Introduction

Mpox, formerly known as monkeypox, is a zoonotic disease caused by the mpox virus (MPXV). The first human case was identified in the Democratic Republic of the Congo (DRC) in 19701. Common symptoms include skin rashes or mucosal lesions that can last 2–4 weeks, often accompanied by fever, headache, back pain, muscle aches, low energy, and swollen lymph nodes2. Most people fully recover; however, pregnant women, children, and people with weakened immune systems are at higher risk for serious illness and death due to complications from mpox. Traditionally, most mpox cases were linked to animal transmission through bites, scratches, or activities such as hunting, skinning, trapping, cooking, playing with carcasses, or eating infected animals. Recent studies have shown that MPXV can also be transmitted from person to person through close contact with patients with mpox. This includes skin-to-skin contact (such as touching or sex) and mouth-to-mouth or mouth-to-skin contact (such as kissing). Moreover, infection can occur through face-to-face exposure to individuals with mpox or contact with contaminated objects such as clothing or linens, as well as through needle injuries in healthcare settings or in community environments such as tattoo parlors3.

MPXV is an enveloped, double-stranded DNA virus belonging to the Orthopoxvirus genus in the Poxviridae family, which also includes variola, vaccinia, cowpox, and other viruses. There are two distinct clades of the virus: clade I (with subclades Ia and Ib) and clade II (with subclades IIa and IIb). Clade II caused the first mpox outbreak outside Africa, which occurred in the United States in 20034. On 6 May 2022, a United Kingdom national returning from Nigeria was confirmed to be infected with MPXV clade IIb5. Subsequently, an outbreak of mpox suddenly emerged and rapidly spread across Europe, the Americas, and eventually all six World Health Organization (WHO) regions6,7,8,9. On 23 July 2022, the WHO declared it as a Public Health Emergency of International Concern (PHEIC). Notably, the global outbreak has primarily affected gay, bisexual, and other men who have sex with men, spreading person-to-person through sexual networks.

In 2024, the number of mpox cases increased, and clade Ib appeared to be the predominant strain. As of 8 September 2024, 15 countries in Africa had reported 5759 confirmed mpox cases, including 32 deaths. On 14 August 2024, under the International Health Regulations, the WHO Director-General declared that the rise in mpox cases in the DRC and their spread to neighboring countries constituted a PHEIC3,10. As of 15 December 2024, in Africa, MPXV clade Ib has been detected in the DRC, Burundi, Kenya, Rwanda, Uganda, Zambia, and Zimbabwe. Additionally, 12 countries outside Africa have reported cases of MPXV clade Ib. Sweden, Thailand, Germany, the United States, and Canada have each detected a single case among travelers from affected countries in East and Central Africa. The United Kingdom has reported five cases: two among travelers from affected countries in East Africa and three household contacts of one of these travelers. India and Pakistan have each reported a single case among travelers from the United Arab Emirates. However, no cases of mpox due to MPXV clade Ib have been reported by the United Arab Emirates to date11.

The first imported mpox case in China was reported in September 2022, and the first domestic mpox case was reported in May 202312,13. As of December 2024, more than 2000 mpox cases had been identified in China, all involving MPXV clade IIb14. On 11 January 2025, the WHO announced the detection of five cases of clade Ib in China. One case was linked to recent travel to the DRC, while four subsequent cases were identified among close contacts15,16. We reported the first confirmed case of MPXV clade Ib in China, identified among the four subsequent cases17. In this study, we present the epidemiological, clinical, and virological characteristics of the case, along with findings from the field investigation. We also discuss the efficient transmission mode of MPXV clade Ib and relevant public health measures to control the potential risk.

Results

Symptoms and hospital admission

The patient, 28-year-old woman from South Africa, was employed as an teacher at a kindergarten in Haiyan County, Jiaxing City, Zhejiang Province, China. On 21 December 2024, she experienced nonspecific discomfort but did not seek medical attention. On 23 December, pinprick-like lesions developed on her arm, accompanied by myalgia. On 25 December, she reported periumbilical, left abdominal, and back pain. A computed tomography scan revealed enlarged inguinal lymph nodes, but no vesicular rash was observed. On 30 December, the 10th day post-onset (DPO), the patient presented to the hospital’s infectious disease department with a headache (afebrile) and widespread vesicular lesions affecting the extremities, face, buttocks, trunk, palms, and dorsal aspects of the hands. Notably, no lesions were observed in the oral cavity, perineum, or anus (Fig. 1). The rash was pruritic, and some lesions were crusted. The attending physician suspected mpox and notified the local Centers for Disease Control and Prevention (CDC). Following diagnosis, the patient was admitted for treatment under isolation and received supportive medical care; no specific antiviral treatment was administered. From the 11th DPO (the second day of hospitalization), no new lesions developed, and recovery progressed rapidly. By the 18th DPO, only vesicles remained on the dorsum of the right foot and in the finger web spaces, while lesions in other areas had crusted or sloughed off. By the 24th DPO (13 January 2025), all lesions had resolved, and the patient was discharged after a total of 15 days of hospitalization.

