Talk:Bat virome

Rabies
Discussion of dogs and arctic fox as transmission vectors is off-topic. Should it be deleted? Aloysiussnuffleupagus (talk) 13:51, 30 January 2020 (UTC)
 * , I removed it, but in the future feel free to be bold and make the change yourself! Enwebb (talk) 21:59, 30 January 2020 (UTC)

Problem with the lead
I have a problem with the lead. Stating that a bat-borne virus is any virus whose PRIMARY reservoir is any species of bat, and then following that with a list of viruses which some have not been proven to be bat-borne. SARS-CoV-2 has not been proven to be bat-borne. I think it's misinforming the public when speculation is used as fact. Please, if others can also review this and discuss here, it would be appreciated. Even the links provided are weak in evidence and do not provide such bold statements as this lead.

"A bat-borne virus is any virus whose primary reservoir is any species of bat. The viruses include coronaviruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); hantaviruses; lyssaviruses such as rabies virus and Australian bat lyssavirus; henipaviruses such as nipah virus and Hendra virus; Lassa virus; Ebola virus; and Marburg virus. Several bat-borne viruses are considered important emerging viruses."

Battykin (talk) 23:39, 28 April 2020 (UTC)
 * , hello again! I started seriously rewriting and expanding this article last month (here's what it looked like in Mid-March, quite different!). While I still have some work to do in covering the viral diversity of bats, it had occurred to me that a new title might be in order. I have just retitled the article to "Bat virome".
 * Because the lead is supposed to be a synopsis of the rest of the article, I often leave redoing the lead for last, once I have finished redoing the body of the article. I did a quick and rough rewrite of the lead just now, but I anticipate that once finished with my rewrite (hopefully in the next week) the lead will be several paragraphs long.
 * Finally, I wanted to provide a note about sourcing. Any content anywhere on Wikipedia that makes any kind of biomedical claim must be cited with a reliable secondary source, preferably published in the last 5 years. We call this policy WP:MEDRS. Secondary sources are things like literature reviews. When we have reviews like this one saying "Evidence from the sequence analyses clearly indicates that the reservoir host of the virus was a bat..." then it is appropriate to include that information on Wikipedia. Enwebb (talk) 03:31, 29 April 2020 (UTC)
 * Finally, I wanted to provide a note about sourcing. Any content anywhere on Wikipedia that makes any kind of biomedical claim must be cited with a reliable secondary source, preferably published in the last 5 years. We call this policy WP:MEDRS. Secondary sources are things like literature reviews. When we have reviews like this one saying "Evidence from the sequence analyses clearly indicates that the reservoir host of the virus was a bat..." then it is appropriate to include that information on Wikipedia. Enwebb (talk) 03:31, 29 April 2020 (UTC)
 * Finally, I wanted to provide a note about sourcing. Any content anywhere on Wikipedia that makes any kind of biomedical claim must be cited with a reliable secondary source, preferably published in the last 5 years. We call this policy WP:MEDRS. Secondary sources are things like literature reviews. When we have reviews like this one saying "Evidence from the sequence analyses clearly indicates that the reservoir host of the virus was a bat..." then it is appropriate to include that information on Wikipedia. Enwebb (talk) 03:31, 29 April 2020 (UTC)


 * Hello again, yourself! I appreciate your replies to my comments and questions! Thank you for taking the time to try and organise this article. My issue with it was the wording seemed too bold and factual, when almost all scholarly sources (I am a doctor, myself) have used words like, "likely originated", or "a similar type of virus". I have never seen one that said "certain", as it is still unknown. The linked source you showed me here that says "clearly indicates" is inaccurate, as that abstract that stated that used a source itself, that says "likely". Therefore, it is misleading. I can show you the source they used for that, as it is linked there- https://www.ncbi.nlm.nih.gov/pubmed/32218527 Here are some statements made from newer research:

"The bat coronavirus, which was the ancestor of SARS-CoV-2, has 19 amino acids on the spike protein that are different from SARS-CoV-2; the pangolin coronavirus only has five amino acids that are different from SARS-CoV-2. Meanwhile, several other research groups have found further experimental evidence of pangolins being infected by coronaviruses highly similar to SARS-CoV-2."

