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Article ; Online: Impact of meteorological factors and population density on COVID-19 pandemic in Saudi Arabia

Khalid J. Alzahrani / Nadim Sharif / Afsana Khan / Hamsa Jameel Banjer / Anowar Khasru Parvez / Shuvra Kanti Dey

Saudi Journal of Biological Sciences, Vol 30, Iss 2, Pp 103545- (2023)

2023

Abstract: Transmission and increase in cases and fatalities of coronavirus disease-2019 (COVID-19) are significantly influenced by the parameters of weather, human activities and population factors. However, study gap on the seasonality of COVID-19 and impact of ... ...

Abstract	Transmission and increase in cases and fatalities of coronavirus disease-2019 (COVID-19) are significantly influenced by the parameters of weather, human activities and population factors. However, study gap on the seasonality of COVID-19 and impact of environmental factors on the pandemic in Saudi Arabia is present. The main aim of the study is to evaluate the impact of environment on the COVID-19 pandemic. Data were analyzed from January 2020 to July 2021. The generalized estimating equation (GEE) was used to determine the effect of environmental variables on longitudinal outcomes. Spearman's rank correlation coefficient (rs) was used to analyze the impact of different parameters on the outcome of the pandemic. Multiple sequence alignment was performed by using ClustalW. Vaccination and fatalities (rs = −0.85) had the highest association followed by vaccination with cases (rs = −0.81) and population density with the fatalities (rs = 0.71). The growth rate had the highest correlation with sun hours (rs = −0.63). Isolates from variant of concern alpha and beta were detected. Most of the reference sequences in Saudi Arabia were closely related with B.1.427/429 variant. Clade GH (54%) was the most prevalent followed by O (27%), GR (9%), G (6%), and S (4%), respectively. Male to female patient ratio was 1.4:1. About 95% fatality and hospitalization were reported in patients aged >60 years. This study will create a comprehensive insight of the interaction of environmental factors and the pandemic and add knowledge on seasonality of COVID-19 in Saudi Arabia.
Keywords	COVID-19 ; Weather ; Population ; Variant of concern ; Vaccination ; Saudi Arabia ; Biology (General) ; QH301-705.5
Subject code	590
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: High prevalence of norovirus GII.4 Sydney among children with acute gastroenteritis in Bangladesh, 2018–2021

Nadim Sharif / Shamsun Nahar Ahmed / Nazmul Sharif / Khalid J. Alzahrani / Meshari A. Alsuwat / Fuad M. Alzahrani / Shamim Khandaker / Nuzhat Haque Monifa / Shoko Okitsu / Anowar Khasru Parvez / Hiroshi Ushijima / Shuvra Kanti Dey

Journal of Infection and Public Health, Vol 16, Iss 7, Pp 1015-

2023 Volume 1022

Abstract: Background: Active molecular surveillance and rapid diagnosis method to track an outbreak of norovirus in Bangladesh is lacking. This study aims to determine the genotypic diversity, molecular epidemiology and evaluate a rapid diagnosis method. Methods: ... ...

Abstract	Background: Active molecular surveillance and rapid diagnosis method to track an outbreak of norovirus in Bangladesh is lacking. This study aims to determine the genotypic diversity, molecular epidemiology and evaluate a rapid diagnosis method. Methods: A total of 404 fecal specimens were collected from children aged below 60 months from January 2018 to December 2021. All samples were analyzed by reverse transcriptase polymerase chain reaction molecular sequencing of partial VP1 nucleotide. Immunochromatography kit (IC, IP Rota/Noro) was evaluated against reference test method. Results: We found norovirus in 6.7 % (27 of 404) fecal specimens. A wide diversity of norovirus genotype including GII.3, GII.4, GII.5, GII.6, GII.7, and GII.9 were detected. Norovirus strain GII.4 Sydney-2012 was the most predominant (74 %, 20 of 27) followed by GII.7 (7.4 %), GII.9 (7.4 %), GII.3 (3.7 %), GII.5 (3.7 %) and GII.6 (3.7 %), respectively. Co-infection of rotavirus and norovirus (19 [4.7 %] of 404) was the most prevalent. We found higher odds of prolonged health impact [OR 1.93 (95 % CI 0.87–3.12) (p = .001)] among patients with co-infection. The incidence of norovirus was significant among the children below 24 months (p = 0.001). Significant relation of temperature with the cases of norovirus was detected (p = 0.001). The IC kit provided high specificity (99.3 %) and sensitivity (100 %) for the detection of norovirus. Conclusions: This study will provide an integrated insight on the genotypic diversity and rapid identification method of norovirus in Bangladesh.
Keywords	Norovirus ; Genotype GII.4 Sydney ; Immunochromatography kit ; Acute gastroenteritis ; Bangladesh ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Subject code	610
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development of high temperature simultaneous saccharification and fermentation by thermosensitive Saccharomyces cerevisiae and Bacillus amyloliquefaciens

