Introductory Chapter: Current Landscape of Animal and Human Virus Treatments

1. Introduction

As the world is currently watching the COVID-19 pandemic unravel to a controlled course, there are still many instances of viral infection outbreaks that occurred. Although there is a downward trajectory, the influenza virus is still a potential threat due to its history of causing pandemics [1]. Moreover, some other viral infections such as HIV/AIDS and Hepatitis are still causing sporadic outbreaks worldwide [2, 3]. However, the discussion about the current situation of human and animal viral outbreaks will not be complete without mentioning the COVID-19 pandemic. As a zoonosis infection, the SARS-CoV-2 virus could infect both humans and animals. Besides humans, it is known to infect cats, dogs, tigers, minks, and others [4, 5, 6]. Henceforth, zoonosis infection will continue to be a challenging research topic. In this respect, several developments in the field of biomedicine and medical biotechnology for dealing with COVID-19 pandemics should be mentioned, as they could be possibly catered to another type of viral infections as well.

2. Current status of COVID-19 drug and vaccine development

As soon as WHO declared the ongoing COVID-19 pandemic in March 2020, several repurposed drugs are prepared. One of them is remdesivir, that previously developed for treating hepatitis C, Ebola, and Marburg virus infections [7, 8, 9, 10, 11]. Although there are mixed results in the clinical settings, remdesivir is currently one of the standard options in COVID-19 treatments [12]. Moreover, more drugs have been rolled out for COVID-19, namely molnupiravir and paxlovid [13, 14]. The aforementioned drugs are working by targeting specific proteins of the SARS-COV-2 virus, such as Mpro and RdRp [15]. Hence, biologics such as antibody treatment are also developed with regeneron ® as one of the examples [16]. However, one of the game changers in the COVID-19 pandemic is always the vaccine development. The successful deployment of new mRNA vaccines, as well as the existing ones such as live attenuated and vectors, have successfully slowed down the infection rate of COVID-19 [17, 18, 19]. While highly promising, some therapeutic approaches are still in their infancy. The development of lead compounds for COVID-19 from natural products is currently still ongoing, mainly in both in vitro and in vivo stages [20]. Moreover, the same condition also occurred with siRNA-based therapeutics [21]. However, the application of natural products and siRNA-based therapeutic for COVID-19 faces several challenges, such as low bioavailability, poor stability, off-target effects, and delivery barriers [22, 23]. Therefore, more research is needed to overcome these limitations and optimize the efficacy and safety of these potential agents. Furthermore, the development of combinatorial strategies that target multiple viral genes or pathways may enhance antiviral activity and reduce the risk of viral resistance [22, 24]. Thus, natural products and siRNA-based therapeutics could offer promising alternatives or adjuncts to conventional treatments for COVID-19 and other coronaviruses. In this regard, the current research progress for COVID-19 will eventually serve as a benchmarking trend that could be applied in other cases.

3. Structural bioinformatics as virology studies instrument

Structural bioinformatics is currently an integral part of the research pipeline in virology studies, as it has provided detailed information about virus’ protein and nucleic acid structures [25, 26, 27]. As such, the annotated information is useful to design drugs and vaccines and gives a push to the development of rational drug design and immunoinformatics as possible solutions for combating viral infections [28, 29, 30]. Moreover, structural bioinformatics is currently under trial for examining phages molecular mechanism [31]. Some of the structural bioinformatics methods and tools for virology research include visualization and analysis of protein structures [32], comparative protein structure analysis [33], protein–protein modeling using cryo-EM restraints [34], biological assembly comparison, and integrating molecular simulation and experimental data. These methods and tools can help to identify and characterize viral proteins and their interactions with host factors, drugs, antibodies, and other viruses. They can also facilitate the discovery of novel targets, inhibitors, and vaccines for viral diseases. However, there are still many challenges and limitations in applying structural bioinformatics to virology, such as the scarcity of experimental data, the complexity of viral dynamics and evolution, and the uncertainty of molecular interactions and mechanisms [35, 36, 37]. Therefore, more efforts are needed to improve the accuracy, efficiency, and applicability of structural bioinformatics methods and tools for virology research.

4. Alternative viral infection diagnostics methods

In the early phase of the COVID-19 pandemic, WHO has elevated NAAT (Nucleic acid amplification test) method such as RT-PCR as a standard instrument for diagnosing the disease. WHO’s stance has been enacted in several of their official documents that dictate the diagnostics protocol in the clinical setting [38, 39, 40]. Due to the limitation of RT-PCR deployment in the early phase of pandemic, WHO also provides guidelines for NAAT alternatives, such as antigen-detecting rapid diagnostic tests [41]. All of WHO’s guidelines on COVID-19 diagnostics are totally in line with their already published guidelines on the establishment of virology laboratory [42]. However, the WHO’s establishment of standard operating procedure (SOP) for virology diagnostics did not deter the development of alternatives method. One of them is the breath analysis by electronic nose (enose) that has been trialed in Indonesia [43, 44]. Similar technology also has been applied in the Netherlands [45]. Unlike standard NAAT and non-NAAT-based diagnostics, enose was developed to detect Volatile Organic Compounds (VOC) that are produced by human cells. It is deemed as a unique and creative application of diagnostics and has huge potential [46]. The other alternative is the bioelectrochemistry-based method. It has been applied in animal viruses with nanoparticle deployment, such as with African Swine Fever Virus (ASFV) [47, 48]. Moreover, it is also trialed in detecting SARS-CoV-2 as well [49]. Despite the development of alternatives, WHO has not changed its stance pertaining to its virology SOPs. In the end, the status of RT-PCR as a standard method for COVID-19 diagnostics is still unchanged up to the publication of this chapter. This condition could serve as a standing ground for more research in this area, as WHO’s SOP will serve as a benchmark for any developed method in virology.

5. Outlook: Bioinformatics as instrument to resolve biomedical problem

Staring in the post-COVID-19 lockdown period, there will be massive integration of Bioinformatics into biological sciences, especially in virology studies. Bioinformatics will serve as an indispensable instrument to resolve biomedical and medical biotechnology problems. Moreover, methods of structural bioinformatics such as molecular simulation is a crucial method to understand the biochemical properties of viruses ([50, 51, 52], p. 201). Thus, the COVID-19 pandemic has taught us that SARS-CoV-2 virus is indeed evolving. In order to comprehend viral evolution, a more sophisticated instrument is needed. The standard tool to do that is definitely the New Generation Sequencing (NGS) instrument. NGS is crucial in the discovery of new SARS-CoV-2 variants such as delta and omicron [53]. Moreover, portable NGS instrumentation such as Oxford Nanopore ® has made the integration of bioinformatics into wet laboratory pipelines more assured than ever. Its versatility and portability have enabled such tools to be used by any life scientist with minimal training time [54]. Sequence analysis, as an integral part of bioinformatics, also plays an important part in Loop-mediated Isothermal Amplification (LAMP) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) diagnostics development [55, 56]. Both of these methods are also trialed for COVID-19 diagnostics as well [57, 58]. Lastly, phages and biologics will possibly play an important role in dealing with viral infection in general [16, 59, 60, 61, 62]. An improved and updated bioinformatics pipeline should be devised to comprehend the potential role of phages and biologics in biomedical applications.

Acknowledgments

The author would like to thank the Research and Community Service Department (LPPM) of the Indonesia International Institute for Life Sciences (i3L) for supporting these studies. The author also declared that there is no competing interest and received no external funding to support this study. The author also declared that Bing ® AI was deployed for web searches, references citation, and editing the text.