September 3, 2026

Kogle-Zanga Biopesticide Boosts Amaranth Yield | IJB 2026

Amaranth, Kogle-zanga, Biopesticide, Pest control, Sustainable agriculture

Drabo Samuel Fogné,  Nikiéma Dominique,  Zézouma Anselme Dao,  Romba Rahim,  Sedogo Sanata, and Gnankine Olivier, from the institute of the Burkina Faso. Wrote a research article about, Kogle-Zanga Biopesticide Boosts Amaranth Yield. Entitled, Role of the Kogle-zanga biopesticide in improving amaranth leaf production in Loumbila. This research paper published by the International Journal of Biosciences | IJB. an open access scholarly research journal on Biosciences. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

Amaranth is a widely consumed traditional vegetable with high nutritional value. However, its production is constrained by both biotic and abiotic factors, which cause significant field damage. To address this issue, farmers often rely on a variety of pesticides, many of which are unregistered and pose risks to both humans and the environment. Hence, there is an urgent need to find alternatives to these synthetic products. In this context, the present study was undertaken to improve amaranth production using Kogle-zanga, a biopesticide. A completely randomized block design with four replications and four treatments was used. The biopesticide’s efficacy was assessed based on pest attack levels, plant growth and development, and leaf yield. The results showed that Kogle-zanga effectively controlled pests. The T3 dose (70 mL/ha) had a more favorable effect on growth, development, and leaf yield compared to the T1 (50 mL/ha) and T2 (60 mL/ha) doses. Among the tested doses, T3 (70 mL/ha) was the most effective. Additionally, the biopesticide enabled amaranth to achieve its potential yield of 1–2 t/ha. Therefore, promoting the use of this biopesticide among producers for amaranth leaf cultivation is essential to protect human health and the environment.  

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Introduction

Burkina Faso is characterised by a Sudano-Sahelian climate and an economy strongly dependent on agricultural and pastoral activities. Agriculture plays a central role in the national economy and remains a major driver of economic growth. It currently contributes approximately 18–19% of the gross domestic product (GDP) (INSD, 2025), while the services sector was the principal contributor to the 4.9% economic recovery recorded in 2024. Agricultural activities continue to be the primary source of employment in the country, with 98.7% of the agricultural workforce employed in the informal sector (INSD, 2025).

With cereal production estimated at 6.1 million tonnes (FAO, 2023), agriculture remains a cornerstone of both the economy and food security in Burkina Faso. Agricultural production is largely dominated by cereals, particularly millet, sorghum, maize, rice and fonio, which occupy more than 60% of cultivated land and contribute over 55% of total crop production nationwide (INSD, 2025). The sustained production levels recorded in recent years further underscore the strategic importance of cereal-based farming systems in the country (FAO, 2023).

This situation is partly due to a long-standing agricultural policy that has prioritised the promotion of food and cash crops to the detriment of fruit and vegetable production. This trend persists today, as subsidies for cereal inputs continue to account for the largest share of the national agricultural budget (INSD, 2025). According to the World Bank (2023), the agricultural sector contributed 1.9 percentage points to the 4.9% economic growth recorded in 2023 and represented 18.59% of the national gross domestic product (GDP). Vegetable crops, particularly onions, tomatoes and cabbages, constitute the second largest group of primary crops after cereals in Burkina Faso. These crops contribute substantially to both food security and the livelihoods of rural households (INSD, 2025). Their production has increased steadily in recent years, largely driven by the expansion of irrigated farming systems and the growing use of agricultural inputs, including fertilisers and pesticides. Improvements in farming practices and the adoption of high-yielding varieties have also contributed to this upward trend (FAO, 2023).