Roni Miah / Ayesha Siddiqa / Udvashita Chakraborty / Jamsheda Ferdous Tuli / Noyon Kumar Barman / Aukhil Uddin / Tareque Aziz / Nadim Sharif / Shuvra Kanti Dey / Mamoru Yamada / Ali Azam Talukder

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 11

Abstract: Abstract Scarcity of energy and pollution are two major challenges that have become a threat to all living things worldwide. Bioethanol is a renewable, ecological-friendly clean energy that may be utilized to address these issues. This study aimed to ... ...

Abstract	Abstract Scarcity of energy and pollution are two major challenges that have become a threat to all living things worldwide. Bioethanol is a renewable, ecological-friendly clean energy that may be utilized to address these issues. This study aimed to develop simultaneous saccharification and fermentation (SSF) process through high temperature-substrate adaptation and co-cultivation of S. cerevisiae with other potential amylolytic strains. In this study, we adapted our previously screened thermosensitive Saccharomyces cerevisiae Dj-3 strain up-to 42 °C and also screened three potential thermotolerant amylolytic strains based on their starch utilization capability. We performed SSF fermentation at high temperature by adapted Dj-3 and amylolytic strains using 10.0% starch feedstock. Interestingly, we observed significant ethanol concentration [3.86% (v/v)] from high temperature simultaneous saccharification and fermentation (HSSF) of adapted Bacillus amyloliquefaciens (C-7) and Dj-3. We attribute the significant ethanol concentration from starch of this HSSF process to C-7’s high levels of glucoamylase activity (4.01 U/ml/min) after adaptation in starch (up-to 42 °C) as well as Dj-3's strong glucose fermentation capacity and also their ethanol stress tolerance capability. This study suggests the significant feasibility of our HSSF process.
Keywords	Medicine ; R ; Science ; Q
Subject code	660
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019–2022

Nadim Sharif / Khalid J. Alzahrani / Shamsun Nahar Ahmed / Afsana Khan / Hamsa Jameel Banjer / Fuad M. Alzahrani / Anowar Khasru Parvez / Shuvra Kanti Dey

PLoS ONE, Vol 17, Iss

2022 Volume 8

Abstract: In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient ... ...

Abstract	In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient information to reduce the health burden of the pandemic. This study focused to conduct worldwide genomic surveillance. About 7.6 million genomic data were analyzed during 2019 to 2022. Multiple sequence alignment was conducted by using maximum likelihood method. Clade GK (52%) was the most predominant followed by GRY (12%), GRA (11%), GR (8%), GH (7%), G (6%), GV (3%), and O (1%), respectively. VOC Delta (66%) was the most prevalent variant followed by VOC Alpha (18%), VOC Omicron (13%), VOC Gamma (2%) and VOC Beta (1%), respectively. The frequency of point mutations including E484K, N501Y, N439K, and L452R at spike protein has increased 10%-92%. Evolutionary rate of the variants was 23.7 substitution per site per year. Substitution mutations E484K and N501Y had significant correlation with cases (r = .45, r = .23), fatalities (r = .15, r = .44) and growth rate R0 (r = .28, r = .54). This study will help to understand the genomic diversity, evolution and the impact of the variants on the outcome of the COVID-19 pandemic.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019-2022.

