Rights statement: This is the peer reviewed version of the following article: Shabbir MZ, Ul‐Rahman A, Zahid MN, Munir M. Genetic characterization of small ruminant morbillivirus from recently emerging wave of outbreaks in Pakistan. Transbound Emerg Dis. 2018;65:2032–2038. https://doi.org/10.1111/tbed.12964 which has been published in final form at https://onlinelibrary.wiley.com/doi/abs/10.1111/tbed.12964 This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.
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Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
}
TY - JOUR
T1 - Genetic characterization of small ruminant morbillivirus from recently emerging wave of outbreaks in Pakistan
AU - Shabbir, Muhammad Zubair
AU - Ul-Rahman, Aziz
AU - Zahid, Muhammad Nauman
AU - Munir, Muhammad
N1 - This is the peer reviewed version of the following article: Shabbir MZ, Ul‐Rahman A, Zahid MN, Munir M. Genetic characterization of small ruminant morbillivirus from recently emerging wave of outbreaks in Pakistan. Transbound Emerg Dis. 2018;65:2032–2038. https://doi.org/10.1111/tbed.12964 which has been published in final form at https://onlinelibrary.wiley.com/doi/abs/10.1111/tbed.12964 This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.
PY - 2018/12/6
Y1 - 2018/12/6
N2 - Peste des petits ruminants (PPR) is an endemic and highly infectious disease of several tropical countries, including Pakistan. Despite exhaustive vaccination, outbreaks are on the rise annually across different parts of the country. Clinical outcomes are largely employed to diagnose disease, while comprehensive genomic features of prevailing field strains of SRMV largely remain elusive. Here, we present comparative sequence-based phylogenomics of field strains from three districts representing different agro-livestock production systems during an emerging wave of outbreaks in 2015, together with the first complete genome sequencing of a strain from Pakistan. The analysis revealed clustering of study strain (SRMV/Lahore/UVAS/Pak/2015) to lineage IV, close to isolates characterized previously from India and China. Investigations of inter- and intralineage genetic distances showed a higher genetic distance between SRMV/Lahore/UVAS/Pak/2015 to lineage III viruses than lineages I and II. The characterized Pakistani strain also showed a high percentage of genetic distance from isolates originated from Nigerian and other African small ruminants. Based on these observations, an integrated cross-protection investigation is warranted in the future, not only to define the protective efficacy of currently applied vaccines, but also to continuously elucidate the genomic and evolutionary nature of circulating viruses in the country to achieve disease eradication by 2030.
AB - Peste des petits ruminants (PPR) is an endemic and highly infectious disease of several tropical countries, including Pakistan. Despite exhaustive vaccination, outbreaks are on the rise annually across different parts of the country. Clinical outcomes are largely employed to diagnose disease, while comprehensive genomic features of prevailing field strains of SRMV largely remain elusive. Here, we present comparative sequence-based phylogenomics of field strains from three districts representing different agro-livestock production systems during an emerging wave of outbreaks in 2015, together with the first complete genome sequencing of a strain from Pakistan. The analysis revealed clustering of study strain (SRMV/Lahore/UVAS/Pak/2015) to lineage IV, close to isolates characterized previously from India and China. Investigations of inter- and intralineage genetic distances showed a higher genetic distance between SRMV/Lahore/UVAS/Pak/2015 to lineage III viruses than lineages I and II. The characterized Pakistani strain also showed a high percentage of genetic distance from isolates originated from Nigerian and other African small ruminants. Based on these observations, an integrated cross-protection investigation is warranted in the future, not only to define the protective efficacy of currently applied vaccines, but also to continuously elucidate the genomic and evolutionary nature of circulating viruses in the country to achieve disease eradication by 2030.
KW - complete genome
KW - genetic distance
KW - Pakistan
KW - per cent identity
KW - phylogenomic analysis
KW - small ruminant morbillivirus
U2 - 10.1111/tbed.12964
DO - 10.1111/tbed.12964
M3 - Journal article
C2 - 30051602
VL - 65
SP - 2032
EP - 2038
JO - Transboundary and Emerging Diseases
JF - Transboundary and Emerging Diseases
SN - 1865-1674
IS - 6
ER -