Among these vegetable species, amaranth (Amaranthus spp.) is an important traditional leafy vegetable valued for its high nutritional potential and widespread consumption (Gelaye, 2023; Netshimbupfe et al., 2023). In addition to its leaves, the seeds are also consumed in various forms (Ajayi et al., 2016; Alemayehu et al., 2015). More generally, leafy vegetables constitute an essential component of diets in many parts of the world, particularly in Africa, Asia and Oceania, where they make significant contributions to nutritional intake and are also used in traditional medicinal practices (Abolaji et al., 2016; Al-Mamun et al., 2016; Bhat et al., 2015). However, amaranth production is frequently constrained by a wide range of biotic pressures, particularly pest infestations, which are among the major causes of yield losses (Ezeh et al., 2015; Mureithi et al., 2017; Seni, 2018). To manage these pests, producers frequently depend on the intensive and often indiscriminate application of synthetic chemical pesticides (Drabo et al., 2017, 2021). Nevertheless, the excessive use of chemical fertilisers and pesticides may adversely affect both the agronomic performance of amaranth and its culinary quality (Ahouangninou et al., 2011; Nampeera et al., 2019). Moreover, the intensive application of synthetic pesticides poses considerable risks to human health and the environment, including contamination of soils and water resources (Acharya et al., 2025), poisoning of producers and consumers (Romba et al., 2020), and the progressive erosion of biodiversity (Knauer et al., 2026). A recent study estimated that the annual avoidable health and environmental costs associated with toxic chemicals in food systems amount to approximately USD 3 trillion (Systemiq, 2025). In addition, the repeated and uncontrolled use of insecticides contributes to the development of resistance among several pest species, thereby reducing treatment efficacy over time and increasing production costs (Bian et al., 2026). These constraints represent a major challenge for agricultural production systems, particularly for vegetable crops that depend heavily on phytosanitary interventions (Schatz et al., 2026).

In response to the growing challenges associated with synthetic insecticides, increasing attention is being directed towards plant-based biopesticides as sustainable alternatives for crop pest management due to their biodegradability, low environmental impact and compatibility with agroecological and integrated pest management approaches. The present study aimed to evaluate the efficacy of Kogle-zanga, a locally produced biopesticide, on pest damage and the agronomic performance of amaranth crops.

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Article source : Role of the Kogle-zanga biopesticide in improving amaranth leaf production in Loumbila  

September 2, 2026

Stem Cells in Type 2 Diabetes Treatment | IJB 2026


Diabetes, Stem cell, Therapy, Tissue regeneration, Glycemic control

Mirza Masroor Ali Beg,  Nilam Bhasker,  Tridiv Katiyar, and Amar Chandra Sharma, from the department of India. Wrote a review article about, Stem Cells in Type 2 Diabetes Treatment. Entitled, Clinical importance of stem cells in T2D treatment: A systematic review.This research paper published by the International Journal of Biosciences | IJB. an open access scholarly research journal on Biosciences. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

Advanced pharmacological treatments have not been able to effectively manage the course of type 2 diabetes mellitus [T2DM] as a result of these challenges to investigate the possible intervention of regenerative medicine such as stem-cell therapies to restore metabolic functions and improve complications of diabetes. The systematic review was done in accordance with PRISMA 2020, PubMed/MEDLINE [2016-2026] were searched on the topic of stem cell therapies in T2DM. Eight studies [RCTs, Phase I-IV trials, observational and case studies] were counted, and they were based on bone marrow-derived MSCs, adipose-derived stromal cells, and umbilical cord-derived MSCs. MSC based therapy has shown high therapeutic promise in T2DM with a consistent improvement in the HbA1C, glycemic control and 8-cell performance, especially using umbilical cord MSCs and bone marrow MSCs. Metabolic results are further improved as a consequence of combination [e.g., in hyperbaric oxygen]. The long-term outcomes such as long-term glycemic control and 8 years of 15 8cell functioning have been reported. The complications that have been reported to have improved notably include wound healing, limb perfusion, and slowed down kidney disease progression. These processes are mediated by β-cell regeneration in patients with long-term diabetes, which demonstrates the benefit of early intervention. Regenerative therapies through stem cells offer an option to treat T2DM. The approaches have the potential to improve glycemic control and result in improvements in complications associated with diabetes.  

