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Introduction to Sars-Cov-2 Research Project Plan

The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus -2 (SARS-Cov-2). The disease originated from Wuhan, China in the month of December 2019. The COVID-19 was declared a “public health emergency” by 30 January 2020 and a pandemic on 11 March 2020. More than 188 countries have been found to be affected by the disease with more than 6.15 million cases and counting (World Health Organization, 2020). The virus is known to spread via respiratory droplets with contingency in the first few days of infection. In Australia, there have been about 7000 confirmed cases (as at the time of writing of this proposal) (Government of Australia, 2020). The transmission of coronavirus between humans and other animals has been a subject of research and extreme precaution since the SARS outbreak.

Regarding the transmission of the SARS-Cov-2, studies have been performed for the domesticated animals where cats have been found to be more susceptible to the viral infection than the dogs in a study by the World Health Organization (Mallapaty, 2020). SARS related viruses have also been common in bats. The aim of this research proposal is to study the emergence of the coronavirus is Australian fauna with respect to the fruit bats. The closely related X-winged and Y-winged bats have been found to be carrying a virus that is closely linked with the virus associated with COVID-19. It is, therefore, crucial to understand the significance of the virus transmission in the fauna. This research will focus on the evolutionary perspective of the X-winged and the Y-winged bats to aid the ongoing research associated with fauna and coronavirus transmission.

Research Questions

  1. What are the characteristic features of the X-winged and the Y-winged bats?
  2. What is the phylogenetic relationship between the X-winged and Y-winged bats?
  3. What are the essential roles of the X-winged and the Y-winged bats in the ecological system?
  4. Is there a possibility of genetic recombination between the X-winged and Y-Winged bats?
  5. Is there a possibility of viral transmission between the X-winged and the Y-Winged bats?
  6. What are the potential harms of the virus identified in bats that is associated with SARS-Cov-2?

Research Aim

To study the phylogenetic relationship between the X and Y winged bats.

Research Objectives

The provided aim will be fulfilled by achieving the following objectives:

  1. Feature analysis of the X-winged and Y-winged bats
  2. Assessment of phylogenetic relationship between the X-winged and Y-winged bats
  3. Role of X-winged and Y-winged bats in the ecological niche as pollinators and seed dispersion
  4. To study the possibility of genetic recombination between the X-Winged and Y-Winged bats
  5. To study if it is possible for X-winged and the Y-winged bats to transmit the virus to each other.
  6. To identify the potential harms of the virus identified in bats that is associated with SARS-Cov-2.

Literature Review of Sars-Cov-2 Research Project Plan

Hu et al. (2015) had studied that bats are often considered as a natural reservoir of a large variety of viruses. The special focus has been provided to the coronaviruses as two major epidemics of SARS and MERS has been known to have originated from the bats. The study illustrates that several bats in China have been known to possess a genetically diverse strain of the identified SARS-like coronavirus that is highly similar to human infecting strains. These strains after genetically related to the human infecting coronavirus and have been found to play a significant role in the transmission and emergence of the disease outbreaks. A comprehensive phylogenetic analysis was also conducted by Holz et al. (2018) who illustrated that the bats are often considered as the carriers of infectious diseases. The study identifies that there has been only limited research on the effects of these pathogens on the bat population. The study identifies that the novel viruses have been identified in the bats. The study focuses on how the incidence of these viruses and ecological overlaps can lead to transmission of the viruses among two different bat species Miniopterusorianaebassanii and Miniopterusorianaeoceanensis.

The premise of the study focuses that in south-eastern Australia, disease of unknown aetiology has been identified as a possible cause for the extensive decline in the southern bent-winged bat population. The viruses were collected from different geographical locations and were tested for coronavirus, ABLV, filoviruses, herpesviruses, and henipaviruses. The study showed that these viruses have a drastic impact on the bat health and impact the biodiversity of the geographical location. The study also illustrated that the rate of infections is higher in the bat species and subspecies that are phylogenetically linked resulting in an increased number of cases due to transmission Zhaou et al. (2020) identifies that the bats act as the asymptomatic reservoirs of the hosts for various zoonotic viruses.

The study of Smith et al. (2016) also validated this study where it screened the bats for beta coronaviruses after the SARS outbreak and provided a proof of concept for the virus-host co-evolution hypothesis. The study also tested for the cross species transmission of the coronaviruses and the enteric tropism of these species providing clear evidence for host specificity of coronaviruses in association with the co-evolution and occasional host shifts. Banerjee et al. (2019) provided a comprehensive analysis of the association of bats with the coronaviruses. The study identifies that there has been a consistent similarity in the zootonic viruses that are associated with the bats and have affected humans and other animals along with the presence of a similar virus in the intermediate host and the reservoir host(Table 1).

