Kariithi Henry M, Christy Nancy, Decanini Eduardo L, Lemiere Stéphane, Volkening Jeremy D, Afonso Claudio L, Suarez David L
Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, Athens, GA 30605, USA.
Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Nairobi P.O. Box 57811-00200, Kenya.
Vet Sci. 2022 Oct 19;9(10):579. doi: 10.3390/vetsci9100579.
Avian metapneumoviruses (aMPV subtypes A-D) are respiratory and reproductive pathogens of poultry. Since aMPV-A was initially reported in Mexico in 2014, there have been no additional reports of its detection in the country. Using nontargeted next-generation sequencing (NGS) of FTA card-spotted respiratory samples from commercial chickens in Mexico, seven full genome sequences of aMPV-A (lengths of 13,288-13,381 nucleotides) were de novo assembled. Additionally, complete coding sequences of genes N ( = 2), P and M ( = 7 each), F and L ( = 1 each), M2 ( = 6), SH ( = 5) and G ( = 2) were reference-based assembled from another seven samples. The Mexican isolates phylogenetically group with, but in a distinct clade separate from, other aMPV-A strains. The genome and G-gene nt sequences of the Mexican aMPVs are closest to strain UK/8544/06 (97.22-97.47% and 95.07-95.83%, respectively). Various amino acid variations distinguish the Mexican isolates from each other, and other aMPV-A strains, most of which are in the G ( = 38), F ( = 12), and L ( = 19) proteins. Using our sequence data and publicly available aMPV-A data, we revised a previously published rRT-PCR test, which resulted in different cycling and amplification conditions for aMPV-A to make it more compatible with other commonly used rRT-PCR diagnostic cycling conditions. This is the first comprehensive sequence analysis of aMPVs in Mexico and demonstrates the value of nontargeted NGS to identify pathogens where targeted virus surveillance is likely not routinely performed.
禽偏肺病毒（aMPV A - D亚型）是家禽的呼吸道和生殖病原体。自2014年在墨西哥首次报告aMPV - A以来，该国未再有其检测报告。通过对墨西哥商业鸡的FTA卡斑点呼吸道样本进行非靶向下一代测序（NGS），从头组装了7个aMPV - A的全基因组序列（长度为13288 - 13381个核苷酸）。此外，从另外7个样本中基于参考组装了基因N（= 2）、P和M（各 = 7）、F和L（各 = 1）、M2（= 6）、SH（= 5）和G（= 2）的完整编码序列。墨西哥分离株在系统发育上与其他aMPV - A菌株聚类，但在一个不同的分支中。墨西哥aMPV的基因组和G基因核苷酸序列与UK/8544/06菌株最接近（分别为97.22 - 97.47%和95.07 - 95.83%）。各种氨基酸变异将墨西哥分离株彼此区分开来，也与其他aMPV - A菌株区分开来，其中大多数存在于G（= 38）、F（= 12）和L（= 19）蛋白中。利用我们的序列数据和公开可用的aMPV - A数据，我们修订了先前发表的逆转录-聚合酶链反应（rRT-PCR）检测方法，这导致aMPV - A的循环和扩增条件不同，使其与其他常用的rRT-PCR诊断循环条件更兼容。这是墨西哥对aMPV进行的首次全面序列分析，证明了非靶向NGS在识别可能未常规进行靶向病毒监测的病原体方面的价值。
