Editorial: Evolution & Genomic Adaptation of Emerging and Re-emerging RNA Viruses

Abstract

Editorial on the Research Topic Evolution & Genomic Adaptation of Emerging and Re-emerging RNA Viruses Emerging and re-emerging infectious diseases are defined as diseases caused by unidentified and reappearing pathogens (NIAID, 2018). RNA viruses are mostly responsible for most of such infectious disease outbreaks (Nichol et al., 2000). One of the key reasons is due to genomic alterations such as spontaneous mutation recombination or reassortment which occurs during adaptation and evolution processes (Nichol et al., 2000). When those genomic changes have been accumulated to a certain level or when the changes are on the antigenic or receptor-binding region, the host immune systems are no longer able to recognize the new variants, resulting in global viral outbreaks (De Wit et al., 2016; Nelemans and Kikkert, 2019; Kikkert, 2020). SARS-CoV-2 and its variants has claimed more than 4.56 million lives from December 2019 until the writing of this manuscript. The high mortality rate emphasizes the importance of continuously monitoring these emerging viruses' evolution and genomic adaptation (WHO, 2021). The purpose of this Research Topic serves to provide an open access platform for an international global team of multidisciplinary researchers and scientists to share their findings on the viral genomic feathers and changes, to provide a platform enabling public health officials to warn the global community of potential and existing epidemics and pandemics, and to develop an analytical platform for researchers to evaluate the outbreak risks, to prepare and to control future pandemics (Huang et al., 2021). In this Research Topic, the authors will present their most recent genomic investigations on these viruses. A total of 28 manuscripts including original research and review have been received, of which 15 were eventually accepted for journal publications after rigorous peer review processes. Based on the viruses involved, these 15 articles can be briefly classified into three groups: positive sense single-strand RNA (+ssRNA) viruses; negative-sense single-strand RNA (-ssRNA) viruses; diagnosis and dynamic single-strand RNA Virus-Host interactions. The first group +ssRNA viruses are the Group IV viruses in the Baltimore classification system (Baltimore, 1971; Cann, 2016), including viruses from Coronaviridae, Picornaviridae, Flaviviridae, Togaviridae. Within this group viruses, Coronavirus is the most researched virus in this topic. Three original research articles discussed the SARS-CoV-2 coronaviruses identified in China, Brazil, and Uruguay, respectively. In China, Song et al. isolated SARS-CoV-2 viruses from the Henan Province, which is adjacent to the Hubei Province, the region which has the highest mortality rate due to the SARS-CoV-2 pandemic within China. They analyzed the samples from different locations to estimate the virus's most recent common ancestor (TMRCA) and evolutionary rate. In Brazil, Resende et al. analyzed 190 SARS-CoV-2 viruses isolated from 13 Brazilian states and found the B.1.1.33-like viruses circulating in Brazil might have been transmitted from Europe or domestically erupted a few weeks before regional outbreaks. Their analysis also indicates public health interventions were successful because the median effective reproductive number (Re) dropped by 66%. In Uruguay, Mir et al. investigated the local virus source and the transmission rate(s). Based on the 122 viruses recovered at Brazilian–Uruguayan border area, they found that the SARS-CoV-2 viruses in the Uruguay border were introduced multiple times independently from Brazil (lineage B.1.1.28 and B.1.1.33). The researchers also revealed in their research that the synonymous and non-synonymous single nucleotide polymorphisms (SNP) are the genetic variations responsible to define the lineages. Castonguay et al. completed the fourth SARS-CoV-2 meta-analysis, which systematically tracked the evolutionary trajectory of SARS-CoV-2 over time, identified emerging mutations, and modeled the structural changes and corresponding molecular interactions. The fifth coronavirus is the avian infectious bronchitis virus (IBV). Jiang et al. identified a critical mutation to determine the host tropism alteration, which is a valuable key in understanding why the coronavirus could jump from one host to another. Porcine Epidemic Diarrhea virus (PEDV) is the last coronavirus discussed in this Research Topic. Li et al. isolated a PEDV, which has been detected to contain a unique insertion in the S1 protein binding by the recombination test. They predicted the structure of this new recombinant and proved its biological correlation by showing this strain had higher pathogenicity than the other viruses isolated in the piglet in vivo challenge. Following the Coronaviridae, Picornaviridae is the second most popular virus family within this topic. In two articles, researchers investigated the Norovirus and Coxsackievirus, which are enteroviruses within the family Picornaviridae. Zuo et al. identified the new Norovirus GII.17 variants, which surpassed the predominant GII.4 genotype causing the Kawasaki variant outbreaks in 2014–2015. Serological analysis showed weak cross-protection to these new variants so attention should be taken to prevent future outbreaks. The corresponding mutated amino acids on antigenic sites were also identified. The second study led by Li's team focused on the Norovirus GII.2 clusters, which caused unprecedented endemic outbreaks in 2016–2017. Eight distinct clusters with increased genetic diversity were characterized with an absence of elevated evolutionary rate. Additionally, the selection pressure was detected, suggesting the outbreak was probably not related to an evolutionary adaptation. The second virus in the Picornaviridae, is the Coxsackievirus A16 (CVA16) and was reported by Nhu et al. This molecular...