Nadim Sharif / Khalid J Alzahrani / Shamsun Nahar Ahmed / Afsana Khan / Hamsa Jameel Banjer / Fuad M Alzahrani / Anowar Khasru Parvez / Shuvra Kanti Dey

PLoS ONE, Vol 17, Iss 8, p e

2022 Volume 0271074

Abstract	In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient information to reduce the health burden of the pandemic. This study focused to conduct worldwide genomic surveillance. About 7.6 million genomic data were analyzed during 2019 to 2022. Multiple sequence alignment was conducted by using maximum likelihood method. Clade GK (52%) was the most predominant followed by GRY (12%), GRA (11%), GR (8%), GH (7%), G (6%), GV (3%), and O (1%), respectively. VOC Delta (66%) was the most prevalent variant followed by VOC Alpha (18%), VOC Omicron (13%), VOC Gamma (2%) and VOC Beta (1%), respectively. The frequency of point mutations including E484K, N501Y, N439K, and L452R at spike protein has increased 10%-92%. Evolutionary rate of the variants was 23.7 substitution per site per year. Substitution mutations E484K and N501Y had significant correlation with cases (r = .45, r = .23), fatalities (r = .15, r = .44) and growth rate R0 (r = .28, r = .54). This study will help to understand the genomic diversity, evolution and the impact of the variants on the outcome of the COVID-19 pandemic.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular epidemiology and surveillance of circulating rotavirus among children with gastroenteritis in Bangladesh during 2014-2019.

Shuvra Kanti Dey / Nadim Sharif / Omar Sadi Sarkar / Mithun Kumar Sarkar / Ali Azam Talukder / Tung Phan / Hiroshi Ushijima

PLoS ONE, Vol 15, Iss 11, p e

2020 Volume 0242813

Abstract: Acute gastroenteritis is one of the major health problems in children aged <5 years around the world. Rotavirus A (RVA) is an important pathogen of acute gastroenteritis. The burden of rotavirus disease in the pediatric population is still high in ... ...

Abstract	Acute gastroenteritis is one of the major health problems in children aged <5 years around the world. Rotavirus A (RVA) is an important pathogen of acute gastroenteritis. The burden of rotavirus disease in the pediatric population is still high in Bangladesh. This study investigated the prevalence of group A, B, and C rotavirus (RAV, RBV, RCV), norovirus, adenovirus (AdV) and human bocavirus (HBoV) infections in children with acute gastroenteritis in Bangladesh from February 2014 to January 2019. A total of 574 fecal specimens collected from children with diarrhea in Bangladesh during the period of February 2014-January 2019 were examined for RAV, RBV and RCV by reverse transcriptase- multiplex polymerase chain reaction (RT- multiplex PCR). RAV was further characterized to G-typing and P-typing by RT-multiplex PCR and sequencing method. It was found that 24.4% (140 of 574) fecal specimens were positive for RVA followed by AdV of 4.5%. RBV and RCV could not be detected in this study. Genotype G1P[8] was the most prevalent (43%), followed by G2P[4] (18%), and G9P[8] (3%). Among other genotypes, G9P[4] was most frequent (12%), followed by G1P[6] (11%), G9P[6] (3%), and G11P[25] (3%). We found that 7% RVA were nontypeable. Mutations at antigenic regions of the VP7 gene were detected in G1P[8] and G2P[4] strains. Incidence of rotavirus infection had the highest peak (58.6%) during November to February with diarrhea (90.7%) as the most common symptom. Children aged 4-11 months had the highest rotavirus infection percentage (37.9%). By providing baseline data, this study helps to assess efficacy of currently available RVA vaccine. This study revealed a high RVA detection rate, supporting health authorities in planning strategies such as introduction of RVA vaccine in national immunization program to reduce the disease burden.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An increasing trend of human sapovirus infection in Japan, 2009 to 2019

Sheikh Ariful Hoque / Koji Nishimura / Aksara Thongprachum / Pattara Khamrin / Ngan Thi Kim Pham / Mohammad Tajul Islam / Nusrat Khandoker / Shoko Okitsu / Yuko Onda-Shimizu / Shuvra Kanti Dey / Niwat Maneekarn / Takeshi Kobayashi / Satoshi Hayakawa / Hiroshi Ushijima

Journal of Infection and Public Health, Vol 15, Iss 3, Pp 315-

An emerging public health concern

2022 Volume 320

Abstract: Background: Human sapovirus (SaV) is an important etiologic agent of childhood diarrhea. This study aims to investigate the burden of SaV infection in childhood diarrhea in Japan from 2009–2019, to understand the changes in SaV infection after the ... ...

