):  
Case Fatality Rate ◽  
Case Fatality ◽  
P Value ◽  
Fatality Rate ◽  
Purposive Sampling

Demam Berdarah Dengue (DBD) adalah penyakit menular yangdisebabkan oleh virus Dengue dan ditularkan melalui gigitan nyamukAedes aegypti. Dinas Kesehatan Provinsi Riau melaporkan jumlah kasusDBD sebanyak 277 dan Case Fatality Rate (CFR) DBD sebesar 1,4% padatahun 2016, di mana kasus terbanyak berasal dari Kota Pekanbaru yaitu58 kasus dengan CFR sebesar 0%. Adapun, CFR DBD di wilayah kerjaPuskesmas Payung Sekaki meningkat dari 0% pada tahun 2015 menjadi0,7% pada tahun 2016. DBD merupakan penyakit berbasis lingkunganyang dapat dicegah dengan melakukan tindakan pengendalian vektor,antara lain dengan pemberantasan sarang nyamuk (PSN) dan tindakanpencegahan lainnya. Akan tetapi, partisipasi aktif masyarakat dalam PSNmasih rendah dan kurang. Tujuan penelitian adalah untuk mengetahuihubungan PSN 3M Plus dengan kejadian DBD di wilayah kerja PuskesmasPayung Sekaki Kota Pekanbaru tahun 2017. Penelitian ini dilakukan padabulan Agustus tahun 2017. Desain studi penelitian ini adalah observasionaldengan pendekatan kasus kontrol. Jumlah sampel kasus dipilih denganteknik total sampling yaitu 40 kasus, sedangkan sampel kontrol dipilihdengan teknik purposive sampling yaitu 80 kontrol. Analisis datamenggunakan uji regresi logistik ganda. Hasil analisis multivariatmenunjukkan bahwa kebiasaan menggunakan obat nyamuk palingdominan menjelaskan perubahan variabel kejadian DBD (p-value = 0,092;OR = 2,76; 95% CI = 0,85-8,87). Variabel praktik M1 (menguras TPA),keberadaan kawat kassa nyamuk dalam ventilasi rumah, kebiasaanmenggantung pakaian, dan kebiasaan menggunakan obat nyamukberhubungan dan merupakan faktor risiko kejadian DBD di wilayah kerjaPuskesmas Payung Sekaki Kota Pekanbaru

scholarly journals Covid-19 High Attack Rate Can Lead to High Case Fatality Rate

2021 ◽  
Author(s):  
Tareef Fadhil Raham
Keyword(s):  
Mortality Rate ◽  
Attack Rate ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Positive Influence ◽  
P Value ◽  
Fatality Rate ◽  
Mean Values ◽  
Paired Samples ◽  
Significant Difference

Background: During the current Covid-19 pandemic case fatality rate (CFR) estimates were subjected to a lot of debates regarding the accuracy of its estimations, predictions, and the reason of across countries variances. In this context, we conduct this study to see the relationship between attack rate (AR) and CFR. The study hypothesis is based on two: 1- evidence suggests that the mortality rate (MR) has a positive influence on case fatality ratio (CFR), 2- and increase number of Covid-19 cases leads to increased mortality rate (MR). Material and methods: Thirty countries and territories were chosen. Inclusion criterion was > 500 Covid-19 reported cases per 10,000 population inhabitants. Data on covid-19 cases and deaths was selected as it was on March 10, 2021. Statistical methods used are descriptive and one-sample Kolmogorov-Smirnov (K-S), the one-way ANOVA, Levene, least significant different (LSD), and matched paired-samples T-tests. Results: ANOVA test showed a significant difference at P<0.01 among all studied groups concerning AR and CFR mean values. Group of countries with MR ≥ 15 death / 104 inhabitants recorded the highest level of crude mean CFR and AR values, and recorded the highest gap with leftover groups, especially with countries reported MR of <10 death/ 104 inhabitants. There were independence 95% confidence intervals of mean CFR and AR values between countries with ≥ 15 death / 104 MR and countries with MR of <10 death /104. There was a significant difference between countries with MR ≥ 15 death / 104 inhabitants and countries with MR of <10 death / 10 4 inhabitants groups through least significant difference (LSD) test for CFR%( 0.042 p-values) and Games Howell (GH) test for AR/104 (p-value 0.000). Conclusions: CFR has a positive significant association with AR.

