Genetic Diversity of Omicron Spike Variants in Vietnam | IJB 2022

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 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.  

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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Article source : Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene in Vietnam   

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Crop Protection and Human–Wildlife Conflict in Côte d’Ivoire | JBES 2025

 

Koffi Kouamé Christophe,  Ouffoue Affoué Eugénie Naomie,  Gagbé Dalié Sylvestre, and Beda Alex, from the institute of the Côte d’Ivoire. Wrote a research article about, Crop Protection and Human–Wildlife Conflict in Côte d’Ivoire. Entitled, Household socio-agricultural profiles and the adoption of crop protection strategies in human-wildlife conflict contexts: Insights from western Côte d’Ivoire around mount Sangbé National Park. 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

In rural sub-Saharan Africa, proximity to protected areas and habitat fragmentation intensify human-wildlife conflicts, particularly through crop-raiding. This study examines how household socio-agricultural profiles influence the adoption of protection strategies against wildlife incursions. The study took place near mount Sangbé national park in Côte d’Ivoire and involved surveying 121 farming households from three villages through structured interviews, complemented by field observations and expert consultations. Nineteen wildlife species were identified as crop raiders, with granivores and rodents, especially the grass cutter, red-headed quelea, and patas monkey, causing significant damage to rice, cassava, and cocoa. A hierarchical classification revealed four distinct household clusters, differentiated by landholding size, education level, age structure, and proximity to the park. Binary indicators were constructed for each method to evaluate protection practices and visualized by cluster. Strategies were grouped into physical deterrents, agroecological measures, and community-based interventions. A bias-reduced multinomial logistic regression was conducted using adjusted score equations to obtain stable estimates. Results show that field guarding is the most widely used strategy, especially among educated households with smaller landholdings, while traditional hunting and trapping are more common among older, less educated households with larger farms. Passive tolerance was positively associated across all clusters, suggesting widespread reliance on non-confrontational coping mechanisms. Scarecrows and trapping methods showed low or negative adoption rates, indicating limited perceived effectiveness. These findings underscore the need to tailor mitigation strategies to household-specific capacities and spatial contexts. The study advocates for agroecological and community-based approaches to enhance resilience and sustainability in buffer zones near protected areas.

Introduction

In rural regions of sub-Saharan Africa, agricultural systems are increasingly subjected to ecological and social pressures resulting from habitat fragmentation, expansion of cultivated areas, and proximity to protected zones. These factors exacerbate humanwildlife conflicts, particularly via wildlife encroachments into subsistence crops, a phenomenon extensively documented in buffer zones adjacent to natural reserves (Dibloni et al., 2020; Chepkwony et al., 2025). Such crop-raiding events jeopardize food security, economic stability, and the psychological well-being of farming households (Barua et al., 2013; Nyhus, 2016). Crop-raiding, defined as the incursion of wild animals into cultivated fields, results in direct economic losses and indirect effects on the mental health and social cohesion of farmers (Hill, 2005; Galley and Anthony, 2024). These conflicts are further aggravated by land pressure, habitat degradation, and inadequate compensation or prevention mechanisms (Asaye et al., 2024).

While forest ecosystems provide essential services that enhance rural resilience to climate change, their proximity also increases exposure to crop-raiding, especially in low-diversity farming systems. This paradox highlights the need for integrated approaches that balance conservation and agricultural productivity. Agroecology is a theoretically grounded and operational framework to address this dual challenge. Rooted in ecological principles and local knowledge, agroecology promotes crop diversification, sustainable soil management, and landscape-level planning. It offers practical strategies such as vegetative barriers, agroforestry, and community-based surveillance systems that can mitigate wildlife incursions while enhancing ecosystem services (Altieri, 1995; Bommarco, 2024; Dickman, 2010; Wezel et al., 2009).

Despite growing recognition of crop-raiding impacts, existing research remains fragmented and overly focused on direct economic losses. It often neglects the socio-territorial and behavioral dimensions that shape household responses and rarely incorporates agroecological or resilience-based perspectives. Moreover, the socio-agricultural typologies of farming households and their influence on the adoption of mitigation strategies are insufficiently characterized. This study fills these gaps by analyzing the complex interactions between household socio-agricultural profiles, crop-raiding dynamics, and protection strategies. It adopts a differentiated and sustainability-oriented approach to managing human-wildlife conflicts in rural areas adjacent to protected zones. Specifically, the study identifies the plant and animal species involved in crop-raiding events, characterizes the socio-agricultural profiles of affected households, evaluates the protection strategies adopted based on household profiles and geographic location, and statistically models the influence of household characteristics on mitigation methods.

