A transdisciplinary approach to disease ecology: Emerging coronaviruses

Humankind is currently facing the effects of an unparalleled pandemic that has impacted healthcare, social, and economic systems worldwide. Numerous studies have been published since the SARS-CoV-2 outbreak began in Wuhan, China. Most have focused on virology, epidemiology, pathogenesis, and therapeutic medicine, having been centered by reactive strategies to control the pandemic. Meanwhile, publications addressing the ecological, evolutionary, and anthropogenic drivers of virus emergence, and potential strategies to prevent future outbreaks have been sparse. Here, we highlight the necessity of complementary and transdisciplinary insight and methodologies from an integrated perspective to study emergent diseases. It is paramount to situate the consistently associated factors to understand the complexity of the current pandemic. Disease ecology can examine information to recognize the causes of emergence while appraising the role of interactions among pathogens, domestic animals, wildlife, and humans, integratively. Here we draw on a variety of disciplines and perspectives, from evolutionary biology, biogeography, ecology, molecular epidemiology and integrative health, to address the emergence of coronaviruses, with particular emphasis on SARS-CoV-2. We describe the process of the surfacing of zoonotic diseases, highlighting the interactions among wildlife, domestic animals, and humans, as well as the genetic, evolutionary, ecological, and anthropogenic processes that favor coronavirus epidemics and epizootics. We discuss specific results related to coronavirus investigations conducted in Mexico based on disease ecology methodologies. Finally, we describe alternative approaches for understanding and preventing future outbreaks and we suggest strategies to entice integrative and transdisciplinary research within the One Health/Ecohealth paradigm.

Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates

Peste des petits ruminants virus (PPRV) causes disease in domestic and wild ungulates, is the target of a global eradication programme and threatens biodiversity. Understanding the epidemiology and evolution of PPRV in wildlife is important, but hampered by the paucity of wildlife-origin PPRV genomes. In this study, full PPRV genomes were generated from three Mongolian saiga antelope, one Siberian ibex and one goitered gazelle from the 2016/2017 PPRV outbreak. Phylogenetic analysis showed that for Mongolian and Chinese PPRV since 2013, the wildlife and livestock-origin genomes were closely related and interspersed. There was strong phylogenetic support for a monophyletic group of PPRV from Mongolian wildlife and livestock, belonging to clade of lineage IV PPRV from livestock and wildlife from China since 2013. Discrete diffusion analysis found strong support for PPRV spread into Mongolia from China and phylogeographic analysis indicated Xinjiang Province as the most likely origin, although genomic surveillance for PPRV is poor and lack of sampling from other regions could bias this result. Times of most recent common ancestor (TMRCA) were June 2015 (95% HPD: August 2014 to March 2016) for all Mongolian PPRV genomes and May 2016 (95% HPD: October 2015 to October 2016) for Mongolian wildlife origin PPRV. This suggests that PPRV was circulating undetected in Mongolia for at least six months before the first reported outbreak in August 2016, and that wildlife were likely infected before livestock vaccination began in October 2016. Finally, genetic variation and positively-selected sites were identified that might be related to PPRV emergence in Mongolian wildlife. This study is the first to sequence multiple PPRV genomes from a wildlife outbreak, across several host species. Additional full PPRV genomes and associated metadata from the livestock-wildlife interface are needed to enhance the power of molecular epidemiology, support PPRV eradication and safeguard the health of the whole ungulate community.

Contributions of Genetic Evolution to Zika Virus Emergence

Mosquito-borne Zika virus (ZIKV) was considered an obscure virus causing only mild or self-limited symptoms until the explosive outbreaks in French Polynesia in 2013–2014 and in the Americas in 2015–2016, resulting in more than 700,000 cases of the disease, with occasional miscarriage and severe congenital birth defects, such as intrauterine growth restriction, fetal microcephaly, and other neurodevelopmental malformations. In this review, we summarized the evolution of ZIKV from a mundane virus to an epidemic virus. ZIKV has acquired a panel of amino acid substitutions during evolution when the virus spread from Africa, Asia, Pacific, through to the Americas. Robust occurrence of mutations in the evolution of ZIKV has increased its epidemic potential. Here we discussed the contributions of these evolutionary mutations to the enhancement of viral pathogenicity and host-mosquito transmission. We further explored the potential hypotheses for the increase in ZIKV activity in recent decades. Through this review, we also explored the hypotheses for the occurrence of the recent ZIKV epidemics and highlighted the potential roles of various factors including pathogen-, host-, vector-related, and environmental factors, which may have synergistically contributed to the ZIKV epidemics.