Fig. 1
Fig. 1
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Skin rashes on the right arm, abdomen, back, and foot.

During the patient’s hospitalization, a total of 59 samples were collected, including 36 skin lesion swabs obtained from various body sites, 12 detached scabs, 7 oropharyngeal swabs, 2 urine samples, 1 rectal swab, and 1 plasma sample (Table 1). Of these, 55 samples tested positive for MPXV by polymerase chain reaction (PCR), with Ct values ranging from 18.10 to 36.00. While the positivity rate for oropharyngeal swabs was 42.9%, all other specimen types had a positivity rate of 100%. Samples collected on the 11th DPO showed the highest viral load of MPXV in the skin lesions, followed by the oropharyngeal swabs, while the plasma showed comparatively lower viral loads. The oropharyngeal swabs turned negative, with no detectable virus by the 16th DPO. However, the skin lesion samples, urine samples, and scab specimens continued to test positive through the 20th DPO. Notably, the scab samples consistently exhibited high viral loads (Ct values of <30) throughout the testing period. These findings emphasize the clinical relevance of our epidemiological data and set the stage for our subsequent epidemiological investigation.

Table 1 PCR Test Results of Different Specimen Types from the Patient at Various Days Post-Onset
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Epidemiological investigation

The patient reported no history of smallpox or mpox vaccination. She had not left Haiyan County, Jiaxing City, in the 21 days prior to illness onset, except for traveling to Guangzhou City, Guangdong Province, on 14–15 December and 28–29 December. Because of language barriers and other challenges, the patient engaged in a few local social activities in Haiyan County. Apart from daily teaching, which included high-fiving and other classroom interactions along with the use of teaching materials, she spent most of her time at home and ordered food delivery for each meal.

On 14 December 2024, the patient flew to Guangzhou, Guangdong Province and had sexual contact with male Friend A on the same day. She also had dinner and engaged in ceremonial kissing and hugging with male Friend B. In addition, she spent approximately 2 h in a room with Friend C. The patient reported no other history of sexual contact and returned Haiyan County by plane on 15 December (Fig. 2). After her illness onset, she made a brief round trip between Haiyan County and Guangzhou on 28–29 December.

Fig. 2
Fig. 2
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Timeline of illness onset and activities of the first confirmed human infection with mpox clade Ib virus in China.

The source tracing investigation and related responses revealed that Friend A flew from the DRC on 4 December and arrived at Guangzhou, China, on 5 December before traveling to Yunnan Province later that same day. He returned to Guangzhou on 13 December. Friend A reported no recent mpox-related symptoms, such as fever or rash. However, a physical examination on 10 December showed the following abnormalities: low white blood cell count of 3.32 × 109/L (reference range: 3.5–9.5 × 109/L), low neutrophil count of 1.57 × 109/L (reference range: 1.8–6.3 × 109/L), low hematocrit of 50.4% (reference range: 40.0%–50.0%), high eosinophil percentage of 8.1% (reference range: 0.4%–8.0%), high basophil percentage of 1.5% (reference range: 0.0%–1.0%), and high aspartate aminotransferase concentration of 44.0 U/L (reference range: 0–40 µ/L). A throat swab from Friend A was collected on 2 January 2025. Environmental swabs were also collected from his two residences: Apartment A in Yunnan Province (where he lived from 5–11 December) and Apartment B in Guangzhou, Guangdong Province (where he had been living since 19 December) Quantitative PCR (qPCR) revealed that his throat swab was negative, but five environmental samples tested positive. These included two swabs from a razor (Ct 36.3 and 37.03) in Apartment A and swabs from the bed (Ct 34.28), refrigerator (Ct 37.44), and sofa (Ct 38.12) in Apartment B. Despite the environmental contamination, Friend A reported that he had purchased the razor for personal use on 11 December but had not used it since and had left it at the patient’s home. These findings suggest that Friend A had likely been shedding the virus beginning on 11 December. By contrast, Friends B and C reported no suspected symptoms of mpox in the 21 days before and after their date of contact with the patient. Their throat swabs and environmental samples from their residences were all negative. Furthermore, no mpox cases had been previously reported in Haiyan County. Based on the positive nucleic acid results from Friend A’s environmental samples, the abnormalities in his routine blood tests, and the exclusion of other possible sources of infection, Friend A is considered the likely origin of the patient’s infection.