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Introduction

T2DM is a complicated metabolic condition with a combination of insulin resistance, progressive pancreatic 2-cell dysfunction, and chronic hyperglycemia resulting in the severe complications related to diabetes such as foot ulcers, kidney disease, and critical limb ischemia (Zhao et al., 2017). Despite development and advances in pharmacological care, the number of patients with progressive disease and complications remains high, over the last few years, regenerative medicine, such as stem cell-based therapy, has been growing fast and is being as a clinical option for the diabetic treatment (Zhao et al., 2017). There is developing evidence that cell-based regenerative therapies can have a beneficial effect on pancreatic activity and metabolic control. Indicatively, platelet-derived mitochondria have been reported to express embryonic stem cell markers and improve pancreatic islet cell function in humans which suggests a new way of metabolic recovery in diabetes (Zhao et al., 2017). Bone marrow-derived cell therapies have been shown to have a potential beneficial effect in diabetes management, such as tissue regeneration and muscle control. It has been clinically demonstrated that bone marrow mesenchymal stem cell transplantation has proven to be effective in the treatment of diabetic complications, including long-term treatment of severe diabetics such as recurrent cases of lower limb bullosis diabeticorum (Chen et al., 2018). Moreover, there are randomized controlled trials conducted on combination therapies, including autologous bone marrow stem cell transplantation combined with hyperbaric oxygen therapy, which depict therapeutic effectiveness in persons with T2DM (Estrada et al., 2019). Vascular complications in diabetes have also been proven to be treated with the help of stem cell therapies. Long-term outcomes of extracting bone marrow mesenchymal stem cell [BMMSCs] or bone marrow mononuclear cells [BMMNCs] have been shown to have positive results in diabetic critical limb ischemia patients and foot ulcer patients (Lu et al., 2019).

Moreover, adipose-derived stromal cells and stromal vascular fraction cells showed their regenerative potential in reversing chronic diabetic foot ulcers, by enhancing wound-healing process (Carstens et al., 2021; Soria-Juan et al., 2021). An additional mesenchymal stem cell source of the umbilical cord has also undergone clinical trials and reported safety and the possibility of an effective outcome in adults with type 2 diabetes to enhance metabolic parameters (Zang et al., 2022; Zang et al., 2023). These regenerative treatments have facilitated tissue repair through mechanisms such as angiogenesis, immunomodulation, and enhanced microvascular circulation.

Also, recent studies have been investigating the mesenchymal stromal cell therapy with regards to diabetic kidney disease, noting its safety and initial effectiveness in the enhancement of renal outcomes (Habiba et al., 2024). The clinical outcomes of stem cell therapies can differ depending on the disease duration and disease, which was proved to affect the efficacy of the autologous bone marrow-derived mesenchymal stem cell transplantation (Velikova et al., 2024). Experimental and clinical research has been building evidence that stem cell-based therapies and regenerative medicine technologies can provide a prospective tool in enhancing metabolic regulation and intervention of the complications that can be linked to type 2 diabetes mellitus. Nevertheless, there is need to carry out additional research and properly designed clinical trials to determine the safety, longterm efficacy, and clinical applicability of these emerging therapeutic interventions. Thus, the current review aimed to summarize the stem cell-based therapies of type 2 diabetes, and especially highlight recent clinical developments, the current challenges in the field, and the future outlook of regenerative diabetes care.

Reference

Carstens MH, Quintana FJ, Calderwood ST, Sevilla JP, Ríos AB, Rivera CM. 2021. Treatment of chronic diabetic foot ulcers with adipose-derived stromal vascular fraction cell injections: Safety and evidence of efficacy at 1 year. Stem Cells Translational Medicine 10, 1138–1147.