scholarly journals Konseling WhatsApp Gateway untuk Meningkatkan Kesiapsiagaan Masyarakat dalam Menghadapi Covid-19

2021 ◽  
Vol 8 (03) ◽  
pp. 244-249
Author(s):  
Riris Andriati ◽  
Fenita Purnama Sari Indah ◽  
Andiyan Andiyan ◽  
Marta Desri Ayu
Keyword(s):  
Case Fatality Rate ◽  
Case Fatality ◽  
T Test ◽  
P Value ◽  
Fatality Rate ◽  
Quasi Experiment

Sampai 31 Maret 2020, Indonesia melaporkan 1.528 kasus terkonfirmasi C dengan 136 kematian dan tingkat kematian (case fatality rate) 8,9%. Pandemi Covid-19 membuat aktifitas menjadi serba terbatas, tidak terkecuali dengan penyebaran informasi sehingga edukasi intensif dibutuhkan untuk membentuk kesiapsiagaan masyarakat. Tujuan penelitian ini adalah untuk mengetahui pengaruh konseling melalui WhatsApp terhadap kesiapsiagaan masyarakat Villa Pamulang Depok dalam menghadapi Covid-19. Penelitian ini menggunakan metode quasi experiment yang bersifat analitik dan one group pretest-posttest design. Sampel dalam penelitian ini berjumlah 44 orang yang diperoleh dengan teknik proportional sample. Responden diberikan edukasi melalui WhatsApp selama 14 hari. Pengaruh penyebaran informasi melalui WhatsApp diukur dengan menggunakan paired sampel t-test. Hasil penelitian menunjukkan adanya hubungan antara penyebaran informasi Covid-19 melalui WhatsApp terhadap kesiapsiagaan masyarakat Villa Pamulang Depok dalam mengahadapi Covid-19 dengan p-value=0,004. Hasil penelitian juga menunjukkan perbedaan kesiapsiagaan Covid-19 sebelum dan sesudah pemberian informasi Covid-19 melalui WhatsApp. Penelitian ini diharapkan dapat menambahkan pengetahuan terhadap kesiapsiaagan masyarakat sebagai upaya pencegahan Covid-19.

scholarly journals Correlation between COVID-19 case fatality rate and percentage of BCG vaccination: is it true the vaccine is protective?

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Aliae A. R. Mohamed Hussein ◽  
Marwa Rashad Salem ◽  
Samar Salman ◽  
A F Abdulrahim ◽  
Nasrallah A. Al Massry ◽  
...  
Keyword(s):  
Vaccination Coverage ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Epidemiological Studies ◽  
Protective Role ◽  
Main Body ◽  
Fatality Rate ◽  
Vaccination Policy ◽  
Bcg Vaccination ◽  
Different Populations

Abstract Background The observations of some recent epidemiological studies offer hope for a reduced impact of COVID-19 for countries which practice universal BCG vaccination policy. Main body This report provides a correlation between the case fatality rates of COVID-19 and the percentage of BCG vaccination coverage in 183 most affected countries. The main objective of this observational ecologic report is to evaluate possible effects of the previous BCG vaccination in different populations and the epidemic outcomes specially the rates of severe/critical cases and case fatalities. The analysis is preliminary since it is based on constantly rolling data while the COVID-19 pandemic is still unfolding. Conclusion Our findings seem to support the fact that an older BCG vaccine may have a protective role in avoiding severe/critical SARS-CoV2 pneumonia and relatively decrease its fatalities.

scholarly journals 1373Severe acute respiratory infection with high mortality rate in Sana'a city, 2018-2019 Yemen

2021 ◽  
Vol 50 (Supplement_1) ◽  
Author(s):  
Manal Mahsoon ◽  
Yasser Ghaleb ◽  
Riham Al-dubaiee ◽  
Mohamed Al Amad
Keyword(s):  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Control Program ◽  
Case Definition ◽  
Influenza Viruses ◽  
P Value ◽  
Fatality Rate ◽  
Severe Acute Respiratory Infection