Environmental samples were collected from the patient’s living space, workplace, and other locations she visited. Of the 95 environmental samples collected, 8 tested positive for MPXV, with Ct values ranging from 27.79 to 37.98. Positive samples were found in her living room, at her workplace, and in a classroom; on chair armrests used during meals with a family; and on the door handle of a car belonging to a kindergarten staff member. However, no mpox virus was successfully cultured from any of the environmental samples.

Contact tracing

In total, 211 contacts were identified and classified according to their risk of infection (Table 2). Among those at high risk, one house cleaner had cleaned the patient’s room on 30 December and was exposed to potential contaminants. Two taxi drivers had prolonged close contact with the patient in confined spaces (approximately 1 h 20 min). One kindergarten staff member had multiple long-term close contacts with the patient. A family of four had meals with the patient ~ 1 h 10 min. Eighteen individuals (17 children and 1 staff member in her residential community) were classified as medium risk because of their direct physical contact with the patient. All remaining contacts were considered general contacts, having shared the same space without direct interaction. Serum antibody tests were later conducted on five close contacts, and all results were negative.

Table 2 Contacts of the first confirmed mpox clade Ib case, China, October 2024
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Different management measures were implemented based on the contact’s risk level. All contacts were monitored for 21 days and instructed to report any symptoms. High-risk contacts were required to remain at home in quarantine for the first 7 days, after which they underwent an additional 14 days of follow-up. Both high- and medium-risk contacts were sampled on the 7th day after their last exposure to the patient and tested for mpox. During the 21-day observation period, 13 individuals developed nonspecific symptoms (7 had fever, 2 had cough, 2 had pharyngitis, 1 developed vomiting, and 1 had a stuffy nose). Specimens were collected from all symptomatic individuals. All samples tested negative for mpox; however, two were positive for H1N1 influenza A, and one was positive for metapneumovirus.

Virus detection

The qPCR result from the patient’s first throat swab sample was positive for mpox nucleic acid, with a Ct value of 22. Using Nanopore sequencing technology, we obtained the complete genome of MPXV from samples taken from a skin lesion on the arm and from the throat swab. The genome was 195,313 bp in length, and the strain was designated MPXV ZJ-JX-2025. The sequencing results indicated that the mpox virus isolate in this study belonged to genotype Ib (Fig. 3). All publicly available MPXV clade Ib sequences with > 85% genome coverage were collected from the global public databases NCBI and GISAID.

Fig. 3: Phylogenetic tree analysis of the 378 MPXV clade Ib sequences from GISAID.
Fig. 3: Phylogenetic tree analysis of the 378 MPXV clade Ib sequences from GISAID.
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The red area represents the MPXV clade Ib sequence first isolated in China (mpxv strain ZJ-JX-2025), the yellow area represented the MPXV clade Ib sequences originating from Democratic Republic of Congo (hMpxV/Congo/BZV-LNSP-CG001/2024, hMpxV/Congo/BZV-LNSP-CG018/2025, hMpxV/Congo/BZV-LNSP-CG021/2025, hMpxV/Congo/BZV-LNSP-CG022/2025).

The phylogenetic analysis showed that the genome sequence of MPXV strain ZJ-JX-2025 was most closely related to sequences from the DRC (hMpxV/Congo/BZV-LNSP-CG001/2024, -CG018/2025, -CG021/2025, and -CG022/2025), all collected from December 2024 to February 2025. As expected, given the conserved nature of the mpox virus genome, ZJ-JX-2025 also showed close similarity to other sequences, including those originating from Thailand (hMpxV/Thailand/NIC-31/2024), Kenya (hMpxV/Kenya/KEMRI-00107/2024), and Uganda (hMpxV/Uganda/UVRI-MP512/2024).