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Article source : Household socio-agricultural profiles and the adoption of crop protection strategies inhuman-wildlife conflict contexts: Insights from western Côte d’Ivoire around mount Sangbé National Park 

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Lignocellulolytic Bacteria for Sugarcane Trash Biodegradation | IJB 2024

Viji Jayabalan and Neelanarayanan Periyasamy, from the institute of the India. Wrote a research article about, Lignocellulolytic Bacteria for Sugarcane Trash Biodegradation. Entitled, Diversity of lignocellulolytic bacteria in native soil of sugarcane trash and to assess their biodegradation potential. 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 main goal of this research was to investigate the diversity of lignocellulolytic bacteria in the native soil of sugarcane trash and to assess their biodegradation potential. From naturally degrading sugarcane waste, bacteria were identified. 35 distinct bacterial species were discovered; these bacteria were then employed to determine each one’s potential for breaking down the lignin and cellulose found in sugarcane waste. After selecting a potential strain of bacteria, Congo red and iodine tests were created for the purpose of screening bacterial species, and they were then utilized to further the biodegradation of sugarcane waste. Thirteen of the thirty-five investigated bacterial species generated cellulase and ligninase enzymes, and Pseudomonas fluorescens was identified in the secondary screening as a suitable strain among these. Hence, this P. fluorescens was employed in the degradation of sugarcane waste. When this lingo-cellulolytic bacterium was introduced to sugarcane waste, the rate of degradation of the waste was enhanced. Significant reduction in lignin and cellulose contents were observed in sugarcane trash inoculated with P. fluorescens compared to other experiments. P. fluorescens lowered the C:N ratio in soil-mixed sugarcane waste from 70:1 to 10:1. The macronutrients of the compost taken from experimental trays seeded with P. fluorescens showed a substantial increase as well. It is evident from these results that the P. fluorescens, lingo-cellulolytic bacteria may be used for the degradation of sugarcane trash. Hence, we conclude that P. fluorescens can be recommended for the degradation of sugarcane trash which would result in the production of good quality compost containing higher amounts of total nitrogen, total potassium and total phosphorus contents.

Introduction

Sugarcane is one of the most significant cash crops in India and is extremely essential to both the agricultural and industrial economies of the nation. One of the world's top producers of sugarcane is India. India produces 320 million tonnes of sugarcane annually. In Tamil Nadu, 102 tonnes of sugarcane are produced per acre (Mohan and Ponnusamy, 2011).

More than 3000 ha of sugarcane are grown in the Tiruchirappalli district of Tamil Nadu, with an average production of 100 tonnes ha-1. Over 6.5 million tonnes of sugarcane waste are created year when the crop is harvested. The state government of Tamil Nadu, through Krishi Vigyan Kendra, Sirugamani, and Tiruchirappalli District, conducted numerous education and training initiatives on how to effectively manage trash from harvested sugarcane, although trash burning is still a common practise (Dhanushkodi et al., 2019). By releasing harmful gases into the atmosphere, such as methane and carbon dioxide, this activity pollutes the atmosphere and endangers both human health and the ecosystem. Moreover, this approach significantly depletes the soil of minerals, micronutrients and microbes.

The two best alternatives for managing sugarcane waste effectively are composting and mulching, but both require a lot of work. The combined approaches of composting with microbial inoculants can be used to reduce this issue, and it currently attracts a lot of interest from researchers (Swetha et al., 2010).

The aforementioned facts make it clear that using microorganisms is necessary for the efficient and rapid decomposition of sugarcane waste. The breakdown process is typically accelerated by the microorganisms that are naturally present in the garbage. In this work, we looked into a biological technique for employing bacteria to hasten the breakdown of the main chemical components found in the waste from sugarcane. It is one of the greatest options for quickly turning the available, unused organic biodegradable wastes, such as sugarcane garbage, into compost.

This study aims to examine the diversity of lingocellulolytic bacteria in native soil, or naturally decomposing sugarcane waste sites, and afterwards to test their biodegradation capacity in order to make recommendations to farmers in the future.

Reference

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Article source : Diversity of lignocellulolytic bacteria in native soil of sugarcane trash and to assess their biodegradation potential  

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Scaling Management of Invasive Prosopis juliflora | JBES 2025

Filbert T. Meela,  From the institute of the,  Tanzania Forestry Research Institute, Morogoro, Tanzania. Linus K. Munishi, From the institute of the,  School of Life Sciences and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania. Richard A. Giliba, From the institute of the, School of Life Sciences and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania. Wrote a review article about, Scaling Management of Invasive Prosopis juliflora. Entitled, Challenges in scaling management of the invasive tree Prosopis juliflora: A review. 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