"Neither the bat betacoronaviruses nor the pangolin betacoronaviruses sampled thus far have polybasic cleavage sites. Although no animal coronavirus has been identified that is sufficiently similar to have served as the direct progenitor of SARS-CoV-2, the diversity of coronaviruses in bats and other species is massively undersampled."

While I believe there are strong similarities and the likelihood of a bat species being a possible host, I still think it's misleading to use words like "certain". I also think it's important for the public to know that the fact that bats have always been used as samples is another reason why they find more viruses in them. Other animals do not get the same amount of testing. Here is an article regarding that:

https://www.merlintuttle.org/2020/01/30/wuhan-coronavirus-leads-to-more-premature-scapegoating-of-bats/

I appreciate your feedback! Battykin (talk) 04:36, 29 April 2020 (UTC)
 * , because SARS-CoV-2 is relevant to human health, we have to follow WP:MEDRS in the kinds of sources we're allowed to use. We can't use anything on merlintuttle.org. Instead, we have to use secondary sources, like literature reviews from peer-reviewed journals, or statements from groups like the CDC or WHO.
 * As Wikipedians, we don't get to decide if these secondary sources published in peer review journals are accurate or not. We cannot draw our own conclusions from the source material&mdash;that's known as original research. While I'm not using the word "certain" in this article in any context related to SARS-CoV-2, I do use the phrasing found in the review, which is "clearly indicates". Enwebb (talk) 14:49, 29 April 2020 (UTC)
 * As Wikipedians, we don't get to decide if these secondary sources published in peer review journals are accurate or not. We cannot draw our own conclusions from the source material&mdash;that's known as original research. While I'm not using the word "certain" in this article in any context related to SARS-CoV-2, I do use the phrasing found in the review, which is "clearly indicates". Enwebb (talk) 14:49, 29 April 2020 (UTC)


 * I realise that merlintuttle.org is not considered a primary source. That was just added to show the part about how bats are often used as samples compared to other animals, hence, the reason they find more viruses in them. Merlin, however is a bat specialist who has published books regarding them. The rest of what I wrote was regarding the research performed by medical researchers who are active in COVID-19 studies. The article that said "clearly indicates" used a reference that does not state that, and states, "likely". This would not be considered original research, since it's the article itself that was used as a reference: https://www.ncbi.nlm.nih.gov/pubmed/32218527 The above quoted statements were also from researchers active in the virology studies of the genome. Surely, those would be considered primary sources, and not original? Thanks. Battykin (talk) 19:03, 29 April 2020 (UTC)
 * , the article is clear that there is research bias in how bats are surveyed for viruses relative to other animals (Bats compared to other viral reservoirs). The role of review articles is to synthesize and summarize the primary sources, drawing overarching conclusions. Wikipedia prefers secondary sources because it is more reliable for an expert to summarize the body of work in their field than for a Wikipedia editor to attempt to do so by building from primary sources. I'm also unsure what distinction you're making between "primary" sources and "original" sources. Can you be more clear with what you mean?
 * We're a bit limited right now with timing: because it's a recent and ongoing event, there hasn't been time for many different secondary sources to be published. The best course of action now would be to identify various reliable secondary sources and try to use language that matches the stance taken by a majority of them. Enwebb (talk) 19:31, 29 April 2020 (UTC)
 * I think that is part of why I had a problem with the article. The fact that Cov-2 is a novel virus and research is still active, which I have been keeping up with, as my field is in medicine. All articles that I have read, including CDC and WHO statements, none have used words like "clearly indicates". The one article that was referenced here with those words had a reference of its own next to that statement, which when I opened it up, it made no mention of such. It was like all other articles I have read that state the uncertainty and unknown. Seeing how you have been trying to fix this article, I will leave it to you. However, if you need medical references, let me know, as I collect them. I just would like this article to be more neutral. Even if I am an advocate for bats, among other wildlife, I am a human doctor, so I am not here for bias in favor of bats. I am just aware of the long history of the media vindicating bats with no actual evidence of them being the hosts to a lot of viruses. I hope that makes more sense. Battykin (talk) 22:55, 29 April 2020 (UTC)
 * My whole MS thesis was on an endangered bat species, so I'm very sympathetic to the persecution bats face worldwide. I'm a big fan of Merlin Tuttle and understand why he's been outspoken against "virus hunting" for several years now. If you find secondary sources or statements from bodies like the WHO or CDC that contradict what I've written, I'm happy to revise the article further. Enwebb (talk) 02:11, 30 April 2020 (UTC)
 * That is wonderful to hear. I'm glad you understand what I am saying :) When I have a little more time, I will post some references here from medical sources that are considered reliable. I can come up with primary and secondary sources. I have a lot saved. This article will take some work. I appreciate the time you put in it as you have shown me what it looked like before. Keep up the good work! I will do what I can to help :) Battykin (talk) 03:18, 30 April 2020 (UTC)
 * That is wonderful to hear. I'm glad you understand what I am saying :) When I have a little more time, I will post some references here from medical sources that are considered reliable. I can come up with primary and secondary sources. I have a lot saved. This article will take some work. I appreciate the time you put in it as you have shown me what it looked like before. Keep up the good work! I will do what I can to help :) Battykin (talk) 03:18, 30 April 2020 (UTC)