Compared with the MPXV strain DQ011155.1 (MPXV strain Zaire_1979-005, complete genome), our analysis identified 141 nucleotide sites with missense mutations. When compared with other clade Ib sequences, we found 35 mutations in hMpxV/Congo/BZV-LNSP-CG001/2024, 25 mutations in hMpxV/DRC/HGRK-23/2024, 19 mutations in hMpxV/Sweden/PHAS-506/2024, 26 mutations in hMpxV/DRC/HGRK-45/2023, 20 mutations in hMpxV/Thailand/NIC-31/2024.

Discussion

After the emergence of a new sub-lineage of MPXV clade I, the WHO declared the upsurge of mpox in the DRC and its spread to a growing number of African countries to constitute a PHEIC on 14 August 202418. The new clade Ib of MPXV is estimated to have emerged in mid-September 2023 in the DRC and has since spread to Burundi, Kenya, Rwanda, Uganda, and other countries. In addition, travel-associated clade Ib cases have been confirmed in several other regions, including European countries (Sweden, Germany, and the United Kingdom), Southeast Asian countries (Thailand and India), and the United States, where they have also caused continued clustered outbreaks within families19,20,21. Although a few published studies have revealed sustained human outbreaks of clade I and suggested its association with more severe clinical symptoms, the currently available data remain limited22,23.

The current case was the first confirmed infection with MPXV clade Ib in China, notably involving a female patient infected through heterosexual contact. This was confirmed through epidemiological investigation, virus sequencing, and phylogenetic analysis. As such, the case holds value for exploring symptom presentation, clinical course, modes of transmission, virus shedding dynamics, and risk management strategies. These insights will contribute to a better understanding of the epidemiology of MPXV clade Ib and the development of effective case management strategies.

Clinical features

We examined the clinical features of this clade Ib case. A retrospective investigation revealed that the patient first experienced nonspecific discomfort, followed 2 days later by the appearance of pinprick-like lesions on the arms. Widespread skin rashes affecting the extremities, face, buttocks, trunk, palms, and dorsum of the hands were observed by the 10th DPO. However, no lesions were identified in the oral cavity, perineum, or anus. This clinical pattern differed from clade Ia outbreaks reported elsewhere, where 89% of patients had genital skin lesions, and the mean lesion density was highest in the genital area among adults.

In addition to the above-described typical symptoms, this patient also presented with abdominal pain, back pain, and headache. A computed tomography scan revealed inguinal lymphadenopathy. These signs and symptoms were nonspecific and contributed to the difficulty of achieving an early diagnosis. Attention should be paid to such nonspecific symptoms, which may be mistaken for other common viral infections (e.g., respiratory or intestinal infections) in the early stages of mpox. It is therefore important to strengthen the differential diagnosis to ensure that patients are assessed promptly and accurately. This requires clinicians to maintain a high level of vigilance and diagnostic sensitivity, enabling timely viral testing and screening to guide appropriate treatment options and avoid misdiagnosis and delays in care.

Previous studies have shown that vaccination against smallpox can provide cross-protective immunity against mpox, potentially reducing disease severity and transmission risk24. The severity of disease is higher for clade 1a (case fatality rate of up to 12%) than for other clades (case fatality rate of 0.0%–3.6%)3. The patient in this case had not been vaccinated against smallpox or mpox; however, she did not develop severe symptoms. Given the evolving nature of MPXV, ongoing research and robust public health responses remain essential for managing potential future outbreaks.

Pathogenetic features

Since the emergence of the newly identified MPXV clade I in September 2023, limited data have been available on viral shedding dynamics in patients infected with clade Ib. To address this, we analyzed virus detection across various sample types and examined temporal viral load trends to gain further insight. In total, 59 consecutive samples were obtained from different body sites during hospitalization. Skin lesions showed higher viral loads than oropharyngeal swabs, as indicated by lower Ct values. Additionally, skin lesion swabs maintained stable viral loads up to the 20th DPO, in contrast to oropharyngeal swabs, which showed a notable decline and turned negative by the 16th DPO. Our data suggest that skin lesion swabs are the most sensitive sample type for diagnostic purposes, supporting the WHO-recommended sampling strategy and aligning with previous research22,25. Notably, urine samples in this case exhibited viral loads and clearance dynamics comparable to those of skin lesions, an observation that contrasts with prior studies in which urine yielded the lowest positivity rates22,26. It remains unclear whether clade Ib contributes to the high and consistent viral load observed in urine. Further investigation into the shedding kinetics of MPXV clade Ib is warranted. These findings also emphasize the importance of multisite sampling to enhance diagnosis sensitivity. Stable and high MPXV loads were observed in detached scabs collected from bedclothes during hospitalization, underscoring the need for strengthened disinfection procedures, personal protective measures, and strict nosocomial infection prevention guidelines for healthcare workers.

