Virus prevalence and occurrence
As shown in Table 1, different types of viruses were detected in all provinces with the exception of Jiangsu province where no virus was detected. All of the viruses were present in the different provinces with the exception of KBV and ABPV, which were not detected. BQCV was the most prevalent virus and was present in 18 % of the A. mellifera apiaries and in seven provinces. CSBV was found in 38.9 % of the A. cerana apiaries and in seven provinces. In contrast, BQCV was detected in 22 % of the A. cerana apiaries and CSBV was found in 2.6 % of the A. mellifera apiaries. The following frequencies were obtained for the remainder of the viruses: IAPV was detected in 7.9 % of the A. mellifera apiaries and 5.6 % of the A. cerana apiaries; CBPV was found in 15.8 % of the A. mellifera apiaries and was not detected in A. cerana; SBV was identified in 5.3 % of the A. mellifera apiaries and 16.7 % of the A. cerana apiaries; DWV-A was found in 13.2 % of the A. mellifera apiaries and 5.6 % of the A. cerana apiaries; DWV-B was found in 10.5 % of the A. mellifera apiaries and was not detected in the A. cerana apiaries; AmFV was found in 13.2 % of the A. mellifera apiaries and 11.1 % of the A. cerana apiaries; and DWV-C/KV was found in 10.5 % of the A. mellifera apiaries and 11.1 % of the A. cerana apiaries.
BQCV was the most common virus and accounted for 84.6 % among the tested samples in each province (Figure 1A). The second highest frequency virus was CSBV (61.6%), followed by another 3 viruses at equal frequency (53.8 %; DWV-A, AmFV and DWV-C/KV). The least frequent viruses were IAPV and DWV-B with 30.8 %. The number of honey bee viruses in A. mellifera was higher than that in A.cerana in the same province (Figure 1B) with the exception of Chongqing and Yunnan, which gave priority to keeping A. cerana. The number of viruses in A. mellifera in Zhejiang was the same as that of A. cerana. Liaoning province had the highest number of viruses, with 9 viruses in A. mellifera and only one in A. cerana. Similarly, there were 7 viruses in A. mellifera in Inner Mongolia and Heilongjiang and no viruses were detected in A. cerana.
Co-infection of viruses in each province
The co-occurrence of more than one virus in one province was fairly common in both the A. mellifera and A. cerana apiaries (Table S3 and Table S4). In A. mellifera, virus co-infection varied from 2 to 6 viruses. Co-infection with 2 viruses represented 28.9 % of the occurrences, 3 viruses represented 31.6 %, 4 viruses represented 15.7 %, 5 viruses represented 10.5 % and 6 viruses represented 7.89 %. Among the multiple co-infections, BQCV and CBPV co-infection was the most common 2 virus co-infection and accounted for 10.53 %. IAPV, SBV and CBPV was the highest percentage 3 virus co-infection with 7.89 %, followed by BQCV, CBPV and AmFV, IAPV, SBV and CSBV, and IAPV, DWV-A and DWV-B. IAPV, BQCV, DWV-A and DWV-B was the most common 4 virus co-infection with 13.16 %. In contrast, fewer co-infections were detected in A. cerana compared to A. mellifera (Table S4). Virus co-infections in A. cerana primarily involved 2 and 3 viruses. Simultaneous infections with 2 viruses were detected in 61.11% and with 3 viruses in 16.67% of the apiaries. The most prevalent co-infection was SBV and CSBV in A. cerana, accounting for 22.22 %. Co-infection with 4 viruses (IAPV, BQCV, DWV-A, and DWV-B) was significantly higher than the other co-infections in A. mellifera, (χ2=12.61, P=0.00038, df=1) (Table S5), whereas in A. cerana co-infection with 2 viruses was significantly more common than the other co-infection types (e.g., BQCV and CSBV; χ2=0.0009, P=0.02, df=1) (Table S6).