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Soria-Juan B, Garcia-Arranz M, Llanos Jiménez L, Aparicio C, Gonzalez A, Mahillo Fernandez I. 2021. Efficacy and safety of intramuscular administration of allogeneic adipose tissue-derived mesenchymal stromal cells in diabetic patients with critical limb ischemia: Study protocol for a randomized controlled trial. Trials 22, 595. DOI: 10.1186/s13063-021-05430-2.

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Wu Z, Huang S, Li S, Cai J, Huang L, Wu W, et al. 2024. Bone marrow mesenchymal stem cell and mononuclear cell combination therapy in type 2 diabetes mellitus: A randomized controlled study with 8-year follow-up. Stem Cell Research and Therapy 15, 339.

Xu J, Zgheib C, Hodges MM, Caskey RC, Hu J, Liechty KW. 2017. Mesenchymal stem cells correct impaired diabetic wound healing by decreasing ECM proteolysis. Physiological Genomics 49, 541–548.

Zang L, Li Y, Hao H, Liu J, Cheng Y, Li B, et al. 2022. Efficacy and safety of umbilical cord-derived mesenchymal stem cells in adults with type 2 diabetes: A randomized placebo-controlled phase II trial. Stem Cell Research and Therapy 13, 180.

Zang L, Li Y, Hao H, Liu J, Zhang Q, Gao F. 2023. Efficacy of umbilical cord-derived mesenchymal stem cells in type 2 diabetes assessed by continuous glucose monitoring. Stem Cells Translational Medicine 12, 775–782.

Zhang J, Suo M, Wang J, Liu X, Huang H, Wang K, Liu X, Sun T, Li Z, Liu J. 2024. Standardisation is the key to the sustained, rapid and healthy development of stem cell-based therapy. Clinical and Translational Medicine 14(4), e1646. DOI: 10.1002/ctm2.1646.

Zhao Y, Jiang Z, Delgado E, Li H, Zhou H, Hu W. 2017. Platelet-derived mitochondria display embryonic stem cell markers and improve pancreatic islet β-cell function in humans. Stem Cells Translational Medicine 6, 1684–1697.

Article source : Clinical importance of stem cells in T2D treatment: A systematic review 

September 1, 2026

Plant-Based Biopesticides Against Rice Green Leafhopper | IJB 2026

Bioefficacy, Indigenous, Plant-based, Biopesticides, GLH

Diosa G. Alasaas,  Angelina T. Gonzales,  Ricardo Casauay, and Mayflor D. Compra, from the institute of the Philippines. Wrote a research article about, Plant-Based Biopesticides Against Rice Green Leafhopper. Entitled, Bioefficacy testing of indigenous plant-based biopesticides against green leafhopper (GLH) of rice. This research paper published by the International Journal of Biosciences | IJB. an open access scholarly research journal on Biosciences. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

In the Philippines, rice is the major staple crop but its production is affected by insect pests such as the rice green leafhopper (GLH). This study assessed the efficacy of three indigenous plant-based biopesticides namely: Hagonoy (Chromolaena odorata), Lantana (Lantana camara), and Makabuhay (Tinospora crispa) against GLH under laboratory and nursery conditions. The aqueous and ethanolic extracts were prepared at a ratio of 100 g plant material to 1 L solvent and applied at different concentrations. Based on the results of phytochemical analysis, it reveals that Lantana camara and Hagonoy contained the highest number of secondary metabolites in the aqueous and ethanolic extracts, respectively. Under laboratory conditions, Cypermethrin obtained the 100% GLH mortality, however the Makabuhay at 40 mL showed statistically comparable efficacy with 93.33% mortality after one hour of application. In nursery trials at 56 days after transplanting, all three plant extracts obtained mortality rates comparable to Cypermethrin. These findings indicate that the tested biopesticides, particularly Makabuhay, have potential as environmentally friendly alternatives for GLH management, although further field validation is recommended. 

