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)

Aloysiussnuffleupagus, 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)

Battykin, 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)

Enwebb 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)

Battykin, 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—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)

Battykin, 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)

Battykin 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)

Enwebb 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)

Battykin Hello. I am reviewing this article - so I am supposed to decide whether it has a neutral point of view. Enwebb 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)

Velayinosu, 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)

GA Review

This review is transcluded from Talk:Bat virome/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Chidgk1 (talk · contribs) 11:47, 7 July 2020 (UTC)

GA review – see WP:WIAGA for criteria

Hello @Enwebb: - I am glad you are explaining this important and topical subject. As I know almost nothing about it yet I am afraid I am going to be taking up your time with lots of naive questions. And if any of my suggestions do not make sense scientifically fell free to reject them but please explain why in layman's terms.

Chidgk1 thank you so much for taking on this review! Enwebb (talk) 03:27, 8 July 2020 (UTC)

1. Is it well written?

   A. The prose is clear and concise, and the spelling and grammar are correct:

• • Question: Does the word "assemblage" have a special meaning or could it be replaced by "group" or "set"? Would it make sense for the first sentence to be simplified to "The bat virome is the group of viruses which infect bats."?
    • Changed to "group". Keeping "associated with" rather than "infect" because "infect" denotes that it causes disease, and this is not an article about viruses that cause disease in bats. Enwebb (talk) 21:04, 13 July 2020 (UTC)
      • Ah I see. But in Asymptomatic carrier "infected" is used. Alternatively what do you think about shortening "associated with" to "hosted by"?
  • Q: Could there be a clause in the lead and/or "viral diversity" section explaining STING in layman's terms if it is important enough?
  • Q: The last sentence in the lead could perhaps be clarified as the word "conversely" confuses the meaning a bit for me. But before we figure out whether it can be improved can I ask you what is the most diverse order of mammals?
    • The most diverse mammal order is the rodents :) In the section "Bats compared to other viral reservoirs", I talk about two recent reviews. One review found that bats do have more zoonotic viruses than most mammal groups, though not significantly more than rodents and primates (rodents, bats, and primates were not significantly different from each other). In contrast, a second review found that bats do not have more zoonotic viruses than any other group relative to how diverse they are. So the two reviews are offering different answers to the question, "Are bats special as zoonotic viral reservoirs"? The first review is essentially saying, yes, they're special, but not more so than rodents and primates, and the second review says no, bats aren't special at all. Enwebb (talk) 03:27, 8 July 2020 (UTC)
      • Ah I see thanks. Perhaps a lot of research was done between 2015 and 2020, so should we consider the 2015 review to be superseded by the 2020 review do you think? After answering that question would you like to try improving that sentence first or shall I have a shot at it? Chidgk1 (talk) 06:27, 8 July 2020 (UTC)
        • Revised. Enwebb (talk) 21:04, 13 July 2020 (UTC)
  • Q: If we simplified "Number of viral sequences" to "Number of kinds of virus" or ""Number of species of virus" would that still be correct?
    • "Species" would be incorrect, as it is not interchangeable with sequence. "Viral sequence" is the language used by the source. Enwebb (talk) 21:04, 13 July 2020 (UTC)
  • Q: Would it not be the fact that they go into torpor or hibernate that make them better hosts, rather than the ability to do so or is there something about the ability even if they don't?
  • Q: Is rabies the only lyssavirus confirmed to kill them? Maybe tweak sentence to clarify.
    • No, at least one other lyssavirus can be fatal to bats (Lagos bat virus). Enwebb (talk) 03:27, 8 July 2020 (UTC)
  • Q: Would it be useful to also have a % in the virus family table?
    • added. Enwebb (talk) 21:04, 13 July 2020 (UTC)
  • Q: Do you think it would be better to have one or two more tables? For example the "Hantaviruses" section has a list which could be a table maybe? But I am not sure because in the table in "reoviruses" is it important to know the year identified? And would not some of those be hosted both by bats and humans?
    • I don't really see use of tables applies to the criterion of "well-written". Host just means whether the virus was isolated from a human or a bat. Enwebb (talk) 21:04, 13 July 2020 (UTC)

1. B. It complies with the manual of style guidelines for lead sections, layout, words to watch, fiction, and list incorporation:

   Q: Is there a good reason for some subsections being very short or would you like to combine some (perhaps as bullet points)?

   Each subsection is about a family of viruses, with the exception of Lyssavirus, which is a genus. Some subsections are short because not a lot of research has been done about those particular bat viruses. And several virus families are only represented by a few sequences identified from bats. Enwebb (talk) 21:04, 13 July 2020 (UTC)

   I went ahead and changed the subsection lyssaviruses to Rhabdoviruses and added more about non-lyssavirus rhabdoviruses. Enwebb (talk) 19:53, 14 July 2020 (UTC)

2. Is it broad in its coverage?

   Perhaps it would be worth mentioning how research on this fits in to the global virome project.

   Are there any predictions for the future e.g. any idea what proportion of the bat virome remains to be discovered?