Through phylogenetic analyses of clade Ib sequences from the GISAID database, we found that the sequence from the present case shared a close genetic relationship with strains originating from the DRC. The timeline also aligns with the period during which clade Ib was introduced into China, suggesting that the virus was geographically imported27. A previous study also revealed that the genetic sequence of MPXV in this case was predominantly clustered with MPXV clade Ib sequences28. Future studies are needed to further define the functional and epidemiological significance of these mutations, which will help to guide risk assessment as well as prevention and control strategies for mpox.

Transmission pathways

According to the WHO, intimate contact—including kissing, hugging, touching, sexual contact, and mother-to-fetus transmission—is the primary mode of mpox transmission29. While many cases have been linked to transmission among men who have sex with men, our detailed epidemiological investigation confirmed that heterosexual sex can also lead to infection. Furthermore, research conducted in Africa has revealed a higher prevalence of infection among household contacts1, particularly children. However, the patient in this case lived alone and had limited close contact with family members3. Aside from possible droplet exposure, such as shared meals and spending more than 1 h in a taxi with others, the patient’s occupation also involved physical touch and close interaction with children. To assess the risk of transmission by exposure type, we conducted a thorough evaluation during contact management. Environmental samples were retrospectively collected to provide evidence-based data supporting the risk assessment.

Based on direct contact and environmental evidence—including positive swabs from a restaurant chair on the 4th DPO, positive swabs from the armrest of a private car used by the patient on the 5th DPO, and multiple positive environmental swabs from the patient’s residence—8 close contacts were identified and classified as high-risk among the total 211 contacts. None of these individuals became infected during the 21-day follow-up period. Our study provides preliminary observational findings on the transmission potential of MPXV clade Ib, suggesting that non-sexual contact—such as sharing a confined indoor space, intermittent direct physical touch, face-to-face conversation within 1 meter, or riding in the same car for more than 1 h—might not constitute efficient transmission routes for this clade. Other studies have reported the possibility of contracting mpox through contaminated items such as clothing or bedding, needlestick injuries in healthcare settings, or in community environments such as tattoo parlors30.

Despite the possibility of contact with contaminated surfaces, no viral transmission was observed from these exposures. Some studies have shown that individuals may be infectious before the onset of visible symptoms, although this is considered rare. Others suggest that mildly ill patients may be infectious for a few days before and after symptom onset, which can make early detection difficult31,32. In addition, mildly symptomatic individuals may still transmit the virus via droplets during active illness, especially in confined spaces22. Because of the limitations of epidemiological investigation techniques, the traceability investigation for Friend A was conducted long after his arrival from the Congo. By that time, he may have recovered and tested negative for viral nucleic acid. Although Friend A reported no recent mpox-related symptoms such as fever or rash, the presence of viral nucleic acid in his environment indicates the possibility that asymptomatic or mildly symptomatic individuals can transmit the virus.

Public health implications

The emergence of the first case of mpox drew significant attention from local government units. The patient was immediately placed in isolation, her clinical course was closely monitored, and health surveillance and management measures were implemented for individuals at key risk. Authorities rapidly and comprehensively investigated risk points and controlled at-risk groups. A detailed investigation was conducted to trace close contacts in kindergartens, nursing homes, hospitals, taxis, shared meal environments, and other settings the patient had visited during the 4 days prior to illness onset.

In addition, an epidemiological investigation was carried out, including detailed and accurate tracing of the patient’s activities during the 21 days prior to illness onset, investigation of possible sources of infection, and coordination with other provinces for joint investigations and surveys. Environmental sampling and final disinfection were carried out in kindergartens, nursing homes, hospitals, and other relevant locations.

In summary, we confirmed the first case of MPXV clade Ib in China and described the clinical characteristics of the patient. She presented with disseminated vesicular lesions involving the extremities, face, buttocks, trunk, palms, and dorsum of the hands, with no lesions observed in the oral cavity, perineum, or anus. The oropharyngeal swab turned negative by the 16th DPO, while skin lesion samples, urine samples, and scab specimens remained positive through the 20th DPO. Consecutive scab samples consistently exhibited high viral loads throughout the testing period, indicating that infection can persist for an extended duration.