Abstract Background The burden of influenza and severe acute respiratory infection (SARI) in conflict countries such as Yemen is exacerbated due to limited resources and the collapse of the health system. The aims are to describe epidemiology of SARI, determine influenza detection and case fatality rates among SARI patients. Methods We used a descriptive analytical study design. All SARI patients who meet WHO case definition during 2018-2019 from Sana'a city were included. Nasopharyngeal samples were examined by polymerase chain reaction. A soft copy of data that collected by surveillance staff was obtained from the National Influenza Control Program (NICP). Case fatality rate and detection rate were calculated and P value &lt; 0.05 used for statistical significant. Results 1447 SARI patients were reported: 73% males, 54% aged 15- &lt; 50 years. Comorbidity was among 27% (387) of them: (57% cardio-vascular diseases and 50% diabetes). Samples of 934 (64%) SARI patients were tested and influenza viruses were detected in 141 (15%) patients (13% type A and 2% type B). Higher influenza viruses were detected in winter months (November – February) (17% vs 9%, P &lt; 0.001). Overall SARI fatality rate was 19% (276), significantly higher among patients with comorbidity (26% vs 16%, P &lt; 0.001) confirmed influenza (30% Vs 15%, P value &lt; 0.001) and not receiving antiviral (51% vs 17%, P &lt; 0.001) than relevant groups. Conclusions SARI patients in Yemen had a high case-fatality rate particularly SARI patients with confirmed influenza. Introduce influenza vaccination for the risk group should be considered. Key messages Influenza and SARI cases are high in Yemen and progress to death.

scholarly journals Impact of COVID-19 Pandemic on Refugees, Migrants and Asylum Seekers Living in Camps and Reception and Identification Centers in Greece in the Pre-Vaccination Period, February 2020 to May 2021. Summary of Epidemiological Findings

2021 ◽  
Author(s):  
Spiros Sapounas ◽  
Konstantinos Mitrou ◽  
Alexandros Georgios Asimakopoulos ◽  
Garyfallia Antoniou ◽  
Ioanna Papari ◽  
...  
Keyword(s):  
General Population ◽  
Asylum Seekers ◽  
Case Fatality Rate ◽  
Clinical Manifestations ◽  
Case Fatality ◽  
Population Data ◽  
Epidemiological Data ◽  
P Value ◽  
Fatality Rate ◽  
Notification Rate

Abstract Background: Protection of refugees, migrants, and asylum seekers living in open hosting camps (HCs) and reception and identification centers (RICs) has been a priority since the beginning of the COVID-19 pandemic. We present the epidemiological data of COVID-19 infection in HCs/RICs in Greece from February 2020 to May 2021, before the initiation of the onsite vaccinations.Methods: Case confirmation was performed by rapid antigenic test and/or RT-PCR. Data were retrieved from the National COVID-19 registry. The notification rate by type of accommodation facility, by sex and ethnicity and the mean age of cases, were calculated for HCs, RICs and general population. Data on clinical manifestations, and disease severity (admissions to intensive care unit (ICU) / case fatality rate) were analysed.Results: Of the 397,497 recorded domestic COVID-19 infection cases, 2,609 (0.7%) regarded HCs/RICs; of them 1,566 (60%) were identified in 27 HCs and 1,043 (40%) in six RICs. The notification rate was 542 and 380 cases per 10,000 population in HCs/RICs and the general population, respectively (p-value<0.001).Up to February 2021 the occurrence of cases in HCs/RICs did not follow the occurrence of cases in the general population. After March 2021 the course of the outbreak in HCs/RICs and the general population was similar.The median age of cases in HCs/RICs and the general population was 27 (range:0-81) and 44 (range:0-106), respectively (p<0.001). Twenty-four different ethnicities were reported among migrant cases; 51% were from Afghanistan, 13% from Syria, 6% from Kongo and 5% from Somalia.Overall, 48% and 80% of cases, respectively in HCs/RICs and the general population were symptomatic (p<0.001). Five (0.2%) cases in HCs/RICs were admitted to the ICU compared to 10,426 cases (3.0%) in the general population (p-value <0.001). Case fatality rate was 3% in the general population and 0.08% in HCs/RICs (p-value <0.001).Conclusion: Recorded COVID-19 infections were less severe in migrants living at HCs/RICs than the general population, however, the number of identified cases was high and measures for the prevention of transmission should be strengthened.

scholarly journals Impact of lockdown on Covid-19 Case Fatality Rate and Viral Mutations Spread in 7 Countries in Europe and North America.