 * Hello. I am reviewing this article - so I am supposed to decide whether it has a neutral point of view. I wonder if either of you are aware of any new research confirming or refuting the cited MacKenzie et al. paper? Is there a majority view amongst researchers yet re the possible bat origin of Cov-2? Chidgk1 (talk) 09:01, 8 July 2020 (UTC)

From https://www.nature.com/articles/d41586-020-01541-z and https://www.nytimes.com/2020/07/08/health/coronavirus-origin-china-lucey.html it now seems to be a consensus view?

Note to self
Found another review article here that could be good to finish this off and finally nominate for GA. Enwebb (talk) 19:04, 12 May 2020 (UTC)

classification
The article uses the Baltimore classification system as the basis for creating sections. Baltimore groups have to do with how viruses create their mRNA, but this article does not discuss molecular & cellular biology much. Also, various Baltimore groups are polyphyletic, so grouping unrelated viruses together may give the average reader the impression that the families within a Baltimore group are related. E.g. the dsDNA section has three families, Adenoviridae, Herpesviridae, and Papillomaviridae. These three families belong to three different realms and since virus realms have no genetic relation to each other these three families are unrelated, so grouping them together via Baltimore groups when the lower taxa are united by genetic relation may misinform readers, especially since Baltimore classification isn't explained in the article.

ICTV taxonomy is the official system used, so I think before being promoted to GA it may be better to reorganize the sections to place the current lower taxa into the realms they belong to. If a realm is too long, then its kingdoms can be subsections. Orthornavirae may be long, so its phyla can be used for subsections. A section for "other viruses" can be created for viruses not assigned to a realm. I can rearrange the article to show what it would look like with the new structure. If this is done, then some parts of the text will have to be changed to deemphasize Baltimore groups and make greater mention of higher taxa. Velayinosu (talk) 00:26, 19 May 2020 (UTC)
 * , I was following this review in how it talked about bat viruses. It went group by group through the Baltimore classification system. I think that following the usage of a secondary source is a fine rationale for using the organization system that I did. Enwebb (talk) 21:20, 19 May 2020 (UTC)
 * Okay after looking at the review I understand now. Good job on the article and good luck with GA. Velayinosu (talk) 22:41, 19 May 2020 (UTC)