Detection of virulence genes of APEC (avian pathogenic Escherichia coli) isolated from poultry in Noakhali, Bangladesh

Hossain, Farzana; Islam, Saiful; Islam, Aminul; Islam, Shariful; Ahmed, Firoz

doi:10.3329/brc.v7i1.54253

Cited by 13 publications

(11 citation statements)

References 14 publications

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“…The present data-based study examines the global association between meteorological factors and Monkeypox cases. Various vector-borne zoonotic viral diseases including COVID-19, dengue, Chikungunia, malaria, Ebola, and Zika are increasing with changes in climatic conditions [ 31 , 32 , 33 , 34 , 35 ]. Previous studies have shown that meteorological factors affect the growth and activity of respiratory viral diseases including SARS-CoV [ 36 , 37 , 38 ].…”

Section: Discussionmentioning

confidence: 99%

Association between Global Monkeypox Cases and Meteorological Factors

Islam

Sangkham

Tiwari

et al. 2022

IJERPH

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The emergence of an outbreak of Monkeypox disease (MPXD) is caused by a contagious zoonotic Monkeypox virus (MPXV) that has spread globally. Yet, there is no study investigating the effect of climatic changes on MPXV transmission. Thus, studies on the changing epidemiology, evolving nature of the virus, and ecological niche are highly paramount. Determination of the role of potential meteorological drivers including temperature, precipitation, relative humidity, dew point, wind speed, and surface pressure is beneficial to understand the MPXD outbreak. This study examines the changes in MPXV cases over time while assessing the meteorological characteristics that could impact these disparities from the onset of the global outbreak. To conduct this data-based research, several well-accepted statistical techniques including Simple Exponential Smoothing (SES), Auto-Regressive Integrated Moving Average (ARIMA), Automatic forecasting time-series model (Prophet), and Autoregressive Integrated Moving Average with Explanatory Variables (ARIMAX) were applied to delineate the correlation of the meteorological factors on global daily Monkeypox cases. Data on MPXV cases including affected countries spanning from May 6, 2022, to November 9, 2022, from global databases and meteorological data were used to evaluate the developed models. According to the ARIMAX model, the results showed that temperature, relative humidity, and surface pressure have a positive impact [(51.56, 95% confidence interval (CI): −274.55 to 377.68), (17.32, 95% CI: −83.71 to 118.35) and (23.42, 95% CI: −9.90 to 56.75), respectively] on MPXV cases. In addition, dew/frost point, precipitation, and wind speed show a significant negative impact on MPXD cases. The Prophet model showed a significant correlation with rising MPXD cases, although the trend predicts peak values while the overall trend increases. This underscores the importance of immediate and appropriate preventive measures (timely preparedness and proactive control strategies) with utmost priority against MPXD including awareness-raising programs, the discovery, and formulation of effective vaccine candidate(s), prophylaxis and therapeutic regimes, and management strategies.

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Section: Discussionmentioning

confidence: 99%

Association between Global Monkeypox Cases and Meteorological Factors

Islam

Sangkham

Tiwari

et al. 2022

IJERPH

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“…In order to better understand how this virus spreads, additional research is needed about natural animal reservoirs and the evolving and changing epidemiology of the virus. 24,25,50 limitations Overall, 17 relevant articles were screened for comprehensive data extraction. However, there are also some limitations hardly could avoid.…”

Section: Discussionmentioning

confidence: 99%

“…[22][23][24] It remains as an important tool to express the fatality of the disease. [25][26][27] The CFR of MPXD can inform specific interferences and the public health scenario of this virus; the ratio of confirmed death patients and diagnosed positive patients number which is converted as a percentage. 8 The children are more vulnerable to MPXD and thus, the severity or fatality of MPXD is related to patient conditions and comorbidities.…”

Section: Introductionmentioning

confidence: 99%

An Estimation of Five-decade Long Monkeypox Case Fatality Rate: Systematic Review and Meta-analysis

Islam¹,

Ahammed²,

Noor³

et al. 2022

J. Pure Appl. Microbiol.

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On July 23, 2022 the World Health Organization (WHO) has announced the Monkeypox disease (MPXD) as a worldwide public health issue. This study conducts a systematic review and meta-analysis to determine the overall case fatality rate (CFR) of MPXD worldwide during 1970–2022. The tenure-tracked MPXD outbreaks associated with CFR were calculated based on available published data from six different periods (i.e., 1970-79, 1980-89, 1990-99, 2000-09, 2010-19, and 2000-2022). A total of 229 peer-reviewed accessible articles were investigated, of which, 17 articles met the inclusion and exclusion criteria. Most of the studies on MPXD CFR were published in the Democratic Republic of the Congo (DRC) providing 47% of data for the current meta-analysis. The overall pooled CFR of MPXD was 4.14% (range: 0.62% – 9.51%) during 1970–2022. In this study, total of 379 death cases were found from published MPXV based research articles where the pooled estimate CFR was 1.87%. The pooled CFR was higher during the earlier outbreak of the MPXD such as 10.71% in 1970-1979. With the progress of time, the CFR from MPXD followed a decreasing trend and reached 5.38% in 1980-1999 and 4.45% in 2000-2022. Young male children aged< 10 years were found to experience the worst outcome with a CFR of >73.0%. This is the first meta-analysis using 52 years of data which indicates that the CFR of MPXV is decreasing from previous years. The findings of this meta-analysis might be paramount for the policymakers to tackle MPXD and minimize the overall CFR of MPXD through strategic actions.

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“…Over 2 years, the SARS-CoV-2 virus has evolved through multiple new mutations and various genetic variants, such as Alpha (B.1.1.7) with seven, Beta (B.1.351) with nine, Gamma (P.1) with 12, Delta (B.1.6, B.1.6.2) with 17, Omicron (B.1.1.529) and Neocov variant with 32 new mutations in the spike protein gene ( Ahmed et al, 2021 ; Chakraborty et al, 2022a ; Chakraborty et al, 2022b ; Chakraborty et al, 2022c ; Chakraborty et al, 2022d ; Chakraborty et al, 2022e ). These variants have spread to various regions of the world, and among them, variants of concern (VOCs) such as Delta, Omicron, and their sub-lineages have caused significant risk to public health ( Hossain et al, 2021 ; Islam et al, 2021 , Islam et al, 2022a ). However, the number of fatalities caused by various SARS-CoV-2 variants fluctuates considerably ( Islam et al, 2022b ; Islam et al, 2022c ; Islam et al, 2022d ).…”

Section: Introductionmentioning

confidence: 99%

“…Among the three significant mutations that the spike protein RBD carries, E484K is situated in a loop region away from direct hACE2 (human angiotensin-converting enzyme 2) contact, while mutations in P.1: N501Y and K417T interact with human ACE2 (hACE2). ( Faria et al, 2021 ; Hossain et al, 2021 ; Chandran et al, 2022 ). Compared with the first strain (alpha strain) of SARS-CoV-2, the Delta variant B.1.617.2 has 23 mutations.…”

Section: Introductionmentioning

confidence: 99%

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development

et al. 2023

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Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates.Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models.Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible.Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.

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Detection of virulence genes of APEC (avian pathogenic Escherichia coli) isolated from poultry in Noakhali, Bangladesh

Cited by 13 publications

References 14 publications

Association between Global Monkeypox Cases and Meteorological Factors

Association between Global Monkeypox Cases and Meteorological Factors

An Estimation of Five-decade Long Monkeypox Case Fatality Rate: Systematic Review and Meta-analysis

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development

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