From 15 April to 31 May 2022, we conducted an observational study in four Omicron-infected patients with advanced pancreatic and biliary cancer (Group 1) in the Oncology Department of the Seventh People’s Hospital of the Shanghai University of Traditional Chinese Medicine (TCM). Omicron infection was clinically defined, referring to WHO diagnostic criteria. At three time points (Days 0, 7, and 14 after the diagnosis of Omicron infection), lymphocyte subsets, cytokines, white blood cell count, blood biochemistry, and tumor markers were detected for Omicron-infected cancer patients; a 45-day clinical observation was conducted, and the data of tumor diagnosis, clinical disease course, and previous tumor treatment were collected. To clarify the effects of Omicron infection on the medical condition of patients with advanced pancreatic and biliary cancer, four non-Omicron-infected cancer patients (Group 2), four Omicron-infected non-cancer-afflicted subjects (Group 3), and four non-Omicron-infected non-cancer-afflicted subjects (Group 4) were included in this study at the same time to serve as controls, and their blood samples were collected at the same time points to detect lymphocyte subsets and cytokines. The subjects in Groups 1 and 2 were paired by age, sex, body mass index (BMI), pathological diagnosis, tumor stage, and tumor co-morbidities. Omicron-infected patients were defined as patients diagnosed with advanced pancreatic and biliary cancer using pathological or clinical evidence whose RT-PCR test result was positive. The non-cancer-afflicted subjects were enrolled by caregivers. All 16 subjects had no history of COVID-19 infection. The vaccination status of 16 subjects is shown in Table 1 . This study was approved by the Ethics Committee of the Seventh People’s Hospital of Shanghai University of TCM and is under the jurisdiction of Shanghai epidemic prevention policies, regulations, and laws. In the Seventh People’s Hospital of the Shanghai University of TCM, all subjects received face-to-face interviews and signed written informed consent forms ( Figure 1 ).

We retrospectively analyzed the clinical diagnosis and treatment records, nursing records, laboratory examination results, and imaging examination data of Omicron-infected and control cancer patients. The admission data for these subjects involved the period of 7 February to 31 May 2022. The epidemiological, clinical, laboratory, and imaging examination data of patients were collected and entered into electronic case report forms (CRFs). The CRFs were reviewed and checked by independently two investigators. If incapable of being obtained from electronic medical records, epidemiological and clinical symptom data were determined by the investigators through communication with patients and their families.

In this study, pharyngeal swab samples and blood samples of subjects were collected and then sent to the standardized SARS-CoV-2 testing laboratory. The pharyngeal swab samples were tested using fluorescent RT-PCR approved by the National Medical Products Administration (NMPA, former: State Food and Drug Administration (SFDA)). The RT-PCR test results indicated SARS-CoV-2 Omicron Variant (Omicron) in the respiratory samples.

The primary examination included whole blood cell count, blood biochemistry (liver function, renal function, and electrolytes), tumor markers, lymphocyte subsets, cytokines, RT-PCR, and antibody tests of biliary samples for cancer patients, only lymphocyte subsets and cytokines for non-cancer patients, as well as additional RT-PCR and serum antibody tests of pharyngeal swab samples for Omicron-infected patients.

In view of previous studies and explorations on COVID-19 treatment and considering the clinical symptoms of Omicron infection, Omicron-infected subjects were administrated with Lianhua Qingwen capsules 1.4 g tid p.o. Oxygen inhalation support (e.g., nasal catheter oxygen inhalation) was provided upon blood oxygen saturation (SaO₂). The pharyngeal swab samples of subjects diagnosed as Omicron infection were daily tested by RT-PCR till discharge, death, or a negative RT-PCR result.

To describe the changes of lymphocyte subsets and cytokines in the body at different stages of disease after Omicron infection, cytokines (IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, IFN-γ, IFN-α, and TNF-α), lymphocyte subsets (total T-cell%, total T-cell count, helper/inducer T-cell%, helper/inducer T-cell count, cytotoxic T-cell%, cytotoxic T-cell count, helper T-cell/cytotoxic T cell, total B cell%, total B cell count, NK cell%, and NK cell count) and serum antibodies (IgG antibody and IgM antibody) of subjects in four groups were tested on Days 0, 7, and 14 after the diagnosis of Omicron infection. T-cell subsets were detected using BD Bioscience kits, and cytokines were detected using Raisecare kits. The above test results of subjects in the other three groups were used as controls for cross-comparison.

