West Nile Virus sequence missing collection date

[victorlin]

Describe the possible issue

PP_000HJBT.4 / AF260968.1 / "Eg101" is missing a well-known collection date.

Evidence of the problem

No collection date on the sequence page.

Suggested change

Collection date should be 1951. Evidence from Lanciotti et al. (2002) which was published by authors listed in AF260968.1:

Egypt 1951 (Eg101; Accession No. AF260968)

It could also be 1950 according to Melnick et al. (1951), which is listed as reference for Egypt 1951 in Lanciotti et al.:

In the course of an “antibody survey,” carried out in July 1950, one of us (J.R.P.), collected serum from 251 Egyptians …

Full list of affected sequences

PP_000HJBT.4

[emmahodcroft]

Agree that it seems clear the sample is from either 1950 or 1951 - but actually quite hard to say which. Looking generally at other publications, seems there were outbreaks both years and potentially serosurveys both years?

This publication does say "WNV was first isolated in Egypt in 1950 in north of Cairo, where serosurveys was conducted in 251 individuals; ... [3]" - referencing Taylor et al. 1956 (I don't have access to full text). This would seem to corroborate Melcick et al above with a year of 1950?

[emmahodcroft]

Was able to get access to Taylor et al. 1956 which states:

the virus again came to attention when in the summer of 1950 Dr. John R. Paul collected a series of bloods from children in the Sindbis sanitary district [...] for the purpose of examining for antibodies against the polio-myelitis virus. In the process of these examinations West Nile virus was found in the blood of three of 250 children (Melnick, Paul et al. 1951).

This indeed seems to support 1951 article....

A second article I located, Southam and Moore 1954, (unfortunately also not openly available) states:

Since that report [referring to a Southam and More 1951 paper], there have become available three new isolates of West Nile virus known as Egypt 101, Egypt 21 and Egypt 19 (Melnick et al., 1951).

So this also quite explicitly links Egypt 101 (Eg101) to Melnick et al. 1951, which would again give the year 1950 as isolation.

My guess is that the year of publication and year of sampling (being so close) got mixed up at some point, not helped by the fact that there were outbreaks in 1951 and presumably more sampling too.

In addition, in case of interest, the Southam and More 1954 article states:

The three Egypt isolates of West Nile virus were obtained as the third passage in mouse brain or in chick embryos. Stocks for clinical use were made from this original material by one further passage in the same host.

Of course between this paper and whenever these were sequenced - who knows the additional passage history...!

[victorlin]

Does Pathoplexus support custom date ranges? "Either 1950 or 1951" can be represented as 1950-01-01/1951-12-31 in Augur.