2020 ◽  
Author(s):  
Maria Pachetti ◽  
Bruna Marini ◽  
Fabiola Giudici ◽  
Francesca Benedetti ◽  
Silvia Angeletti ◽  
...  
Keyword(s):  
Case Fatality Rate ◽  
Biological Significance ◽  
Case Fatality ◽  
Pairwise Comparison ◽  
P Value ◽  
Fatality Rate ◽  
Standard Case ◽  
Diagnostic Pcr ◽  
Number Of Patients ◽  
Public Data

Abstract Background: Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the first coronavirus disease 2019 (COVID-19) outbreak in China and has become a public health emergency of international concern. SARS-CoV-2 outbreak has been declared a pandemic by WHO on March 11th, 2020 and the same month several Countries put in place different lockdown restrictions and testing strategies in order to contain the spread of the virus. Methods: The calculation of the Case Fatality Rate of SARS-CoV-2 in the Countries selected was made by using the data available at https://github.com/owid/covi-19-data/tree/master/public/data. Case fatality rate was calculated as the ratio between the death cases due to COVID-19, over the total number of SARS-CoV-2 reported cases 14 days before. Standard Case Fatality Rate values were normalized by the Country-specific ρ factor, i.e. the number of PCR tests/1 million inhabitants over the number of reported cases/1 million inhabitants. Case-fatality rates between Countries were compared using proportion test. Post-hoc analysis in the case of more than two groups was performed using pairwise comparison of proportions and p-value was adjusted using Holm method.We also analyzed 487 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 from January 2020 to April 2020 in Italy, Spain, Germany, France, Sweden, UK and USA. SARS-CoV-2 reference genome was obtained from the GenBank database (NC_045512.2). Genomes alignment was performed using Muscle and Jalview software. We, then, calculated the Case Fatality Rate of SARS-CoV-2 in the Countries selected. Results: In this study we analyse how different lockdown strategies and PCR testing capability adopted by Italy, France, Germany, Spain, Sweden, UK and USA have influenced the Case Fatality Rate and the viral mutations spread. We calculated case fatality rates by dividing the death number of a specific day by the number of patients with confirmed COVID-19 infection observed 14 days before and normalized by a ρ factor which takes into account the diagnostic PCR testing capability of each Country and the number of positive cases detected. We notice the stabilization of a clear pattern of mutations at sites nt241, nt3037, nt14408 and nt23403. A novel nonsynonymous SARS-CoV-2 mutation in the spike protein (nt24368) has been found in genomes sequenced in Sweden, which enacted a soft lockdown strategy.Conclusions: Strict lockdown strategies together with a wide diagnostic PCR testing of the population were correlated with a relevant decline of the case fatality rate in different Countries. The emergence of specific patterns of mutations concomitant with the decline in case fatality rate needs further confirmation and their biological significance remains unclear.

scholarly journals Impact of lockdown on Covid-19 Case Fatality Rate and Viral Mutations Spread.

2020 ◽  
Author(s):  
Maria Pachetti ◽  
Bruna Marini ◽  
Fabiola Giudici ◽  
Francesca Benedetti ◽  
Silvia Angeletti ◽  
...  
Keyword(s):  
Case Fatality Rate ◽  
Biological Significance ◽  
Case Fatality ◽  
Pairwise Comparison ◽  
P Value ◽  
Fatality Rate ◽  
Standard Case ◽  
Diagnostic Pcr ◽  
Number Of Patients ◽  
Public Data

Abstract BackgroundSevere acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the first coronavirus disease 2019 (COVID-19) outbreak in China and has become a public health emergency of international concern. SARS-CoV-2 outbreak has been declared a pandemic by WHO on March 11th, 2020 and the same month several countries put in place different lockdown restrictions and testing strategies in order to contain the spread of the virus. MethodsThe calculation of the Case Fatality Rate of SARS-CoV-2 in the countries selected was made by using the data available at https://github.com/owid/covi-19-data/tree/master/public/data. Case fatality rate was calculated as the ratio between the death cases due to COVID-19, over the total number of SARS-CoV-2 reported cases 14 days before. Standard Case Fatality Rate values were normalized by the country-specific ρ factor, i.e. the number of PCR tests/1 million inhabitants over the number of reported cases/1 million inhabitants. Case-fatality rates between countries were compared using proportion test. Post-hoc analysis in the case of more than two groups was performed using pairwise comparison of proportions and p-value was adjusted using Holm method.We also analyzed 487 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 from January 2020 to April 2020 in Italy, Spain, Germany, France, Sweden, UK and USA. SARS-CoV-2 reference genome was obtained from the GenBank database (NC_045512.2). Genomes alignment was performed using Muscle and Jalview software. We, then, calculated the Case Fatality Rate of SARS-CoV-2 in the countries selected ResultsIn this study we analyse how different lockdown strategies and PCR testing capability adopted by Italy, France, Germany, Spain, Sweden, UK and USA have influenced the Case Fatality Rate and the viral mutations spread. We calculated case fatality rates by dividing the death number of a specific day by the number of patients with confirmed COVID-19 infection observed 14 days before and normalized by a ρ factor which takes into account the diagnostic PCR testing capability of each country and the number of positive cases detected. We notice the stabilization of a clear pattern of mutations at sites nt241, nt3037, nt14408 and nt23403. A novel nonsynonymous SARS-CoV-2 mutation in the spike protein (nt24368) has been found in genomes sequenced in Sweden, which enacted a soft lockdown strategy.ConclusionsStrict lockdown strategies together with a wide diagnostic PCR testing of the population were correlated with a relevant decline of the case fatality rate in different countries. The emergence of specific patterns of mutations concomitant with the decline in case fatality rate needs further confirmation and their biological significance remains unclear.