The plasma levels of cytokines and lymphocyte subsets in four groups were compared with standard parametric and non-parametric tests, and then the polygram and histogram were plotted to visualize the overall levels and dynamic changes of cytokines and lymphocyte subsets in different groups. The quantitative data were presented as mean ± standard deviation or inter-quartile range (IQR). The qualitative data were expressed as percentages (%). GraphPad Prism 9.3.1 software and SAS 9.4 software were used for analysis. P <0.05 indicated a statistically significant difference.

The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report.

A total of 16 subjects in the Second Department of Oncology of the Seventh People’s Hospital of Shanghai University of TCM were included from 15 April to 31 May 2022. Since the diagnosis of Omicron infection, 45-day clinical observation has been performed. The observation results showed that three subjects died separately at Days 11, 25 (Day 9 after negative conversion), and 13 after Omicron infection, and they were all Omicron-infected patients with advanced cancer. In the 16 subjects, there were nine (56%) males and seven (44%) females; there were four (100%) males in Omicron-infected cancer patient group and three (75%) males and one (25%) female in non-Omicron-infected cancer patient group, four (100%) females (the caregivers of cancer patients with positive Omicron infection) in Omicron-infected healthy subject group, as well as two (50%) males and two (50%) females in non-Omicron-infected healthy subject group. The age and BMI of subjects in the four groups were 62.75, 59.5, 59, and 53 years, as well as 23.58 kg/m², 21.6 kg/m², 25.83 kg/m², and 23.32 kg/m², respectively. All subjects had no history of COVID-19 infection. The detailed information on subjects in the four groups is shown in Table 2 .

Patient No. 1 was diagnosed with cholangiocarcinoma (stage: cT3N0M0, IIB) over 4 months ago without any underlying diseases. On 26 February 2022, the patient was admitted to the hospital, and the examination indicated common duct obstruction with obstructive jaundice, hypoproteinemia, and electrolyte disturbance. The patient received nasobiliary drainage, artificial liver support, and symptomatic support treatment during hospitalization ( Supplementary Figure 1 ). On 15 April 2022, the RT-PCR test results of the pharyngeal swab sample and the bile sample were positive, and the antibody test results of the serum sample and the bile sample were negative for IgM antibodies and negative for IgG antibodies ( Table 3 ). After Omicron infection, the patient presented cough and expectoration without other common symptoms or signs of COVID-19 infection and then received antiviral treatment with Lianhua Qingwen capsules. Also, symptomatic support treatment was performed for jaundice, hypoproteinemia, and electrolyte disturbance, and the patient’s general state was stable. On 4 May 2022, the RT-PCR test result of the pharyngeal swab sample was negative, and thereafter, such RT-PCR tests were repeated continuously for 14 days, all with a negative result ( Table 3 ).

Patient No. 2 was diagnosed with hilar cholangiocarcinoma (stage: cT3N0M0, IIIA) over 4 months ago and previously underwent a radical gastrectomy. On 2 March 2022, the patient was admitted to the hospital for biliary drainage and replacement but received symptomatic support treatment during hospitalization due to the lack of a decrease in jaundice-related indexes and the co-morbidities of hepatic cirrhosis, cholecystolithiasis, hypoproteinemia, ascites, splenomegaly, hepatic insufficiency, and hepatic encephalopathy ( Supplementary Figure 2 ). On 15 April 2022, the RT-PCR test results of the pharyngeal swab sample and the bile sample were positive, while the antibody test results of the serum sample and the bile sample were negative for IgM antibodies and negative for IgG antibodies ( Table 3 ). After Omicron infection, the patient had no symptoms or signs of COVID-19 infection and received antiviral treatment with Lianhua Qingwen capsules but presented aggravation in the medical condition. On 20 April 2022, the ultrasonography indicated 1,000 ml of ascites, and the test results showed severe jaundice and hepatic insufficiency. After symptomatic treatment, the patient had no improvement and then died clinically on 26 April 2022. The cause of death was multiple organ failure, which was related to underlying diseases.