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Introduction

Rice production in the Philippines plays a vital role in ensuring the country's food security and contributing to its economy. The Philippines is among the world's leading rice-producing countries, accounting for approximately 2.8% of global rice production. Rice is the staple food of the Filipino population and serves as the primary source of dietary carbohydrates (Palanog et al., 2019). Beyond its nutritional value, rice provides what anthropologists describe as the physiological sensation of satiety. It is consumed daily by millions of Filipinos, particularly low-income households, and serves as the primary livelihood of millions of rice farmers throughout the country.

The annual per capita consumption of rice in the country is estimated at 109.5 kg, which provides 56% of the calories, 37% of the proteins, and 3.8% of the fats required per person per day . In the Philippines, rice is seen as an effective delivery system for food fortification because of its high per capita consumption (109 kg/person/day) Palanog et al., 2019. Similarly, Roy et al. (2011) reported that more than half of the world's population relies on rice as its primary staple food.

Despite its importance, rice production is constrained by several factors, including unfavorable climatic conditions and the incidence of insect pests and diseases. These problems significantly reduce crop productivity and farmers' income. Annually, farmers lose an estimated average of 37% of their rice yield due to insect pests, diseases, and weeds, International Rice Research Institute (IRRI). To lessen these losses, many farmers are highly dependent on synthetic pesticides. However, this practice has resulted in several adverse effects such as the development of pesticide resistance, environmental pollution, pesticide residues in agricultural products, and detrimental on beneficial organisms and other nontarget species.

To reduce the massive use of chemical pesticides, several indigenous plant species possess natural pesticidal properties and offer effective, affordable, and environmentally safe. Plant species such as lantana (Lantana camara L.), hagonoy (Chromolaena odorata (L.) R.M. King and H. Rob.), and makabuhay (Tinospora crispa (L.) Hook. f. and Thomson) contain bioactive compounds with insecticidal, antifeedant, and repellent properties that have demonstrated potential for managing insect pests (Ahmad et al., 2016; Raj and Syriac, 2016).

The development of indigenous plant-based biopesticides presents a promising opportunity to reduce dependence on synthetic pesticides while promoting sustainable rice production. Such ecofriendly pest management strategies can contribute to effective insect pest control, environmental conservation, improved farmer health and safety, and the long-term sustainability of rice farming systems in the Philippines. Thus, this study aimed to determine the effectiveness of indigenous plant based biopesticide against green leafhopper of rice, compare the efficacy of indigenous plant based biopesticide with the standard insecticide used for insect pest of rice, and generate bioefficacy data to support the registration of the product with Fertilizer Pesticides Authority (FPA) in the Philippines.

Reference

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Emeziem DM, Iwu IC. 2024. GC-MS characterization of phytochemicals and antimicrobial properties of Chromolaena odorata leaf harvested from South Eastern Nigeria. Asian Journal of Biochemistry, Genetics and Molecular Biology 16(7), 85–97. DOI: 10.9734/AJBGMB/2024/v16i7393

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Palanog AD, Calayugan MIC, Descalsota-Empleo GI, Amparado A, Inabangan-Asilo MA. 2019. Zinc and Iron Nutrition Status in the Philippines Population and Local Soils. Frontiers in Nutrition 6, 81. DOI: 10.3389/fnut.2019.00081

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Article source : Bioefficacy testing of indigenous plant-based biopesticides against green leafhopper (GLH) of rice 

August 31, 2026

Heavy Metal Risks in Iligan Dumpsite Soil | JBES 2025

Arsenic, Chromium, Dumpsite, Potential ecological risk, Health risk

Shekinah Ruth R. Manupac,  Hernando P. Bacosa,  Johniel E. Babiera,  Wella T. Tatil,  Jaime Q. Guihawan and Peter D. Suson, from the different institute of the Philippines. Wrote a research article about, Heavy Metal Risks in Iligan Dumpsite Soil. Entitled, Chromium and arsenic in an abandoned open dumpsite soil in Iligan, Philippines: A comprehensive ecological and health risk analysis. This research paper published by the Journal of Biodiversity and Environmental Sciences | JBES. an open access scholarly research journal on Environmental Sciences. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

