Review Paper

Term Paper Guideline

Term Paper Guideline

Draft Due: October 24, 2020

Term paper critique due; November 7, 2020

Final Report Due: November 20, 2020

Please read the article by Zhou et al. (2020) (uploaded in D2L) and write a review of the paper. Please follow the guideline and the rubric below. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579: 270–273 (2020) https://www.nature.com/articles/s41586-020-2012-7 Please watch the following video first before reading the paper https://www.youtube.com/watch?time_continue=145&v=Q_4fIkc2k6g&feature=emb_log o Study Guide: General Background: As you are all aware, the novel coronavirus (Covid 19) infection became pandemic. This paper reports the first findings on this virus at the early stages of this pandemic (submitted January 20th, 2020). As we learned in the lecture, coronavirus belongs to an enveloped RNA virus group. I have highlighted some questions in each section. Please include the answer to these questions in your review. Abstract: Summary ➢ This section summarizes its findings. Note how the first two sentences describe the

background, and the third sentence starts talking about their finding. An abstract should mostly contain the findings, not an introduction. Your abstract should follow this, and the introduction should not exceed more than 30 % of the abstract.

The main article-each paragraph is labeled as P1, P2…. P1: This is an introduction. P2: This section describes the isolation and sequencing of Covid19 genome. It has much technical jargon. You only need to understand that they sequenced the viral genome from multiple patient samples and found they belong to the Coronavirus group. Pan-Cov PCR primer: PCR uses DNA replication methods, and you need primers to start the replication. If you put primers that have the matching sequence in

the sample (infected sample), you will amplify the DNA. They used primers that work for most coronavirus. What does “aetiological agent” mean? Please look it up. P3, P4: they analyzed the sequenced genome and compared it with other viruses. ORF (Open Reading Frame): From the DNA sequences, you can find promoters and where RNA transcription can start. In the predicted RNA sequences, a continuous stretch of codons that begins with a start codon (usually AUG) and ends at a stop codon can be found and called ORF. ORF is a section of the gene that codes for a protein. Fig. 1B shows ORF locations on Covid19 genome. Fig 1C shows how similar the DNA sequence (x-axis 0 to ~30,000) to other Coronaviruses Fig. 1D phylogenic tree P5: To develop a test to differentiate Covid19 to other coronaviruses, they need a part of the genome sequence unique to Covid 19. They need to find most different sequence.

1) They suggest that the disease is transmitted by airborne transmission. What was the observation that led to this suggestion?

P6: They tested whether they can use antibodies against SAR to detect Covid19, and they could. Don’t worry about the details in this section. P7: They isolated and established a pure culture. Since it is a virus culture, you need to have host cells. Vero E6 and Huh7 cells are cells from a monkey and a human serving as host cells for the virus. They did several tests to confirm what they isolated were indeed Covid19. P8: Since the host receptor for SARS-Cov is known (ACE2), they wanted to test whether Covid19 also uses the same receptor. They concluded ACE2 is indeed the receptor for the Covid19.

2) How did they show ACE2 is the receptor? The Fig.3 is the data showing it. Please interpret its results.

P9: Discussion/Concluding Remarks.

3) In the discussion, they mention "Koch Postulate." Based on what you learned about the 4 steps of Koch's Postulate, describe which step did the authors accomplished and by what experiments.

Maximum 3 pages- 1” margin on all side, typed

• Title page-not included in the 3-page limit • Abstract: Brief (<250 words) summary of the paper.

The rest of the content could be freestyle, but make sure to include the following content. Follow the guidelines provided.

• Begin with a summary of relevant background information and statement of the major question being addressed.

• A discussion of the experimental approaches- explaining the question/hypothesis, methodology, results, and interpretation of the data (1 page),

• a summary of the overall conclusions, including a discussion of whether hypotheses were supported or not, and the strengths and weaknesses of the paper (1/2 pages).

• A bibliography, not part of the 3-page limit, should be included. For the term paper, following the correct bibliography format is important. You can use any bibliography format typically found in a scientific journal. This includes “in-text” citation and detailed information in the “reference” section.

Grading Rubric

Criteria Points

Abstract A concise summary of the paper: This is not an introduction. Do not put more than 30% of the background material in this section.

10

Background 25

Experimental Approaches Include the answers for questions asked above in red (1, 2, 3)

30

Conclusion 15

Overall Organizations/Writing, Reference format 20