Patient No. 3 was diagnosed with pancreatic cancer (stage: cT3N2M1, IV) over 2 months ago ( Supplementary Figure 3 ). On 12 March 2022, the patient was admitted to the hospital. On 24 March 2022, the patient received chemotherapy with the GEMOX regimen (gemcitabine 1.8 g + oxaliplatin 150 mg) after diagnosis. On Day 4 after chemotherapy, the patient felt palpitations and chest distress, and the examination indicated multiple embolisms in the distal right main pulmonary artery and bilateral pulmonary arteries and deep venous thrombosis of the lower limbs. Considering the co-morbidities, including secondary malignancies of the liver, bones, and lymph nodes, hepatic insufficiency, hypoproteinemia, ascites, and hydrothorax, inferior vena cava filter implantation, and symptomatic support treatment, were performed during hospitalization. On 15 April 2022, RT-PCR test results of pharyngeal swab sample and bile sample were positive, the antibody test results of serum sample were weak positive IgM antibody and negative IgG antibody, and those of bile sample were negative IgM antibody and negative IgG antibody ( Table 3 ). After Omicron infection, the patient presented cough, expectoration, and throat pain, without other symptoms or signs of COVID-19 infection, and then received antiviral treatment with Lianhua Qingwen capsules. On 30 April 2022, the RT-PCR test result of the pharyngeal swab sample was negative, and thereafter the daily retest results were all negative. The patient had a poor general state. On 7 May 2022, ultrasonography indicated massive ascites and a poor conscious state, with liver failure, renal failure and electrolyte disturbance, and the daily urine volume was 500 ml; after symptomatic treatment, there was no improvement. On 9 May 2022, patient’s blood pressure (78/47 mmHg) and SaO₂ were both decreased, and SaO₂ was 89%–93% under high-flow oxygen inhalation. On 10 May 2022, the blood pressure and heart rate were further decreased, and the patient died clinically. The cause of death was multiple organ failure, which was related with underlying diseases.

Patient 4 was diagnosed with cholangiocarcinoma (stage: rT2N1M0, IIIB) over 2 years ago ( Supplementary Figure 4 ). On 7 February 2022, the patient was admitted to the hospital, and the examination and test results indicated gastrointestinal hemorrhage, hemobilia, biliary infection, hypoproteinemia, hypokalemia, ascites, and liver abscess. During hospitalization, the patient underwent percutaneous transhepatic cholangial drainage, liver abscess puncture drainage, abdominal puncture drainage, inferior mesenteric artery embolization, and symptomatic support treatment. On 15 April 2022, RT-PCR test results of pharyngeal swab sample and bile sample were positive, the antibody test results of serum sample and bile sample were negative IgM antibody and negative IgG antibody ( Table 3 ). After Omicron infection, the patient had a poor general state, intermittent chest distress, shortness of breath, decreased SaO₂ (min. 85%), fever, cough, expectoration, and restlessness (which all could be transiently relieved after symptomatic support treatment), without other symptoms and signs of COVID-19 infection, and then received antiviral treatment with Lianhua Qingwen capsules. On 28 April 2022, the patient experienced sudden chest distress, shortness of breath, and decreased SaO₂ (55%–59%), and these symptoms were not improved by symptomatic treatment; thus, the patient died clinically. The cause of death was respiratory failure, which was related with Omicron infection.

Before the diagnosis of Omicron infection, there were two cases of jaundice, four cases of hypoproteinemia, three cases of electrolyte disturbance, three cases of hepatic insufficiency, one case of metastasis, four cases of anemia, one case of upper gastrointestinal hemorrhage, one case of hydrothorax, three cases of ascites, and one case of thrombus in Omicron-infected cancer patients. All non-Omicron-infected cancer patients had advanced biliary cancer, in which there were four cases of jaundice, one case of hypoproteinemia, three cases of electrolyte disturbance, three cases of metastasis, two cases of anemia, one case of hydrothorax, and two cases of ascites. The patients’ previous tumor treatments are shown in Table 2 (before the diagnosis of Omicron virus infection). After the diagnosis of Omicron infection, all Omicron-infected cancer patients and three non-Omicron-infected cancer patients did not receive anti-tumor treatment, and only one non-Omicron-infected cancer patient received targeted therapy ( Table 2 ).

Based on previous study reports, lymphopenia (an abnormal decrease in the number of lymphocytes) is an important characteristic of COVID-19 infection (9). To fully evaluate the body immunity of Omicron-infected patients with advanced pancreatic and biliary cancer, we compared the overall test results of lymphocyte subsets among four groups in this study ( Figure 2 ). The findings showed that total T cell% ( Figure 2B ) and CD8⁺ T cell% ( Figure 2F ) in Omicron-infected cancer patients were lower than those in non-Omicron-infected cancer patients (both P <0.01), while CD4⁺T/CD8⁺T ( Figure 2G ), total B cell count ( Figure 2H ), and total B cell% ( Figure 2I ) were higher (P <0.05, P <0.01, and P <0.001). Compared with Omicron-infected non-cancer-afflicted subjects, total T-cell count ( Figure 2A ), total T cell% ( Figure 2B ), CD4⁺ T-cell count ( Figure 2C ), and CD8⁺ T-cell count ( Figure 2E ) in Omicron-infected cancer patients were decreased (P <0.0001, P <0.001, P <0.0001, and P <0.001), while total B cell% ( Figure 2I ) was increased (P <0.01).