Improper municipal solid waste disposal is a critical issue impacting soil quality, mainly through the contamination of heavy metals. This study aims to assess the concentrations of chromium and arsenic in the open dumpsite soil of Iligan City, Philippines, and its impacts on the environment and human health. Currently there is no data on the ecological and human health risks associated with open dumpsites in the Philippines.  The results indicated that while chromium concentrations fell within acceptable limits for agricultural use, arsenic concentrations significantly exceeded the maximum permissible concentrations set by regulatory bodies, posing a serious environmental hazard. The potential ecological risk index classifies the area as having a low ecological risk, yet highlighted a severe risk associated with arsenic. Health risk assessments indicated that both adults and children fall within acceptable levels for both non-carcinogenic and carcinogenic risks. Overall, these findings demonstrate a need for targeted environmental management strategies in Iligan City to mitigate heavy metal contamination, especially arsenic, and to protect the health of local populations. Remediation efforts and ongoing monitoring are essential to prevent further ecological damage and safeguard public health, particularly for vulnerable groups like children. 

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Introduction

Solid waste management (SWM) is a major concern for many countries (Mavakala, 2022). It is estimated that municipal solid waste (MSW) generation in South Asia, Latin America, and Sub-Saharan Africa will double or triple by 2050, making up to 35% of the world’s MSW (World Bank, 2018). Increasing population, urbanization, economic development, and improved living standards in developing countries have led to a significant increase in municipal solid waste generation (Minghua et al., 2009). Improper waste management practices have led to releasing of significant amounts of toxic materials, particularly heavy metals, into the environment, exacerbating environmental concerns. Dumpsites, prevalent in many developing countries, pose a significant risk as they contain an amount of contaminants that can potentially leach into the surrounding soil, including heavy metals like arsenic (As) and chromium (Cr) (Kanmani and Gandhimathi, 2013; Olayiwola et al., 2017). In the Philippines, for instance, which records 14.66 million tons of trash annually, heavy metals in open dumpsites are a significant concern (Ali et al., 2013; Rebuelta-The, 2022). Heavy metals such as As and Cr in dumpsites and their toxic nature and persistence in the environment further raise environmental concerns (Flyhammar et al., 1998; Riber et al., 2005; Sankaran and Ebbs, 2007).

Heavy metal contamination of soil may pose risks and hazards to humans and the ecosystem via direct ingestion or contact with contaminated soil, the food chain (soil-plant-human or soil-plant-animalhuman), drinking contaminated groundwater, reduction in food quality (safety and marketability) via phytotoxicity, reduction in land usability for agricultural production resulting in food insecurity, and land tenure issues (McLaughlin et al., 2000; Ling et al., 2007). It can accumulate in fatty tissues, influence the central nervous system, be deposited in the circulatory system, and disturb the proper functioning of internal organs. For instance, chromium (Cr) compounds can be absorbed by the lungs, gastrointestinal tract, and, to a limited extent, intact skin. This absorption can lead to respiratory tract irritation, an increased risk of lung cancer, and various health issues affecting the kidneys, liver, stomach, and blood (Wilbur, 2012). Similarly, arsenic can lead to severe health effects such as chronic arsenic poisoning and an elevated risk of skin cancer through prolonged exposure to contaminated soil, food, and water (World Health Organization). As a result, it is critical to monitor and balance heavy metal concentrations in various environmental media to minimize hazardous effects on biota.