Impact of hydroxychloroquin/azithromycin protocol on COVID-19 case-fatality rate reduction in Algeria. (Preprint)

2020 ◽  
Author(s):  
Ahmed Youssef Kada
Keyword(s):  
Case Fatality Rate ◽  
Doubling Time ◽  
Case Fatality ◽  
World Health ◽  
Fatality Rate ◽  
Therapeutic Protocol ◽  
First Case ◽  
The World ◽  
The Impact ◽  
At Home

BACKGROUND Covid-19 is an emerging infectious disease like viral zoonosis caused by new coronavirus SARS CoV 2. On December 31, 2019, Wuhan Municipal Health Commission in Hubei province (China) reported cases of pneumonia, the origin of which is a new coronavirus. Rapidly extendable around the world, the World Health Organization (WHO) declares it pandemic on March 11, 2020. This pandemic reaches Algeria on February 25, 2020, date on which the Algerian minister of health, announced the first case of Covid-19, a foreign citizen. From March 1, a cluster is formed in Blida and becomes the epicentre of the coronavirus epidemic in Algeria, its total quarantine is established on March 24, 2020, it will be smoothly alleviated on April 24. A therapeutic protocol based on hydroxychloroquine and azithromycin was put in place on March 23, for complicated cases, it was extended to all the cases confirmed on April 06. OBJECTIVE This study aimed to demonstrate the effectiveness of hydroxychloroquin/azithromycin protocol in Algeria, in particular after its extension to all patients diagnosed COVID-19 positive on RT-PCR test. We were able to illustrate this fact graphically, but not to prove it statistically because the design of our study, indeed in the 7 days which followed generalization of therapeutic protocol, case fatality rate decrease and doubling time increase, thus confirming the impact of wide and early prescription of hydroxychloroquin/azithromycin protocol. METHODS We have analyzed the data collected from press releases and follow-ups published daily by the Ministry of Health, we have studied the possible correlations of these data with certain events or decisions having a possible impact on their development, such as confinement at home and its reduction, the prescription of hydroxychloroquine/azithromycin combination for serious patients and its extension to all positive COVID subjects. Results are presented in graphics, the data collection was closed on 31/05/2020. RESULTS Covid-19 pandemic spreads from February 25, 2020, when a foreign citizen is tested positive, on March 1 a cluster is formed in the city of Blida where sixteen members of the same family are infected during a wedding party. Wilaya of Blida becomes the epicentre of coronavirus epidemic in Algeria and lockdown measures taken, while the number of national cases diagnosed begins to increases In any event, the association of early containment measures combined with a generalized initial treatment for all positive cases, whatever their degree of severity, will have contributed to a reduction in the fatality rate of COVID 19 and a slowing down of its doubling time. CONCLUSIONS In Algeria, the rapid combination of rigorous containment measure at home and early generalized treatment with hydroxychloroquin have demonstrated their effectiveness in terms of morbidity and mortality, the classic measures of social distancing and hygiene will make it possible to perpetuate these results by reducing viral transmission, the only unknown, the reopening procedure which can only be started after being surrounded by precautions aimed at ensuring the understanding of the population. CLINICALTRIAL Algeria, Covid-19, pandemic, hydroxychloroquin, azithromycin, case fatality rate

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