Sexual contact with an asymptomatic patient can result in MPXV transmission. The infection risk associated with other types of exposure requires further study.

Methods

Case definition

According to the mpox prevention and control guideline issued by the National Disease Control and Prevention Administration of China in July 2023, a suspected mpox case is defined as an acute rash with fever or lymphadenopathy who had epidemiological history within 21 days32. Confirmed mpox cases were defined as meeting the criteria for suspected mpox and also met one of the following criteria33: (a) detection of MPXV RNA by a molecular method from patient serum, (b) isolation of MPXV in cell culture.

Investigation and data collection

An epidemiological investigation was conducted by the staff of the Chinese Center for Disease Control and Prevention (China CDC), Zhejiang Provincial Center for Disease Control and Prevention (Zhejiang CDC), Jiaxing Center for Disease Control and Prevention (Jiaxing CDC), and Haiyan Center for Disease Control and Prevention (Haiyan CDC). Exposure history of the patient and information about demographic features, such as age, gender, occupation, and residential address, exposure history, clinical signs and symptoms, date of illness onset and confirmation were collected. Samples including oropharyngeal swab, skin lesion swab, plasma, urine, rectal swab, detached scabs of the patient and swabs of door handles, toilet seats, switches, handrails of patient relevant environment were collected for testing using the assay of reverse transcription-polymerase chain reaction (RT-PCR). The study was conducted in accordance with the Declaration of Helsinki, and ethical approval was conducted by Zhejiang Provincial Center for Disease Control and Prevention. The aims of our study were explained to the patient, and written informed consent was obtained.

Contact tracing

As this is the first confirmed clade Ib mpox case, a highly sensitive contact definition that included all persons who had close contact with the patient 4 days before onset was adopted. A team of experts, comprising epidemiologists, pathogen specialists, and clinical doctors, assessed the risk level of these contacts by evaluating environmental sample test results, the nature of the contact, and the duration of exposure. Indoor contaminated environmental staying, intermittent direct physical touch, face-to-face conversation within 1 meter and sharing a car carriage for >1 h was considered to be at high risk. Direct physical contacts once were considered to be at middle risk, and other general contacts were considered to be at low risk. Health monitoring was conducted, and all contacts were required to report any symptoms for 21 days.

MPXV detection and phylogenetic analysis

Clinical specimens, including vesicular fluid and oropharyngeal swabs, were collected from different sites on different days. The real-time PCR diagnostic kit for the rapid detection of MPXV (Zhuocheng Huisheng Biotechnology Co., LTD, Beijing) was used and showed that the samples were positive for MPXV by the local CDC. The limit of detection (LOD) of the kit is 200 copies/mL. They were then confirmed and identified as MPXV clade Ib by the Zhejiang provincial CDC on December 31th. The assay contains the probe34 with a 5’-reporter molecule (FAM) and a 3’-quencher molecule: (BHQ1) 5’-FAM-ATATTCAGGCGCATATCCACCCACGT-BHQ-3’, forward primer: 5’-AAGACTTCCAAACTTAATCACTCCT-3’ and reverse primer: 5’-CGTTTGATATAGGATGTGGACATTT-3’.

DNA samples were treated with a DNA repair and end-prep kit (BAIYITECH, Hangzhou), which includes enzymes that repair nicks, gaps, and other types of DNA damage. Following DNA repair, native barcodes were ligated to the DNA fragments. These barcodes are unique sequences that allow for multiplexing of samples during sequencing, enabling the identification of individual samples within a mixed library. Then, these adapters are essential for the sequencing process, as they facilitate the binding of DNA fragments to the sequencing flow cell. The library was then loaded onto the flow cell, ensuring an even distribution of the DNA fragments across the surface. After washing the flow cells, the genomic data were read by Nanopore.

The phylogenetic tree was constructed by combining the virus genome sequence from case samples with genome sequences submitted by different institutions. We used 378 clade Ib sequences from GISAID and NCBI at different times (Supplementary Data 1). Phylogenetic tree analysis was conducted using the Maximum Likelihood method with IQ-TREE (version 2.0.3, available at https://github.com/iqtree/iqtree2, accessed on 1 April 2025). The results were handled and visualized with iTOL (https://itol.embl.de/, accessed on 1 April 2025).

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.