   As noroviruses are fairly well known to the public (at least in UK) may be worth mentioning any evidence (or lack of) of zoonosis.

That would require a MEDRS, and I don't see any secondary sources about bat noroviruses (hardly any primary ones, either). Enwebb (talk) 20:53, 14 July 2020 (UTC)

1. Perhaps add a sentence or 2 expanding on possible bat lifestyle link e.g. colonies or link to more info in bat article https://www.sciencedaily.com/releases/2020/07/200709135631.htm

Hello @Enwebb:. I hope you are well. Although the article is mostly OK I think there are a few places where it is still not clear enough for the general reader. I am happy to help with fixing the prose but I don't know enough to be able to do it all by myself. So I am putting this on hold for the moment. If I don't hear from you in the next few days I will ask the Bats Task Force for some expert help. Chidgk1 (talk) 06:19, 12 July 2020 (UTC)

Chidgk1, there are pretty much no active editors at Bats Task Force except for me. I can work more on this today. Enwebb (talk) 20:32, 13 July 2020 (UTC)

Hello again @Enwebb:. Thanks for making more improvements. As you can see prose is the only area which still needs fixing and (although the prose in some other sections would have to be further improved if you go for "featured" in future) I think only the lead is the vital last hurdle to get to "good article". Although we don't need to simplify it as far as an article on Simple English Wikipedia it is still too technical for the general reader. This is not just my opinion but would be shared by another reviewer I am sure.

Obviously because you are an expert and have worked so much on this article it is hard for you to read it as if you were a layman coming fresh to the subject. Therefore I have made an attempt at rewriting the lead. Could you have a look at the below to see whether I have got anything wrong or missed anything vital for a lead, and amend as you think necessary:

The bat virome is the set of viruses which infect bats. Although bats host all types of virus, most of those identified as of 2020 are single stranded RNA viruses in the Coronaviridae and Rhabdoviridae families.

Despite the abundance of viruses associated with bats, they rarely become ill from viral infections, and rabies is the only viral illness known to kill bats. Bat virology has been much researched, particularly bat immune response. Bats' immune systems differ from other mammals in their lack of several inflammasomes, which activate the body's inflammatory response, and they produce interferon less. Although they defend against viruses excess inflammation and interferon can damage the body. Preliminary evidence indicates bats are thus more tolerant of infection than other mammals.

Much research has centered on bats as a source of zoonotic viruses, which can cause disease in humans, and whether bats harbor more of these than other orders of mammals. As of 2020, according to most recent studies, on average a species of bat will host no more zoonotic viruses than another species of mammal or bird. But there are more species of bats than any other order of mammal, bar rodents, and bats in total host more kinds of zoonotic viruses than other orders of mammal, except perhaps rodents.

Some bat-borne viruses are considered important emerging viruses. These zoonotic viruses include the rabies virus, Marburg virus, Nipah virus, Hendra virus, SARS-CoV and SARS-CoV-2. While transmission of rabies from bats to humans usually occurs via biting, most other zoonotic bat viruses are transmitted by direct contact with infected bat fluids like urine, guano, or saliva, or through contact with an infected, non-bat intermediate host. In some cases the intermediate host is known, for example MERS-CoV was transmitted to humans via camels. But how SARS-CoV-2, which causes coronavirus disease 2019, was first transmitted to humans is not yet certain, although the Sunda pangolin is one suspect. It has been speculated that bats may have a role in the ecology of the Ebola virus, though this is unconfirmed. There is no firm evidence that butchering or consuming bat meat can lead to viral transmission, though this has been speculated.

The lead is supposed to be a summary of the rest of the article. Why has the Baltimore classification been removed from your version of the lead? The schema is the scaffold upon which the entire article is built and organized. I also see changes that are null in that I don't think they necessarily make the article simpler (swapping "group" for "set", for example). I also think that it is more complex to have a note in the first sentence to contradict the association that most readers would have with the word "infect". Would you care if I asked for a second opinion on the lead from another editor? Enwebb (talk) 14:25, 17 July 2020 (UTC)

Good idea. I don't want to fail it so I have asked for a second opinion. Hopefully someone can decide which lead is best or merge the best bits from both versions. No need to come back to me unless you have to - I accept whatever they decide and then it can be marked good. Chidgk1 (talk) 19:02, 17 July 2020 (UTC)

Second opinion

• The current lead is a great summary of the article. The lead proposed by the reviewer is harder to follow and less comprehensive   User:Dunkleosteus77 |push to talk  00:28, 18 July 2020 (UTC)

Notes

Good Article review progress box

Criteria: 1a. prose () 1b. MoS () 2a. ref layout () 2b. cites WP:RS () 2c. no WP:OR () 2d. no WP:CV () 3a. broadness () 3b. focus () 4. neutral () 5. stable () 6a. free or tagged images () 6b. pics relevant () Note: this represents where the article stands relative to the Good Article criteria. Criteria marked are unassessed

Chidgk1 (talk) 11:47, 7 July 2020 (UTC)