Prosopis juliflora is an invasive tree species native to Central and South America, is listed among the world’s 100 worst invasive species, severely impacts biodiversity, soil chemistry, human livelihoods, and poses health risks, potentially endangering native species. Despite global efforts to control this species using mechanical, chemical, biological, and integrated methods, it continues to spread, suggesting current strategies are ineffective. This review evaluates the effectiveness of various management approaches and highlights challenges and lessons from global experiences. Findings reveal that management efforts have mostly been small-scale trials, with mechanical, chemical, biological, and integrated methods applied at 12%, 38%, 12%, and 17% scales, respectively. These strategies often fail due to their unsustainability, lack of follow-up, and poor documentation of scalable protocols. Prosopis juliflora‘s adaptability to diverse environments further complicates management. The review underscores the urgent need for sustainable strategies that account for environmental factors and community perceptions. It recommends developing tailored management plans for each country, raising awareness in affected regions, and integrating various control methods to improve effectiveness.

Introduction

Invasive plants are the species or strains that rapidly increase their spatial distribution by expanding into native plant communities (Zedler and Kercher, 2004). Invasive plants may exert a range of impacts on native communities, they can alter resource availability to native plants and fire regimes (Aslan and Rejmanek, 2012). These invasive plants can be introduced in a new area either intentionally or unintentionally and are likely to cause economic or environmental harm or harm to human health. As trade and travel increase worldwide, invasive plant introductions continue to rise through different pathways such as trade and human movement (Mehta et al., 2007). Other drivers include wind, water, floods, birds, animal movements, and transport machines like cars and cargo ships (Hulme, 2009; Lyimo et al., 2009; Mortensen et al., 2009). Invasive plants not only destroy biodiversity but also soil chemistry, hydrology and lower human livelihood and may result in the extinction of native plants, alter the native species composition and spatial distribution (Foxcroft et al., 2006; Ngondya and Munishi, 2021; Rahman et al., 2010) and after establishment their management is often costly and ineffective in the long term (Clewley et al., 2012).

There are three fundamental management objectives when dealing with invasive species and these are as follows: prevention/exclusion; Early detection/rapid assessment; and Control/containment/eradication (Crowley et al., 2017; Mehta et al., 2007; Rejmánek, 2000). How to meet these objectives, in particular within political and economic limitations, is more a question of policy and technology (Mehta et al., 2007). By increasing resources to detect invasive species, managers may increase their chances of finding a species at a smaller population level, lessening the extent of damage and making subsequent control potentially less expensive and more effective (Mehta et al., 2007). Generally there are four methods employed in the control of the invasive plant species including the use of chemical, mechanical removal, biological method that involve release of herbivores and pathogens to manage the invasive plants (Seastedt, 2015; Zachariades et al., 2011) and integrated management which involve in cooperating all possible management approaches for control the invasive species (Ehi-Eromosele et al., 2013). The cost and time for managing these invasive alien plants (IAPs) vary depending on the level of invasiveness and the choice of the management options depending on the scale of invasion.

Management strategies targeting Prosopis juliflora have predominantly been trialed and implemented at a small scale (Shackleton et al., 2016a; Wise et al., 2012a). Despite these efforts, the effectiveness of these management approaches has been limited due to their unsustainable nature, time of intervention, no effective management practices available or not correctly implemented, failure to follow up, replacement by other IAPs, conflicts of stakeholder interests, and no restoration of desired land use. Additionally, once the projects were phased out, there was a lack of further implementation strategies. Prosopis juliflora hereafter referred to as P. juliflora has infiltrated around 54 million hectares worldwide (Shiferaw et al., 2022). It is now on the International Union Conservation of Nature (IUCN) list of the 100 worst invasive species (Mwangi and Swallow, 2008; Shiferaw et al., 2019; Simberloff and Rejmanek, 2019).

The effectiveness of the methods used, time spent in controlling and acceptance of the control methods used have not been systematically documented. Literature on this subject lacks documentation on the extent of efforts and their equity by geography and by types of methods to enable quantification of the magnitude of successes and challenges associated with the efforts taken to management. P. juliflora continues spreading where it is invasive which indicates that management strategies are not always successful. To fill this gap, this review paper focuses on different regions of the world that P. juliflora has colonized and examines whether the control methods applied were able to eradicate the species or reduce further spread. This involves reviewing the existing literature on the reasons for the introduction of P. juliflora, the negative impacts of P. juliflora, factors that contribute to the globally spread of P. juliflora, and control methods of P. juliflora. Further, the review discusses the challenges and lessons learned about the management strategies employed in fighting P. juliflora. This review paper acts as a prerequisite to decisionmakers to come up with a holistic approach to the management of P. juliflora and it provides an edge to prioritizing management options and a knowledge base for fighting against P. juliflora at different stages of invasion.

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