Talk:WikiJournal Preprints/A history of coronaviruses

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Article information

Author: Kholhring Lalchhandama[a][i]ORCID iD.svg 

Kholhring Lalchhandama, A history of coronaviruses, Wikidata Q99522133






plagiarism check[edit source]

Artículo bueno.svg Pass. Report from WMF copyvios tool: 0% Plagiarism, 100% Unique. Flagged terms, like “Department of Life Sciences, Pachhunga University College”, “Severe acute respiratory syndrome-related coronavirus”, “Middle East respiratory syndrome coronavirus (MERS-CoV)” and “International Committee on Taxonomy of Viruses” were appropriate. --Alaa :)..! 13:10, 18 September 2020 (UTC)Reply[reply]

Peer review 1[edit source]


Review by Christopher Burrell ORCID iD.svgWikidata-logo.svg , University of Adelaide

These assessment comments were submitted on , and refer to this previous version of the article

This article contains extensive reviewing of the early literature and an interesting presentation some of the earlier discoveries. However it has a number of serious problems that require thorough correction and editing before the article can be published, otherwise it is likely to add to confusion in the field. I recommend that the author be congratulated on the scope of the article, but that it is reviewed by an authority in the field of coronaviruses

1. Care in distinguishing the name of the disease from the name of the virus. eg COVID-19 is the correct term for the disease, SARS-CoV-2 is the correct name of the virus. The earlier sections should keep this distinction.

2. Balance in breadth and depth. The article is selective in choice of examples. There are 46 coronavirus species and the article should explain the basis for selection. There is little on SARS-CoV-2, but the author may have taken the view that this example is too recent to qualify in a historical article

3. The sections headed “Feline infectious peritonitis virus” and “porcine epidemic diarrhea virus” are confusing. Feline coronavirus (FCoV) can mutate into feline infectious peritonitis virus (FIPV) and the lin k with pigs is obscure.

4. The final section on evolutionary history is too simplistic, and makes no mention of the uncertainty and assumptions associated with these estimates.

5. There are errors in use of terms for naming taxa versus terms for naming viruses themselves. Species names should be in italic script, subspecies and isolates in Roman, eg Avian coronavirus is the species and “Infectious bronchitis” and “Infectious bronchitis Beaudette” are the different virus isolates. “Severe acute respiratory syndrome-related coronavirus”, is the name of the species

6. Section headed Tyrrell and Almeida. The immunological procedure is “to react virus with antibody to form a complex”, not “fuse”.

Response

14 December 2021

I appreciate the insightful comments and suggestions. I hope I address them well:

1. Names of the diseases and viruses are properly written.

2. There are 45 species of coronaviruses (note that under the family Coronaviridae, one group Letovirinae with 1 species is not a coronavirus). History is reflected by landmark events, as such only those that have notable stories are discussed. Undue weight cannot be given to SARS-CoV-2 either.

3. FIPV and FCoV and PTGV are elaborated.

4. Evolutionary history is expanded, yet avoiding systematic analysis as it can be a digression of an encyclopaedic purpose.

5. Names are distinguished; however, for historical context, reader should note that at the time the name was accepted, italics are used (e.g., Bovine coronavirus) but written in regular fonts after demotion to a strain/sub-species (e.g., Bovine coronavirus).

6. Wording corrected.

Peer review 2[edit source]


Review by Stanley Perlman ORCID iD.svgWikidata-logo.svg , University of Iowa

These assessment comments were submitted on , and refer to this previous version of the article

1. Discovery of mouse coronaviruses. These viruses are now all called mouse hepatitis virus, with JHM and A59 representing different strains. JHM is in fact primarily if not solely a pathogen of the central nervous system, while the A59 strains causes hepatitis and enteritis. Other strains of MHV are enteric. Some of these strains cause an endemic infection of mouse vivarium, which are extremely difficult to clear.

2. Severe acute respiratory syndrome-“The infection was believed to have been contained in China, but an infected individual carried it to Hong Kong on 21 February and spread it in the hospital“. The virus was spread within a hotel in Hong Kong as well as in hospitals.

3. “ In October, it was found that the infection was acquired from the masked palm civets (Paguma larvata)”. Chinese ferret badgers and raccoon dogs were also considered possible intermediate hosts.

4. “The origin of the virus is not known. Malayan pangolins (Manis javanica) which are available in the live-animal market in Wuhan city has been studied as a probable source as its virus is closely related to the SARS-CoV-2”-The first sentence is correct but the second one is an overstatement. There are several postulated intermediate hosts, including raccoon dogs and minks but none are proven. The evidence is weak or non-existent for a specific intermediate host.

5. MERS-coronavirus-“In 2013, a study revealed that the virus was 100% genetically identical to the coronavirus of the Egyptian tomb bat (Taphozous perforatus coronavirus HKU4) from Bisha, Saudi Arabia, indicating its origin.” This is no longer believed to be true and the finding likely represented a lab contamination. The sentence should be removed.

6. Feline infectious peritonitis virus-“A new disease that caused inflammation of the abdomen (peritonitis) in cats was reported in 1966,[121] the virus was identified in 1968,[122] and was named by ICTV as Feline infectious peritonitis virus (FIPV) in 1991”. This is true but it is now known that ‘feline coronavirus’ is much more common and causes diarrhea. It is often persistent and during persistence, it mutates to gain ability to infect macrphages, causes FIPV. This section could be modified to include this information.