Abstract	Background: Human sapovirus (SaV) is an important etiologic agent of childhood diarrhea. This study aims to investigate the burden of SaV infection in childhood diarrhea in Japan from 2009–2019, to understand the changes in SaV infection after the introduction of rotavirus (RV) vaccination in Japan in 2011. Methods: Stool samples were collected from children aged ≤ 12 years old with acute gastroenteritis (AGE) who visited outpatient clinics of six prefectures in Japan. The viral RNA was detected by RT-PCR and genogroups and genotypes were determined through sequence-based analysis. Results: Among 5697 stool samples, 318 (5.6%) samples remained SaV-positives showing the highest prevalence in June and 12–24 month aged children. The most predominant genotype was GI.1 (56.8%), followed by GI.2 (19.2%), GII.1 (10.8%), GIV.1 (9.4%), GI.3 (1.7%), GII.2 (1.4%), GII.3 and GII.5 (0.3%). Importantly, an increasing trend (P = 0.016) of SaV infection was observed during this period. In particular, SaV-detection rate was increased significantly (P = 0.033) from 4.3% in pre-rotavirus (RV)-vaccination era to 6.1% in post-RV-vaccination era. We provided evidence that this increase in SaV infection was mainly attributed by coinfections. Conclusions: The upward trend of SaV infection, particularly after the introduction of RV-vaccination, is an emerging concern. Attention should be paid to control this upward trend of SaV infection to ensure maximum benefits of implementation of RV vaccines towards reducing overall childhood diarrhea worldwide.
Keywords	Sapovirus ; Trend ; Rotavirus-vaccination ; Genotypes ; Coinfections ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Subject code	950
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Environmental correlation and epidemiologic analysis of COVID-19 pandemic in ten regions in five continents

Nadim Sharif / Mithun Kumar Sarkar / Shamsun Nahar Ahmed / Rabeya Nahar Ferdous / Nasir Uddin Nobel / Anowar Khasru Parvez / Ali Azam Talukder / Shuvra Kanti Dey

Heliyon, Vol 7, Iss 3, Pp e06576- (2021)

2021

Abstract: Background: Coronavirus disease-2019 (COVID-19) has caused worldwide health emergencies during the last 6 months of 2020. Within very short time, severe acute respiratory coronavirus-2 (SARS-CoV-2) has infected over 64,516,333 people with 1,493,264 ... ...

Abstract	Background: Coronavirus disease-2019 (COVID-19) has caused worldwide health emergencies during the last 6 months of 2020. Within very short time, severe acute respiratory coronavirus-2 (SARS-CoV-2) has infected over 64,516,333 people with 1,493,264 fatalities in 210 countries and regions. Previous studies have reported that environmental factors can affect the viability and transmission of SARS-CoV-2. This study aimed to determine the correlation of environmental factors with COVID-19 pandemic and epidemiology of COVID-19 across nine countries in five continents. Methods: Both environmental and health data were retrieved from various databases during January 1, 2020 to June 30, 2020. Mean value of environmental factors were calculated for weekly and daily cases and fatalities. Spearman correlation test was conducted. Results: In this study, most of the COVID-19 cases and fatalities were detected from regions (New York, Madrid, Lombardy, London and Sau Paulo) with 7 °C–25 °C mean temperature per day, 3 to 6 mean UV index per day and 14 km/h to 22 km/h mean wind velocity per day. Both cases and fatalities increased significantly after removing lockdown in Bangladesh, India, Brazil and South Africa. Over 50% COVID-19 patients were asymptomatic in every country except Brazil and Australia. Fever (>50%) was the most common symptom followed by cough (45%), tiredness (38%) and sore throat (30%), respectively. In India and Bangladesh over 70% of cases were reported in male. Significant correlation of COVID-19 cases with temperature and UV were detected in London, Lombardy, Madrid, New York and Dhaka. Conclusion: This is one of the first cross-country epidemiologic and correlation studies between environmental factors and COVID-19 pandemics. This study will help both local and international health organizations and policy makers to face the COVID-19 challenge.
Keywords	COVID-19 ; Pandemic ; Correlation ; Temperature ; Epidemiology ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	001 ; 333
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Protective measures are associated with the reduction of transmission of COVID-19 in Bangladesh

Nadim Sharif / Khalid J Alzahrani / Shamsun Nahar Ahmed / Rubayet Rayhan Opu / Nayan Ahmed / Aeken Talukder / Raju Nunia / Mysha Samiha Chowdhury / Israt Jahan Nodi / Tama Saha / Ming Zhang / Shuvra Kanti Dey

PLoS ONE, Vol 16, Iss 11, p e

A nationwide cross-sectional study.