Ecological and health risk assessments are essential tools for evaluating the potential impacts of pollutants (Yu et al., 2022). Analyzing soil for toxic metals is vital for understanding environmental pollution and assessing risks to nearby communities (Kasassi et al., 2008; Akanchise et al., 2020; Aja et al., 2021). However, there is currently no data on the ecological and human health risks associated with open dumpsites in the Philippines. This study aims to investigate the distribution of Cr and As in the soil of the vicinity of the abandoned dumpsite in Iligan City, Philippines, and to pre-assess the associated ecological and health risks. The findings will provide a scientific basis for protecting the soil environment and guiding remediation efforts, contributing to minimal environmental impact and reduced health risks.

This study relies on secondary data for the background values of heavy metals, as obtaining primary data from locations several kilometers away from the sampling site would require additional financial resources that are currently unavailable.

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Article source : Chromium and arsenic inan abandoned open dumpsite soil in Iligan, Philippines: A comprehensive ecological and health risk analysis 

August 29, 2026

Genetic Diversity of Omicron Spike Variants in Vietnam | IJB 2022

Genetic diversity, Omicron, SARS-CoV-2, Spike gene, Vietnam.

Quan Ke Thai, Department of Saigon University, 273 An Duong Vuong, Ward 3 District 5, Ho Chi Minh city, Vietnam. Phuoc Huynh, department of aVNU HCMC University of Science, 227 Nguyen Van Cu, Ward 4 District 5, Ho Chi Minh city, Vietnam. Yen Le Thi, department of DSI1191, Saigon University, 273 An Duong Vuong, Ward 3 District 5, Ho Chi Minh city, Vietnam.  Huyen Nguyen Thi Thuong, department of Biology, HCMC University of Education, 280 An Duong Vuong Ward 4 District 5, Ho Chi Minh city, Vietnam. Wrote a research article about, Genetic Diversity of Omicron Spike Variants in Vietnam. Entitled, Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene in Vietnam. This research paper published by the International Journal of Biosciences | IJB. an open access scholarly research journal on Biosciences. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

The recently emerging Omicron is of prime concern because this variant has been the cause of current large outbreaks. Omicron becomes more dangerous when numerous content mutations in the Spike (S) gene lead to more than 30 substitutions of amino acids in spike protein. Omicron variant had been identified as Variants Of Concern (VOC) when it had transmission rate overtake previous VOCs. In this report, we focus on analyzing the genetic diversity of the S gene of Omicron variants in Vietnam. Our results indicate the high level of haplotype diversity when confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037. The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ± 0.0026 and recorded 318 polymorphic sites with the average number of mutations of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion and insertion occurred in the NTD region. Besides, we note conserved mutation in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the S gene provided more correlation between infection and mutation in this gene. Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through the network, in which necessary focus T22917G (L452R), T23018G (F486V), and other novel mutations will appear in the S gene. The network provided the whole picture of Omicron variants in Vietnam, supporting the tracing of the source of a new outbreak in the future.  

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Introduction

The recently emerging Omicron is of prime concern because this variant has been the cause of current large outbreaks. Omicron becomes more dangerous when numerous content mutations in the Spike (S) gene lead to more than 30 substitutions of amino acids in spike protein. Omicron variant had been identified as Variants Of Concern (VOC) when it had transmission rate overtake previous VOCs. In this report, we focus on analyzing the genetic diversity of the S gene of Omicron variants in Vietnam. Our results indicate the high level of haplotype diversity when confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037. The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ± 0.0026 and recorded 318 polymorphic sites with the average number of mutations of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion and insertion occurred in the NTD region. Besides, we note conserved mutation in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the S gene provided more correlation between infection and mutation in this gene. Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through the network, in which necessary focus T22917G (L452R), T23018G (F486V), and other novel mutations will appear in the S gene. The network provided the whole picture of Omicron variants in Vietnam, supporting the tracing of the source of a new outbreak in the future.

