Partial Sequence and Phylogenetic Analysis of The Nucleoprotein Gene of Coronavirus and VP7/VP4 Gene of Rotavirus in Calf Diarrhea

Öz

The rotavirus and coronavirus are etiological agent of neonatal calf diarrhea and they are widespread in the world. In the twenty first century, investigation of infectious agents have accelerated with molecular-based genetic studies. So far as is known, at least 27 distinct G genotypes and 37 distinct P genotypes have been identified. Coronaviruses are divided into four genotypic groups based on their genetic distance. The aim of this study, we investigate the rotavirus and coronavirus infections in calf diarrhea based on molecular analysis. Partial sequencing of the coronavirus nucleoprotein gene fragment and rotavirus VP4 and VP7 gen fragment was performed using specific nested primer pairs and followed phylogenetic analyses. Phylogenetic tree was constructed using reference strains obtained from GenBank. The Erzurum rotavirus strains were involved in G6 and G10 genogroup based on VP7 coding gen region and all rotavirus strain was involved in P[5] genogroup based on VP4 coding gen region. The phylogenetic analysis of coronavirus strains showed that Erzurum strains, deer, giraffe, bat, bovine and human coronavirus strains take part in Beta-coronavirus genogroup. As a conclusion, this is the first investigation of enteric coronavirus and rotavirus based on molecular analyses in Erzurum. This study will provide an advantage for the further studies.

Anahtar Kelimeler

• Bovine,Coronavirus,Erzurum,Molecular characterization,Rotavirus

Buzağı İshallerinde Coronavirusun Nukleoprotein Gen ve Rotavirusun VP7/VP4 Gen Bölgelerinin Kısmi Sekansı ve Filogenetik Analizi

Öz

Dünya genelinde yaygın olarak gözlenen rotavirus ve coronavirus enfeksiyonları, yeni doğan buzağı ishallerinin etiyolojik ajanları arasındadır. Yirmi birinci yüzyılda enfeksiyon ajanlarının incelenmesi, moleküler tabanlı genetik çalışmalarla hız kazanmıştır. Günümüzde enfeksiyonlardan sorumlu rotavirusun bilinen en az 27 farklı G ve 37 farklı P genotipi tespit edilmiştir. Coronaviruslar ise genetik yakınlıklarına göre; dört genotipik gruba ayrılmaktadır. Bu çalışmada, buzağı ishallerine sebep olan rotavirus ve coronavirus enfeksiyonlarının moleküler düzeyde incelenmesi amaçlandı. Coronavirusun nukleoprotein gen bölgesi ve rotavirusun VP4 ile VP7 gen bölgelerine yönelik spesifik primerler kullanılarak kısmi sekansları ve ardından filogenetik analizleri yapıldı. Filogenetik analiz için GenBank’tan elde edilen referans suşlar kullanıldı. VP7 gen bölgesinin analizi sonucunda Erzurum suşlarının G6 ve G10 genotipine, VP4 gen bölgesine göre ise tüm suşların P[5] genotipine ait olduğu tespit edildi. Coronavirus yönünden yapılan filogenetik analiz sonuçlarına göre ise Erzurum suşları; geyik, zürafa, yarasa, sığır ve insan coronavirus suşları ile birlikte beta-coronavirus genogrubu içerisinde toplandığı tespit edildi. Sonuç olarak bu çalışma ile Erzurum’da ilk kez enterik coronavirus ve rotavirus moleküler olarak araştırılmış olup sonraki çalışmalar için bir temel oluşturmuştur.

Anahtar Kelimeler

• Coronavirus,Erzurum,Moleküler karakterizasyon,Rotavirus,Sığır

Kaynakça

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