Molecular Investigation and Risk Assessment of Neonatal Calf Diarrhea in Morocco: Emphasis on Rotavirus and Coronavirus Infections

Neonatal calf diarrhea represents a major health and economic burden in Moroccan cattle farming and remains a leading cause of calf mortality. It is commonly associated with infectious agents such as rotavirus, bovine coronavirus, Escherichia coli, and Cryptosporidium parvum, and is often aggravated by dehydration and electrolyte imbalances. The present study aimed to update the epidemiological profile of viral pathogens involved in neonatal calf diarrhea in Morocco, with particular emphasis on rotavirus group A (RVA) and bovine coronavirus (BCoV). A total of 889 newborn calves from 20 farms located in five Moroccan regions (Casablanca-Settat, Rabat-Salé-Kenitra, Souss-Massa, Fes-Meknes, and Beni Mellal-Khenifra) were included in this cross-sectional observational study. Among them, 130 rectal swabs were collected from diarrheic calves between November 2022 and March 2023 and analyzed using reverse transcription quantitative PCR (RT-qPCR). The results indicated that 34% of diarrheic calves tested positive for RVA and 62% for BCoV, with a co-infection rate of 24%. Infection rates were influenced by several factors, including calf age, geographic region, dam vaccination status, calving rank, production system, and farm size. RVA infection peaked in calves aged 8–14 days, whereas BCoV was most prevalent in calves aged 21–29 days. Notably, RVA positivity was higher in calves born to vaccinated dams (40%) compared to those from unvaccinated dams (20%), while BCoV infection was more frequently detected in calves from heifers than from multiparous cows. Higher infection rates in calves were also observed in intensive farming systems. Overall, these findings confirmed the major role of rotavirus and bovine coronavirus in neonatal calf diarrhea in Morocco and suggest that the limited effectiveness of vaccination may be influenced by herd management, colostrum transfer, and biosecurity practices. The potential mismatch between vaccine and circulating strains highlights the need for continuous molecular surveillance.