appearance of the Delta variant is almost eliminated, breaking the achievements preventing the pandemic in some countries. Delta's rapid transmission is determined mainly by the spike protein's L452R, T478K, and E484Q N501Y mutations (Kumar, Singh et al., 2021) (Fan, Hu et al., 2021). In addition, some substitutions, such as E484K, D614G, and P681H/R, have also been conserved in many different VOC variants (Papanikolaou, Chrysovergis et al., 2022) (Lubinski, Frazier et al., 2021) . Recently, a new variant is thought to be more infectious than the Delta variant and maintains from 30 to 45 mutations in the spike protein (Wei, Shan et al., 2021) (Kumar, Thambiraja et al., 2022). According to PANGO Lineages, this variant belongs to lineage B.1.1.529, named Omicron by WHO and classified as a VOC variant. Since December 2021, Omicron has almost replaced Delta as the primary source of infection infections in the United States (Fall, Eldesouki et al., 2022). After that, the Omicron variant became almost universally dominant and gradually replaced the previously dangerous Delta variant (Chaguza, Coppi et al., 2022).

Vietnam is one of the infrequent countries that has succeeded in controlling the epidemic situation in the early stages of the pandemic outbreak in the world. Vietnam has successfully gone 99 days with no community transmission, and most cases (60%) in Vietnam are due to entry from China, Europe, and the United States (Thai, Rabaa et al., 2021). Examination of genomics indicated that the nucleotide similarity of the sequences in Vietnam in the two outbreaks was very high (minimum 99.96%, mean 99.97%), combined with familiar mutation exhibiting that virus is not competent to silently infect the community from April 2020 (Phuong, Tung et al., 2021). In Vietnam, each epidemic wave corresponds to the emergence of a new variant with a more robust infectious fitness. During the third wave of epidemics (beginning on January 28, 2021), the outbreak in northern Vietnam occurred rapidly with the main contribution of Alpha variants (Chau, Hong et al., 2021). Then, the fourth wave (beginning on April 27, 2021) had been the worst ever experienced by the country. In May 2021, all patients in Vietnam were derived by the Delta variant (Nguyen, Wong et al., 2021). In November, this wave had caused 99.9% of total deaths in the country (Hoang, Pham et al., 2022). The Vietnamese government has had to implement unprecedented strict epidemic prevention measures, including encouraging people to isolate themselves at home, mobilizing the participation of the army and military medics, and setting up field hospitals. However, the epidemic situation had been still difficult to control because the Delta variant has high transmissibility.

After November 2021, when the vaccination rate in Vietnam reached a relatively high threshold, government took to restore social life under "new normal" conditions.

The gradual easing of epidemic prevention measures has facilitated the spread of the virus in the community. The first case confirmed that the Omicron variant was recorded in Vietnam on December 19, 2021. Until March 2022, the Omicron became the primary circulating variant and the cause of infections in the Hanoi capital. On March 12, 2022, Vietnam recorded the highest number of infections ever at 454,179 cases/day. This number is much larger than the previous wave of epidemics caused by the Delta variants. Proposes that Omicron will become the dominant variant in Vietnam shortly. Despite the sudden increase in cases, the mortality rate tends to be the opposite.

The number of deaths caused by the Omicron on March 13, 2022, is 95 cases, and the average of the last seven days is 82. These concerns were lower than Delta's 803 cases on September 1, 2021, and the average of the last seven days in 360 cases (according to Vietnam's Ministry of Health). The current research literature indicates that the Omicron variants are more infectious than previously recorded variants (Ren, Wang et al., 2022) (He, Hong et al., 2021). On the other hand, Omicron can cause symptoms less severe (Callaway and Ledford, 2021) (Kupferschmidt and Vogel, 2021) (Ren, Wang et al., 2022). Even so, the high transmission rate of Omicron will pose a significant challenge for diagnostics and vaccine strategies. Therefore, tracking the genetic shifts of these variants is significant. For these reasons, the genetic diversity of the S gene of Omicron variants isolated in Vietnam was investigated. By constructing a network, the genetic relationship of Omicron variants would be revealed, supporting the tracing of a infection source of a new outbreak in the future.

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