2021 Volume 0260287

Abstract: Coronavirus disease 2019 (COVID-19) pandemic has become a major public health issue globally. Preventive health measures against COVID-19 can reduce the health burden significantly by containing the transmission. A few research have been undertaken on ... ...

Abstract	Coronavirus disease 2019 (COVID-19) pandemic has become a major public health issue globally. Preventive health measures against COVID-19 can reduce the health burden significantly by containing the transmission. A few research have been undertaken on the effectiveness of preventive strategies such as mask use, hand washing, and keeping social distance in preventing COVID-19 transmission. The main aim of this study was to determine the association of the preventive measures with the reduction of transmission of COVID-19 among people. Data was collected during January 06, 2021 to May 10, 2021 from 1690 participants in Bangladesh. A validated questionnaire was used to collect both the online and offline data. Chi-square test and logistic regression analyses were performed to determine the association among the variables. The prevalence of COVID-19 was 11.5% (195 of 1690) among the population. Age, gender, occupation and monthly income of the participants were significantly associated with the likelihood of following the preventive measures. The risk of infection and death reduced significantly among the participants following preventive measures (p = .001). The odds of incidence was lower among the participants using masks properly (OR: 0.02, 95% CI: 0.01-0.43), maintaining social distances (OR: 0.04, 95% CI: 0.01-0.33), avoiding crowded places (OR: 0.07, 95% CI: 0.02-0.19) and hand shaking (OR: 0.17, 95% CI: 0.09-0.41). This study suggests that preventive health measures are significantly associated with the reduction of the risk of infection of COVID-19. Findings from this study will help the policymakers to take appropriate steps to curb the health burden of COVID-19.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Fuel ethanol production using xylose assimilating and high ethanol producing thermosensitive Saccharomyces cerevisiae isolated from date palm juice in Bangladesh

Talukder, Ali Azam / Nihad Adnan / Ayesha Siddiqa / Roni Miah / Jamsheda Ferdous Tuli / Shafia Tasnim Khan / Shuvra Kanti Dey / Noppon Lertwattanasakul / Mamoru Yamada

Biocatalysis and agricultural biotechnology. 2019 Mar., v. 18

2019

Abstract: Four yeasts were isolated from Khejurer Rosh [an overnight natural fermented date palm (Phoenix dactylifera) juice/sap] at low temperature (∼5–15 °C) to produce bioethanol. Cultural, morphological, physiological, biochemical and genetic analysis were ... ...

Abstract	Four yeasts were isolated from Khejurer Rosh [an overnight natural fermented date palm (Phoenix dactylifera) juice/sap] at low temperature (∼5–15 °C) to produce bioethanol. Cultural, morphological, physiological, biochemical and genetic analysis were carried out under various physiological conditions. All 4-strains (Dj-1, Dj-2, Dj-3, and Dj-4) could produce bioethanol and their production rates were further investigated under various carbon sources, growth temperatures, and pHs. Among them, the highest 10% (v/v) bioethanol was estimated from the thermosensitive yeast strain Dj-3, which was grown in the medium containing 18% of total sugars and 0.05% (NH4)2SO4 at optimum temperature and pH of 25 °C and 6.0, respectively. Microscopic study and a partial 26S rDNA (D1/D2 region) sequencing identified Dj-1, and Dj-3 as Saccharomyces cerevisiae, whereas, Dj-2 and Dj-4 strains were, Pichia kudriavzevii, and Debaryomyces hansenii, respectively. The strains Dj-3 and Dj-4 could grow well in the medium containing xylose as the sole carbon source. Our results conclude that the strain Dj-3 is a natural mutant strain of Saccharomyces cerevisiae, which would be an industrially potential candidate for bioethanol production.
Keywords	Debaryomyces hansenii ; Phoenix dactylifera ; Pichia kudriavzevii ; Saccharomyces cerevisiae ; ammonium sulfate ; bioethanol ; carbon ; ethanol ; ethanol production ; genetic analysis ; juices ; mutants ; pH ; ribosomal DNA ; sap ; temperature ; xylose ; yeasts ; Bangladesh
Language	English
Dates of publication	2019-03
Size	p. 101029.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2642052-1
ISSN	1878-8181
ISSN	1878-8181
DOI	10.1016/j.bcab.2019.101029
Database	NAL-Catalogue (AGRICOLA)

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