Coronavirus

Affected host

Intermediate host

Reservoir host (Bat species)

Similar viral strain in affected host

Similar viral strain in reservoir host

PEDV

Pigs

Not yet known

Scotophiluskuhlii

Not yet known

BtCoV/512/05

SADS-CoV

Pigs

Not yet known

Rhinolophus spp.

Not yet known

HKU2-CoV

SARS-CoV

Humans

Himalayan palm civet or racoons

Rhinolophusspp

CoV isolate SZ3 and SZ16

SARS-related CoVs

MERS-CoV

Humans

Dromedary camels

Taphozousperforatus, Rhinopomahardwickii and Pipistrelluskuhlii

MERS-CoV—KFU-HKU 1 and KFU-HKU 13

BatCoVRhhar, BatCoVPikuh, BatCoV Taper

Table 1: Coronaviruses that have been associated with bats and have caused disease in humans and other animals (Banerjee et al.,2019)

Another essential study in light of same is done by Ye et al. (2020) which highlights that the bats can harbour the coronaviruses with extensive genetic diversity. The study provides articulated evidence that these beta coronaviruses are evolutionarily linked and spread closely in species that are closely associated with each other phylogenetically and therefore often jump from these mammals to humans after certain specific mutations. The study elucidates that as the human activity overlaps with the bats the disease outbreaks have become more common with increased incidences of the interspecies transmissions. In respect to the current pandemic, Shereen et al. (2020) provided a comprehensive analysis of how the coronaviruses are linked to bats and how their transmission affects humans.

The focus of the study revolves around the SARS-COV-2 transmission in the humans in the pandemic. The study illustrates that the novel coronavirus which has been identified as the cause of the COVID-19 is associated with the SARS COV-2 virus variant present in the bats. This study is of high significance as it illustrates how the viral variants can be transmitted among the species and cause diseases in human and other animals. The host of these viruses can change through adaptation via mutations. Therefore, the transmission from the bats can either be interspecies or intraspecies (Su et al., 2016). A phylogenetic analysis, therefore, becomes extremely crucial to identify the potential hosts of this virus that may occur via ecological overlaps or by genetic susceptibility to the virus (To et al., 2016).

Research Methodology of Sars-Cov-2 Research Project Plan

The study will use a mixed approach with both primary and secondary studies. The secondary studies will involve the collection of data and analysis of the pre-published research associated with the information about the X-winged and Y-winged bats in the peer-reviewed journals. Only recent research articles and information from reliable sources shall be taken to synthesize the information required for this analysis. The literature will be cited from reliable databases like Elsevier and Scopus to include only highly credible and well-researched information. The selection criteria and inclusion and exclusion of the selected articles will be done using the PRISMA approach. The study will also follow a primary approach where the X-winged and Y-winged bats will be studied for their ecological niche overlaps for a detailed analysis. The study will follow a reverse approach where genetics and the phylogeny will be tested after the assessment of the physical and ecological attributes. The bat species for the X-winged and Y-winged bats were collected and will be assessed for the homologous characteristics. The viral RNA will be collected from the bat samples. The presence of coronavirus will be tested by the PCR analysis for the detection of viral RNA.

The positive and negative controls will be set for a comparative study in the PCR to assess the amplification. The samples will be sequenced analyzed using the Geneious software for the phylogenetic analysis. The individual sequences will be grouped based on the highest incidence of identity and nearly identical sequences. The sequences will be screened for the SNPs (Washburne et al., 2018). The BLAST X algorithm will be used to find the proteins with the highest similarity. A phylogenetic tree will be therefore constructed with the BLOSUM62 matrix. Moreover, a statistical analysis will be conducted by the generation of graphic plots with the screening of the internal and external predictor variables of the coronaviruses. All the factors with significance levels of more than p<0.05 will be considered significant and for p<0.01 will be considered highly significant after the analysis (Góes-Neto et al., 2018).

Project outline

The project will be conducted in a time frame of six months from September 2020- February 2021. The project will be inclusive of the three distinct phases that will involve literature study, experimental and statistical analysis, and result evaluation..