COVID-19 Research: Challenges to Interpret Numbers and Propose Solutions

The response of the scientific community to the COVID-19 pandemic has been unprecedented in size, speed and discovery output. Within months of virus emergence, the SARS-CoV-2 genomics, replication, evolution and dissemination dynamics as well as natural history, infection risk and prognostic factors and biology of the disease have been gradually deciphered. More than 250 articles on COVID-19 published in Frontiers in Public Health have contributed to these insights. We discuss here some of the key research themes and challenges that have been addressed. We provide our perspective on current research issues with surveillance data quality and limitations of epidemiological methods. We warn against the potential misuse or misleading interpretation of public data of variable quality and the use of inadequate study designs for the evaluation of effect of non-pharmaceutical interventions. We conclude by interrogating possible public health strategies for pandemic control as well as discuss the ethical responsibilities and democratic accountability of researchers in their role as experts and policy advisors.

First report of tilapia lake virus emergence in fish farms in the department of Córdoba, Colombia

Background and Aim: In 2016, the tilapia-producing farms in the department of Córdoba, Colombia, had witnessed outbreaks of disease with clinical signs compatible with those caused by the tilapia lake virus (TiLV). This study was conducted to confirm the presence of TiLV in some fish farms in the department of Córdoba. Materials and Methods: A descriptive cross-sectional study was conducted in seven farms using a non-random sampling method from July 2016 to December 2017. A total of 66 fish, including 33 healthy fish and 33 fish with clinical signs, were caught, from which 178 tissue samples of spleen, liver, and brain were collected. RNA was extracted from each organ using TRIzol®. cDNA was synthesized using a retrotranscriptase and a universal amplification primer. The polymerase chain reaction was performed using primers specific to TiLV, in which the primers were amplified in a 491 bp region in segment 3 of TiLV, and the amplicons were sequenced using the Sanger method. Results: Of the seven farms surveyed, 3 (42.85%) had TiLV in the collected fish. Of the 66 collected fish, 18 (27.27%) were infected with TiLV. The virus was detected in the brain (64.3%, 18/28), spleen (61.9%, 13/21), and liver (35.7%, 10/28). The sequences were recorded in GenBank with the codes MH338228, MH350845, and MH350846 . Nucleotide homology analyses revealed that this study's circulating strains exhibited 97% identity with the Israeli strain (GenBank KU751816.1). Conclusion: This is the first official report of TiLV in the department of Córdoba, Colombia. The circulating strains detected in this study exhibited 97% identity with the Israeli strain.

A Phylogenomic and Evolutionary Perspectives of COVID-19

From the time immemorial, all drastic pandemics and associated pathogens have been under the spotlight of research in our attempts to identify, characterise, control and trace back their origin. Quite often such attempts have enabled mankind to find effective solutions to overcome such pathogen outbreaks and turn them to pages of history. In the wake of repeated infections in different corners of the world, its quite essential to evaluate if they are the cruel aftermaths of nature or any manmade error. In such as scenario, recent developments in the molecular evolutionary analysis offer us more information in-depth regarding the virus emergence, molecular epidemiology, virulence and evolutionary concepts, adding to the conventional strategies in viral epidemiology. The nucleotide sequences were retrieved from NCBI. The present study revealed the genetic variability of CoV, 2019-nCoV against previously reported corona viruses. Moreover, the genetic variability of COVID-19 from different affected corners of the globe are evaluated to get a better understanding of their modes and routes of spread across our planet.Such nucleotide sequence-analyzed information gathered from this investigation will definitely assist the intention and implementation of effective pandemic control measures.

Investigating School-Based Support Teams' Roles in Supporting Children With Cerebral Palsy During the National Lockdown

The demand for mainstream South African schools to adopt inclusive education research recommendations is rising exponentially. The COVID-19 pandemic effects compound curriculum access difficulties for children with cerebral palsy. In addition, the COVID-19 virus emergence exposed longstanding home-schooling endangerments. As part of a larger study, this chapter is a sequel to a qualitative, descriptive multiple case study interviewing 15 teachers from three schools, three coordinators of the school-based support teams, and the district-based support team coordinators in Limpopo Province. The study drew from Bronfenbrenner's ecological systems, Piaget's cognitive development, and Vygotsky's sociocultural theories to investigate stakeholders' understanding of inclusive education. During the lockdown period, follow-up online interviews with the school-based support team (SBST) identified a continuous fragmentation of IE stakeholders' responsibilities. They recommended a community of practice (CoP) approach that advocated expediting the implementation of recommendations.