Evolution of Beak and Feather Disease Virus across Three Decades of Conservation Intervention for Population Recovery of the Mauritius Parakeet
, Simon Tollington 1,3, Vikash Tatayah 4, Sion Henshaw 4, Houshna Naujeer 5, Carl Jones 6, Claire Raisin 7, Andrew Greenwood 8 and Jim J. Groombridge 1,*Round 1
Reviewer 1 Report
The authors present an investigation on the prevalence of Beak and Feather Disease virus in fledglings of the Mauritius parakeet (Alexandrinus eques) on Mauritius and assessed patterns of phylogenetic and haplotype diversity based on the replicase protein (Rep) of the virus. An initial outbreak in 2005 was followed by 2 subsequent waves of infection in 2010/2011 and 2013/14 associated with a rapid diversification of the strain of BFDV present within the Mauritius parakeet population.
The manuscript is well written and contains very interesting information worth being published in the journal Diversity.
There are some comments:
Line 98: The heading of this section does not completely reflect the content. It is suggested to change the heading to Mauritius parakeet sampling, DNA extraction, PCR and sequencing
Line 100: The investigation included 1321 blood samples from 45-day old fledglings. How many parent pairs or nests were included? It would be interesting to know about this.
Line 105: please add the exact years of the investigation period
Line 112: Please add the composition of the DIGSOL buffer.
Line 147: It would be important to know about the length of the sequences number of bases) included in the analyses. Please add this information.
Line 148: haplotype: the authors should give a short definition of this term somewhere in the manuscript.
Figure 3: Please add a short note that the colour codes in figure 3a are the same as in figure 3b, and please explain the meaning of the numbers in figure 3a. Please check the legend for the y axis in figure 3b. “Total positives” seems incorrect to me. Does the solid black line represents number of haplotypes? Please add.
Line 178: Please add more information on the occurrence of recombinations. Please add also some information on the occurrence of multiple haplotypes in individual bird samples, as mentioned in the discussion (Line 267).
Line 219-222: These sentences are unclear to me. There is a contradiction between a frequently fatal infection in immature birds up to 3 years of age and a common recovery of diseased birds. Please rephrase.
Line 252: please check citations. These are missing in the list.
Line 265 et seq. The analyses of the investigation presented here are based on a partial rep sequence. Would the authors expect different results based on full-genome sequences or based on the cap gene? A statement should be added to the discussion.
Line 399: Please check reference 46.
Author Response
Reviewers 1:
The authors present an investigation on the prevalence of Beak and Feather Disease virus in fledglings of the Mauritius parakeet (Alexandrinus eques) on Mauritius and assessed patterns of phylogenetic and haplotype diversity based on the replicase protein (Rep) of the virus. An initial outbreak in 2005 was followed by 2 subsequent waves of infection in 2010/2011 and 2013/14 associated with a rapid diversification of the strain of BFDV present within the Mauritius parakeet population.
The manuscript is well written and contains very interesting information worth being published in the journal Diversity.
There are some comments:
Line 98: The heading of this section does not completely reflect the content. It is suggested to change the heading to Mauritius parakeet sampling, DNA extraction, PCR and sequencing
DONE – please see line 99.
Line 100: The investigation included 1321 blood samples from 45-day old fledglings. How many parent pairs or nests were included? It would be interesting to know about this.
DONE – please see line 104.
Line 105: please add the exact years of the investigation period
DONE – please see line 107.
Line 112: Please add the composition of the DIGSOL buffer.
DONE – please see line 114.
Line 147: It would be important to know about the length of the sequences number of bases) included in the analyses. Please add this information.
DONE – sentence added, please see line 149.
Line 148: haplotype: the authors should give a short definition of this term somewhere in the manuscript.
DONE – please see line 84.
Figure 3: Please add a short note that the colour codes in figure 3a are the same as in figure 3b, and please explain the meaning of the numbers in figure 3a. Please check the legend for the y axis in figure 3b. “Total positives” seems incorrect to me. Does the solid black line represents number of haplotypes? Please add.
DONE – Figure 3 legend amended, please see line 191-192. Y-axis label changed to say ‘Number of individuals’
Line 178: Please add more information on the occurrence of recombinations.
DONE – we have removed information on the occurrence of recombination, it is a topic which requires a more in-depth analysis which we are carrying out as a separate study.
Please add also some information on the occurrence of multiple haplotypes in individual bird samples, as mentioned in the discussion (Line 267).
DONE – please see lines 274-276.
Line 219-222: These sentences are unclear to me. There is a contradiction between a frequently fatal infection in immature birds up to 3 years of age and a common recovery of diseased birds. Please rephrase.
DONE – please see line 222-223.
Line 252: please check citations. These are missing in the list.
DONE – please see lines 256 and 426-427.
Line 265 et seq. The analyses of the investigation presented here are based on a partial rep sequence. Would the authors expect different results based on full-genome sequences or based on the cap gene? A statement should be added to the discussion.
DONE – please see lines 271-272.
Line 399: Please check reference 46.
Done – please see line 410-411.
Reviewer 2 Report
This manuscript describes sequences of beak and feather disease virus (BFDV), from Mauritius parakeet, collected from 1993 to 2017. The host is an endangered parrot species and BFDV is and emerging pathogen, making this study more relevant. Sequences from Rep (replicase) are used to reconstruct ML phylogeny and haplotype network from collected samples. These are interpreted in context of avian breeding pairs and BFDV prevalence. There are many limitations to such focused studies (unknown influence of virus spillover from other hosts, effects of host genetic homogeneity in small island populations etc), but the authors provide a nice discussion of these limitations and do not overinterpret the data.
I have only two minor comments:
Fig. 1 – scale bar of the phylogenetic tree should be included
Line 217,218 – “The ability of a pathogen to establish in a host population
has a direct relationship with its virulence and an inverse relationship with its transmission efficiency” … isn’t it the other way round?
Author Response
This manuscript describes sequences of beak and feather disease virus (BFDV), from Mauritius parakeet, collected from 1993 to 2017. The host is an endangered parrot species and BFDV is and emerging pathogen, making this study more relevant. Sequences from Rep (replicase) are used to reconstruct ML phylogeny and haplotype network from collected samples. These are interpreted in context of avian breeding pairs and BFDV prevalence. There are many limitations to such focused studies (unknown influence of virus spillover from other hosts, effects of host genetic homogeneity in small island populations etc), but the authors provide a nice discussion of these limitations and do not overinterpret the data.
I have only two minor comments:
Fig. 1 – scale bar of the phylogenetic tree should be included
DONE – please see Figure 1.
Line 217,218 – “The ability of a pathogen to establish in a host population has a direct relationship with its virulence and an inverse relationship with its transmission efficiency” … isn’t it the other way round?
DONE – please see line 222-223.
