Metagenomic next-generation sequencing for etiological diagnosis of an unexpected rabies case with unclear exposure history
Authors: Wu jing , QI Yingjie , Zhang Wenyan , Liu Lixue , Chen Jiangrong , Yang Yun , Zhang Xuanshun , Liu Xinru , Shi Yuru 
Published: May 2024

Background
Rabies is an acute and lethal zoonotic disease caused by the rabies virus (RABV). After onset, there are no effective drugs or treatment methods. We reported a fatal rabies case with no clear history of animal bites and atypical early clinical symptoms. And unexpectedly, we discovered that unique RABV sequences were detected in the patient's saliva by metagenomic next-generation sequencing (mNGS). The patient was diagnosed with rabies based on the results of saliva mNGS, real-time reverse transcriptase polymerase chain reaction (RT-PCR) conducted by local Centers for Disease Control and Prevention (CDC), the detection of human rabies virus IgG antibodies performed in our laboratory, as well as the clinical symptoms of pruritus, agitation, paralysis, and excessive salivation at disease onset.
Case presentation
A 49-year-old female from Hefei, Anhui Province, China, presented to a local hospital with fever, pruritus, chest distress, and shortness of breath. During the consultation, the patient exhibited agitation and was later admitted to the intensive care unit (ICU) for endotracheal intubation and mechanical ventilation due to worsened agitation and dyspnea. Cerebrospinal fluid (CSF) and blood samples were collected and pathogenic microorganism identification was performed by culture and mNGS. However, all results were negative. In addition, the patient did not display typical rabies-specific symptoms such as aerophobia, hydrophobia or photophobia from onset to admission. Subsequently, saliva samples were collected for mNGS detection following consultation with experts at our hospital. Nucleic acid sequences uniquely aligned to the rabies virus (RABV) were identified in these samples. The result was further confirmed by local CDC through RT-PCR which detected part of the N gene of RABV in the saliva sample. Then the patient was transferred to our hospital's ICU for isolation. Unfortunately, she died on the 10th day of admission due to multiple organ failure. The patient remained in a comatose state during symptomatic supportive medical care in ICU, and the progression of the disease was accompanied by intermittent elevated body temperature, excessive salivation, and limb weakness. The detection of human rabies virus IgG antibodies reported positive during the advanced stage of the disease. We consistently verified with the patient's family member that there was no clear history of animal bites and no history of RABV vaccination. Furthermore, we performed phylogenetic analysis of partial L and G gene sequences of RABV obtained by mNGS (designated HFG23-L and HFG23-G, respectively), the results showed that both HFG23-L and HFG23-G belonged to the China I lineage, and shared 99.7% similarity with the Fengtai strain isolated from dogs in Beijing. The results suggested that the origin of RABV in this case may be a dog from the northern China.
Conclusions
The patient's non-specific prodromal symptom, along with negative culture and mNGS results of blood and CSF, impose challenges on promptly and definitively diagnosing rabies in this case. The identification of unique RABV sequence through mNGS in the patient's saliva sample suggested that mNGS could serve as a valuable screening tool for the etiological diagnosis of rabies, especially when timely laboratory testing was unavailable or when patients lacked a clear exposure history.