Of four Omicron-infected cancer patients, Patient No. 1 still survived, while Patients Nos. 2, 3, and 4 died on Days 11, 25 (Day 9 after negative conversion), and day 13 after Omicron infection, respectively ( Figure 3A ). To further evaluate the relationship between body immunity and disease course and prognosis in Omicron-infected patients with advanced pancreatic and biliary cancer, we compared the test results of lymphocyte subsets among four Omicron-infected cancer patients, only one of whom survived ( Figure 3 ). The findings revealed that CD4⁺T/CD8⁺T ( Figure 3H ), B cell count ( Figure 3I ), and total B cell% ( Figure 3J ) of Patient No. 1 were lower than those of Patient No. 3, while CD8⁺T cell% ( Figure 3G ) and NK cell% ( Figure 3L ) were greater. Compared with Patient No. 2, the total B cell% ( Figure 3J ) of Patient No. 1 was declined, while NK cell% ( Figure 3L ) was elevated. NK cell% ( Figure 3L ) of Patient No. 1 was greater than that of Patient No. 4 (P <0.05). These findings indicated a poor prognosis in Omicron-infected patients with advanced pancreatic and biliary cancer who had decreased T-cell subsets and immunodeficiency.

Studies have suggested that when infecting the epithelial cells, COVID-19 SARS-CoV-2 will be recognized by macrophages and adjacent endothelial and epithelial cells, causing the secretion of massive proinflammatory cytokines (10). To evaluate the effects of Omicron infection on the secretion of proinflammatory cytokines in patients with advanced pancreatic and biliary cancer, we detected the serum cytokine levels of subjects in four groups and then performed a comparative analysis ( Figure 4 ). The results demonstrated that IL-1β ( Figure 4A ) and IL-6 ( Figure 4E ) in Omicron-infected cancer patients were lower than those in non-Omicron-infected cancer patients (P <0.05) and higher than those in Omicron-infected non-cancer-afflicted subjects (P <0.01), respectively. As shown by the clinical observation, four Omicron-infected cancer subjects had different outcomes: Patient No. 1 still survived, while Patients Nos. 2, 3, and 4 died on Days 11, 25 (Day 9 after negative conversion), and 13 after Omicron infection, respectively. To evaluate the relationship between the secretion level of proinflammatory cytokines and the disease outcome in Omicron-infected patients with advanced pancreatic and biliary cancer, we compared the serum cytokine test results of Patient No. 1 and the remaining three patients ( Figure 5 ). The findings indicated that the secretion levels of IL-6 ( Figure 5C ) and IL-10 ( Figure 5E ) in Patient No. 1 were lower than those in Patients Nos. 2 and 4, respectively. These findings indicated T-cell exhaustion and immunodeficiency in Omicron-infected patients with advanced pancreatic and biliary cancer.

Studies have shown that after invading human body, SARS-CoV-2 will infect monocytes and macrophages, and these two types of cells die of cellular inflammatory necrosis (i.e., pyroptosis) and thus release strong inflammatory warning signals. In COVID-19 patients, about 6% of monocytes die of pyroptosis (11). To fully evaluate the immune state of Omicron-infected patients with advanced pancreatic and biliary cancer, we detected and compared peripheral blood monocytes in four Omicron-infected and four non-Omicron-infected patients with advanced pancreatic and biliary cancer ( Figure 5 ). As shown by the results, there was no significant difference in monocyte count ( Figure 5G ) and monocyte% ( Figure 5H ) between the two groups (P >0.05). In four Omicron-infected cancer patients, however, the monocyte count ( Figure 5I ) of surviving Patient No. 1 was smaller than that of Patient No. 3.

Previous studies have revealed that the neutrophil to lymphocyte ratio (NLR), derived neutrophil-to-lymphocyte ratio (dNLR), lymphocyte to monocyte ratio (LMR), platelet to lymphocyte ratio (PLR), and systemic immune-inflammatory index (SII) is closely related to the development and prognosis of tumors. Numerous studies completed after the COVID-19 outbreak suggested that these inflammatory indexes also have a significant correlation with the prognosis of COVID-19 patients (12). In this study, the comparison of inflammatory indexes between Omicron-infected and non-Omicron-infected cancer patients showed no significant differences ( Table 4 ). To further explore the correlation between inflammatory indexes and prognosis, we compared the inflammatory indexes among four Omicron-infected cancer patients, only one of whom survived ( Figure 5 ). The results showed that the dNLR ( Figure 5L ), PLR ( Figure 5O ), and LMR ( Figure 5M ) of Patient No. 1 were lower than those of Patient No. 2, higher than those of Patient No. 2, and greater than those of Patient No. 3, respectively, and there were no significant differences in the other inflammatory indexes ( Figures 5K–N ).

