Data from: Emergence of human calicivirus among diarrhea cases in southwest China

Background: Acute diarrhea is one of serious problems in global public health which cause considerable morbidity and mortality worldwide. Human calicivirus (HuCV) includes norovirus (NoV, genogroup GI and GII) and sapovirus (SaV), and NoV GII genogroup is a leading cause of acute sporadic diarrhea in individual across all age groups. Few studies had been conducted to clarity the characteristics of HuCV in diarrhea cases across all age groups in China. Our study was aimed to assess the HuCV-related diarrhea burden and NoV genotypes distribution in southwest China.
Methods: The study was conducted in four hospitals in Kunming city from June 2014 to July 2015. Stool specimens were collected from 1,121 diarrhea cases and 319 healthy controls in outpatient department. Reverse transcription polymerase chain reaction (RT-PCR) was used to detect the NoV (GI, GII) and SaV. Sequencing was applied to confirm these three viral infection and phylogenetic analyse was performed to determine these genotypes. The demographics information and clinical symptoms of subjects were recorded with structured questionnaire.
Results: HuCV was detected at 11.0% infection rate out of 1,121 diarrhea cases and at 3.4% of 319 non-diarrhea subjects (P<0.0001, OR=3.5, 95% CI 1.8-6.5). The prevalences of NoV genogroup GII and genotype GII.4 in diarrhea cases were significantly higher than those of in healthy controls (P<0.0001, P=0.018, respectively). NoV GII had seasonal prevalence peak in autumn (2=12.2, P=0.0068). No significant differences of age distribution were observed in diarrhea cases infected with GII.4, GII.3, GII.17 and GII.5, but GII.12 was only detected in diarrhea children under five years (2=15.4, P=0.004). NoV GII (n=118, 10.5%) was the most common HuCV subtype in diarrhea cases, followed by SaV (n=3, 0.3%) and NoV GI (n=2, 0.2%). Of 118 strains NoV GII isolated from diarrhea patients. GII.4 (n=55, 46.6%) was predominant strain, followed by GII.3 (n=28, 23.7%), GII.12 (n=25, 21.2%), GII.17 (n=8, 6.8%) and GII.5 (n=2, 1.7%), of 55 strains GII.4, GII.4 Sydney-2012 variant was absolute predominance prevalence (n=52, 94.5%), followed by NoV GII.4-2006b variant (n=3, 5.5%), GII.4 Orleans-2009 variant was not found in diarrhea cases.
Conclusions: It is the first time to detect the HuCV in sporadic diarrhea cases and asymptomatic patients in southwest China. NoV GII was the major genogroup and GII.4 was the most predominant strain detected in diarrhea patients. GII.17 variant was emergence in sporadic diarrhea and might be became predominant strain in diarrhea cases in near future. Rapid, accuracy detection kit need to be developed to help us timely find and treat NoV associated diarrhea cases in clinical setting.