7. Evolutionary History: “Some experimental evidences indicate that animal coronaviruses switch hosts from one mammal to another, such as dog coronavirus (Canine respiratory coronavirus), which originated from a cattle virus (Bovine coronavirus).[146] Zoonotic coronaviruses emerged recently. For instance, there is an evidence that the human coronavirus OC43 (HCoV-OC43) came from cattle around 1890, which makes it also likely the first zoonotic coronavirus.[147] SARS-CoV was transmitted from bats in 1998 (4.08 years prior to the outbreak in 2003),[148] and diverged from bat coronavirus in around 1962. SARS-CoV-2 evolved from bat coronavirus in around 1948.” This paragraph should be modified. It is not known whether canine respiratory coronavirus originated from a cattle virus. The putative 1998 cross species transmission of SARS-CoV is speculative. Finally SARS-CoV-2 may have diverged from other bat CoV in 1948, but it remained a bat virus

Response

18 December 2021

1. JHM and A59 are explained and elaborated. Additional information is also made mentioning rat viruses. By the way, they are officially called Murine coronavirus.

2. The location is added.

3. Possible intermediate hosts are now described.

4. The sentence is modified with additional explanation on other possible hosts.

5. The sentence remains, as I found no evidence of lab contamination (kindly provide if any). Recent literature are consistent with the position that MERS-CoV is bat derived. Also note that Wikipedia has a policy that it is not needed to make right great wrongs as long as reliable sources hold.

6. Alphacoronavirus 1 is revised and updated to incorporate the suggested points.

7. The last paragraph is revised and modified, with additional information.

Editorial comment[edit source]


Comments by Thomas Shafee ORCID iD.svgWikidata-logo.svgWikimedia Community Logo.svg ,

These editorial comments were submitted on , and refer to this previous version of the article

Additional note from an approached virologist who was unable to provide a detailed review but requested for a comment to be passed on:

Please check that the use of virus taxonomy nomenclature is sufficiently (briefly) explained when first used in the article and checked for consistency throughout.

Response

18 December 2021

Copy edits are made to make distinction in nomenclature. However, as the text indicates, the taxonomy is always confusing. As explained above, for historical context, reader should note that at the time the name was accepted, italics are used (e.g., Bovine coronavirus) but written in regular fonts before acceptance or after demotion to a strain/sub-species (e.g., Bovine coronavirus).

Editorial note[edit source]

The editorial board have agreed that this should be accepted and I have added to the technical editor task sheet Rwatson1955 (discusscontribs) 10:14, 21 June 2022 (UTC)Reply[reply]

Editorial note[edit source]

Reviewer #2 made some final suggestions on 26 June 2022:

1. There are now nine HCoV. Two recently identified ones are: Hu-PDCoV, which is a porcine delta coronavirus that crossed species and was identified in Haiti and Hu-CCoV, which was a recombinant canine CoV that was isolated from children in Malaysia with pneumonia

2. HKU4 is believed to be found in Tylonycteris pachypus. This is described in reference 128. As I mentioned in my original review, the Egyptian tomb bat is not the source for the virus and the virus isolated from this bat (100% identity with MERS-CoV) is considered a lab contaminant. another issue is that MERS-CoV is an endemic camel virus at present and occasionally crosses species to infect humans. It likely originated in bats, but the human infection only results from camels. In Saudi Arabia, the camel and human viruses are nearly identical.

3. The numbers of COVID-19 cases and deaths should be updated.

4. Last paragraph: "Although no details are yet available, but it is generally believed that MERS-CoV originated from bat coronavirus (collectively namedSevere acute respiratory syndrome–related coronavirus)[127] specifically suggested to have evolved from the common ancestor of BtCoV-HKU4 and BtCoV-HKU5.[170][171] . Reference 127 is the early manuscript that misidentified MERS-CoV as being identical to a virus from at the Egyptian tomb bat. The nomenclature and information have been corrected over the past 9 years. MERS-CoV is no longer referred to as a Severe acute respiratory syndrome-related CoV.

I have halted acceptance until the above comments are replied to.

Rwatson1955 (discusscontribs) 09:22, 27 June 2022 (UTC)Reply[reply]

Here are my responses:
1. It is interesting to learn new species of HCoV. However, the article does not emphasise on HCoV. As a matter of fact, Hu-PDCoV and Hu-CCoV are not yet recognised by ICTV. The number of coronavirus species is updated.
2. It would be awfully wrong to say “the human infection [of Mers-CoV] only results from camels.” Human-to-human infection is the major transmission, while camel-to-human infection is regarded as less common. The reference is supported and still cited as legitimate by others (see below).
I reiterate my previous response to this comment: “The sentence remains, as I found no evidence of lab contamination (kindly provide if any). Recent literature [see https://doi.org/10.1002/rmv.2150, https://doi.org/10.14202/vetworld.2021.190-199, 10.1016/B978-0-12-801238-3.11634-4, etc.] are consistent with the position that MERS-CoV is bat derived [still upholding Memish et al., 2013]. Also note that Wikipedia has a policy that it is not needed to make right great wrongs as long as reliable sources hold.”
3. COVID-19 statistics are updated.
4. There must be a misreading by this comment: “MERS-CoV is no longer referred to as a Severe acute respiratory syndrome-related CoV.” Nowhere does the manuscript states that MERS-CoV is called Severe acute respiratory syndrome-related CoV. As to the said reference, the justification is as above point 2. I nonetheless changed the wordings for clarity. Chhandama (discusscontribs) 11:09, 29 June 2022 (UTC)Reply[reply]
@Rwatson1955: The author has responded to reviewer 2's comments (see above). Please take a look. OhanaUnitedTalk page 22:16, 11 July 2022 (UTC)Reply[reply]

Editorial note[edit source]

I have reinstated this on the technical editor sheet for acceptance and pdf generation Rwatson1955 (discusscontribs) 07:12, 5 August 2022 (UTC)Reply[reply]