To evaluate the time-course changes in body immunity, we compared the test results of lymphocyte subsets and cytokines over time between Omicron-infected cancer patients and Omicron-infected non-cancer-afflicted subjects. Total T cell% ( Figure 6B ) trended to decrease in Omicron-infected cancer patients but was stable in Omicron-infected non-cancer-afflicted subjects. After Omicron infection, CD4⁺T cell% ( Figure 6D ) had no obvious change in both cancer patients and non-cancer-afflicted subjects at the early stage but trended to decline at the late stage. The B-cell count ( Figure 6H ) of Omicron-infected non-cancer-afflicted subjects was evidently increased at the early stage but trended to decrease at the late stage, while that of Omicron-infected cancer patients trended to increase generally; in the time-course changes of other lymphocyte subsets, there was no significant difference between the two groups ( Figures 6A, C, E–G, I–K ). At the early stage of Omicron infection, IL-1β ( Figure 7A ) trended to decrease in both cancer patients and non-cancer-afflicted subjects; at the late stage, it remained at a low level without apparent fluctuation in cancer patients but trended to a marked increase in non-cancer-afflicted subjects. IL-2 ( Figure 7B ) had a change trend like IL-1β. In both cancer patients and non-cancer-afflicted subjects, IL-4 ( Figure 7C ), IL-5 ( Figure 7D ), IL-12p70 ( Figure 7H ), IL-17 ( Figure 7I ), IFN-α ( Figure 7J ), and TNF-α ( Figure 7L ) all trended to significantly decrease at the early stage and markedly increase at the late stage of Omicron infection. The overall level of IL-6 ( Figure 7E ) in Omicron-infected cancer patients was higher than that in Omicron-infected non-cancer-afflicted subjects, with a decreasing trend at the early stage; however, IL-6 in non-cancer-afflicted subjects was kept at a low level and had no obvious changes in the whole process of Omicron infection. IL-10 ( Figure 7G ) trended to decrease in Omicron-infected cancer patients and Omicron-infected non-cancer-afflicted subjects at the early stage, and its increase in non-cancer-afflicted subjects was higher than that in cancer patients at the late stage. IL-8 ( Figure 7F ) and IFN-γ ( Figure 7K ) had a declining trend in both cancer patients and non-cancer-afflicted subjects at the early stage but no significant changes at the late stage. The above-mentioned serum cytokine time-course changes further indicated that Omicron-infected patients with advanced pancreatic and biliary cancer had T-cell exhaustion and immunodeficiency.

Of the four Omicron-infected cancer patients, Patient No. 1 still survived. This patient was admitted to the hospital on 26 February 2022, with the co-morbidities of hypoproteinemia, electrolyte disturbance and severe jaundice (total bilirubin TBIL 618.9 μmol/L). After nasobiliary drainage, artificial liver support, and symptomatic support treatment, there was a significant improvement in liver function. On 4 April 2022, TBIL was tested at 102.3 μmol/L. On 15 April 2022, RT-PCR test results of pharyngeal swab sample and bile sample were positive, and the antibody test results of serum sample and bile sample were negative IgM antibody and negative IgG antibody ( Table 3 ). After Omicron infection, the patient presented cough and expectoration without other common symptoms and signs of COVID-19 infection, and then received antiviral treatment with Lianhua Qingwen capsules. During Omicron infection, the patient had normal SaO₂, a poor mental state, generalized weakness, as well as jaundice, hypoproteinemia, and electrolyte disturbance; after symptomatic treatment, the patient’s general state became stable, and there was no apparent aggravation of symptoms. Time-course detection of lymphocyte subsets and cytokines is shown in Supplementary Figures 5 , 6 . On 30 April 2022, TBIL was tested at 29.8 μmol/L. On 4 May 2022, RT-PCR test result of pharyngeal swab sample was negative ( Table 3 ). On 15 May 2022, the patient’s test results indicated aggravated liver dysfunction with TBIL 81.4 μmol/L; after active symptomatic treatment, the patient had an improved state. On 21 May 2022, TBIL was tested at 37.8 µmol/L. Now this patient has stable disease without jaundice.