The Gantt chart for this study has been given below

Date

Tasks

1-Sep-20; 30-Sep-20

1-oct-20; 31-oct-20

1-Nov-20; 30-Nov-20

1-Dec-20; 31-Dec-20

1-Jan-21; 31-Jan-21

1-Feb-21; 28-Feb-21

Literature study

Sample collection

Morphological analysis

Molecular experimentation

Phylogenetic analysis

Statistical analysis

Analysis of results

Evaluation

Writing and compilation of data

Table2: Gantt chart for the work flow of this experimentation

Justification ofSars-Cov-2 Research Project Plan

This study focuses on finding the phylogenetic relationship between the fruit bats that are X-winged and Y-winged. This difference primarily exists in the wing shape of the bat. For this analysis, a combined study approach with secondary data analysis from the published data, morphological analysis of the bat features, and molecular and phylogenetic analysis will be performed. The research objectives 1,3,4, and 6 will be fulfilled by the literature search and analysis of the available data. The research objectives 2 and 5 of this study will be fulfilled with the primary approach where the molecular and phylogenetic analysis will reveal the incidence and overlap of the novel coronavirus or the SARS-COV-2 in the X-winged and Y-winged fruit bats in Australia. This research will serve to be of prime significance in the current analysis of the ongoing pandemic as it will help in the identification of potential overlap along with the phylogenetic proximity of the fruit bats that have been found to be associated with the viral strain of coronavirus closely linked to SARS-CoV-2 in the humans. 

However, this study is not inclusive of the factors like horizontal gene transfer of the virus and the transmission rates that must be kept into consideration. Also, the statistical significance and generalization of the study will be based on the number of samples collected for the assessment. The molecular analysis must be done in replicates to ensure the validity of the research. 

References for Sars-Cov-2 Research Project Plan

Banerjee, A., Kulcsar, K., Misra, V., Frieman, M., & Mossman, K. (2019). Bats and coronaviruses. Viruses, 11(1), 41.

Góes-Neto, A., Diniz, M. V., Carvalho, D. S., Bomfim, G. C., Duarte, A. A., Brzozowski, J. A., ... & Andrade, R. F. (2018). Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method. PeerJournal,6, 4349.

Government of Australia (2020). COVOD-19 health alert. Retrieved from: https://www.health.gov.au/news/health-alerts/novel-coronavirus-2019-ncov-health-alert

Holz, P. H., Lumsden, L. F., Druce, J., Legione, A. R., Vaz, P., Devlin, J. M., &Hufschmid, J. (2018). Virus survey in populations of two subspecies of bent-winged bats (Miniopterusorianaebassanii and oceanensis) in south-eastern Australia reveals a high prevalence of diverse herpesviruses. PloS One, 13(5).

Hu, B., Ge, X., Wang, L. F., & Shi, Z. (2015). Bat origin of human coronaviruses. Virology Journal, 12(1), 221.

Mallapaty, S. (2020). Coronavirus can infect cats — dogs, not so much. Nature,98(4),8 https://www.nature.com/articles/d41586-020-00984-8

Shereen, M. A., Khan, S., Kazmi, A., Bashir, N., & Siddique, R. (2020). COVID-19 infection: origin, transmission, and characteristics of human coronaviruses. Journal of Advanced Research.

Smith, C. S., De Jong, C. E., Meers, J., Henning, J., Wang, L. F., & Field, H. E. (2016). Coronavirus infection and diversity in bats in the Australasian region. Ecohealth, 13(1), 72-82.

Su, S., Wong, G., Shi, W., Liu, J., Lai, A. C., Zhou, J., ... & Gao, G. F. (2016). Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends in Microbiology, 24(6), 490-502.

To, K. K., Hung, I. F., Chan, J. F., & Yuen, K. Y. (2016). From SARS coronavirus to novel animal and human coronaviruses. Journal of Thoracic Disease, 5( 2), 103.

Washburne, A. D., Morton, J. T., Sanders, J., McDonald, D., Zhu, Q., Oliverio, A. M., & Knight, R. (2018). Methods for phylogenetic analysis of microbiome data. Nature Microbiology, 3(6), 652-661.

World Health Organization (2020). Coronavirus. Retrieved from: https://www.who.int/health-topics/coronavirus

Ye, Z. W., Yuan, S., Yuen, K. S., Fung, S. Y., Chan, C. P., &Jin, D. Y. (2020). Zoonotic origins of human coronaviruses. International Journal of Biological Sciences, 16(10), 1686.

Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., ... & Chen, H. D. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270-273.

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