A scientific journey from airport testing to genomic sequencing that uncovered the first imported BA.4 case in Guangdong Province
On April 29, 2022, a routine international flight touched down at Guangzhou Baiyun International Airport after departing from Amsterdam. Among the passengers was a 20-year-old Chinese woman who had completed her COVID-19 vaccination series and tested negative before departure. Like all arriving passengers, she underwent routine SARS-CoV-2 testing at the airport. The next day, public health authorities received an unexpected result: positive for COVID-19. The patient was immediately transferred to a specialized hospital for isolation and treatment, launching a scientific investigation that would uncover something remarkable—the first imported case of the Omicron subvariant BA.4 in China 1 .
This incident represented more than just another COVID-19 case. It marked the arrival of a new Omicron subvariant that was already causing concern among virologists worldwide. The discovery triggered an intensive scientific response to characterize the virus and understand its potential implications for China's pandemic response. The identification and analysis of this case provided a crucial window into the continuing evolution of SARS-CoV-2 and the relentless work of scientists tracking its movement across the globe.
First identification of Omicron BA.4 in China, highlighting global viral spread.
Immediate genomic sequencing and analysis to understand the variant's characteristics.
Illustrated the continuous evolution of SARS-CoV-2 and importance of surveillance.
When scientists at the laboratory received the patient's sample, they immediately began the painstaking process of genomic sequencing to decipher the genetic code of the virus that had infected her. Using the Illumina MiniSeq platform, they assembled the complete viral genome, allowing them to compare its mutations against known variants 1 .
The results revealed that this was no ordinary Omicron virus. The genomic analysis showed the virus belonged to the Omicron BA.4 sublineage, characterized by a distinctive pattern of mutations in the spike protein—the part of the virus that enables entry into human cells. The BA.4 variant possessed a total of 30 amino acid mutations and 5 deletions in the spike protein gene, creating a genetic profile that differed significantly from earlier Omicron subvariants 1 .
The L452R mutation was familiar to virologists, as it had been a defining feature of the Delta variant that caused devastating waves of COVID-19 in 2021. This mutation was known to enhance the binding affinity between the virus and human ACE2 receptors, potentially making the virus more infectious 2 3 .
The F486V mutation was more unusual and concerning. Analysis of global databases revealed this mutation had appeared in only 54 of 10 million sequenced coronavirus genomes before BA.4 emerged. Scientists recognized that mutations at the F486 location were associated with reduced neutralizing activity from antibodies, suggesting this change might help the virus evade immunity from prior infection or vaccination 3 .
| Mutation | Location | Function | Present in Other Variants |
|---|---|---|---|
| L452R | RBD | Enhances binding to ACE2 receptors; increases infectivity | Delta variant |
| F486V | RBD | Reduces antibody recognition; promotes immune escape | Rare in previous variants |
| 69-70 deletion | NTD | May enhance infectivity; causes S-gene target failure | Alpha variant, Omicron BA.1 |
| Q493 reversion | RBD | Wild-type amino acid; may affect antibody binding | Not in other Omicron subvariants |
Table 1: Key Spike Protein Mutations in BA.4 Compared to Other Variants
Additionally, BA.4 shared the 69-70 deletion in the spike protein with the Alpha variant and Omicron BA.1. This deletion provided a practical benefit for detection—it caused S-gene target failure in certain PCR tests, creating a proxy marker that allowed laboratories to quickly suspect potential BA.4 cases without full genomic sequencing 3 .
The confirmation of BA.4 involved a multi-step laboratory investigation that combined cutting-edge technology with meticulous analytical methods. The process began when the patient tested positive during routine quarantine screening on April 30, 2022. A nasopharyngeal swab sample was immediately retested on May 1 for confirmation before being sent for advanced genomic analysis 1 .
Scientists used the Illumina MiniSeq platform, a workhorse of modern genomics, to sequence the viral genome from the patient's sample. This technology works by fragmenting the viral RNA into small pieces, converting it to DNA, then amplifying and sequencing these fragments. Sophisticated software reassembles these fragments into a complete genomic sequence by comparing them to reference sequences 1 .
Once the sequence was assembled, researchers employed phylogenetic analysis—a method that reconstructs evolutionary relationships among viruses based on genetic similarities. They compared the patient's virus sequence with others in global databases and discovered it clustered closely with a BA.4 sequence detected in Denmark around the same time (GISAID: EPI_ISL_12648960). This phylogenetic relationship suggested possible transmission routes and provided insights into the global spread of this emerging subvariant 1 .
Flight arrival from Amsterdam
Patient enters China
Initial positive SARS-CoV-2 test
Case detection
Confirmatory test positive
Case confirmation
Genomic sequencing completed
BA.4 subvariant identification
Phylogenetic analysis
Determination of similarity to Danish BA.4 sequence
Table 2: Timeline of BA.4 Detection and Analysis in the Guangdong Case
The entire process—from sample collection to genomic characterization—took just five days, demonstrating the remarkable speed of modern viral surveillance systems. The sequence was promptly deposited in the National Genomics Data Center under accession number WGS025540, making it available to researchers worldwide 1 .
The detailed genetic analysis provided crucial insights into why BA.4 was concerning to public health experts. The combination of mutations gave BA.4 two distinct advantages over its viral predecessors: enhanced transmissibility and immune evasion capabilities.
The phylogenetic analysis revealed that BA.4 and its close relative BA.5 likely originated from a common ancestor in mid-November 2021, around the same time other Omicron lineages were emerging. This suggested parallel evolution occurring within a potentially discrete reservoir—possibly immunocompromised individuals with chronic infections or animal hosts—that allowed the virus to accumulate mutations without immediate selective pressure from population immunity 3 .
Bayesian phylogenetic methods demonstrated that BA.4 and BA.5 were genetically distinct from other Omicron lineages despite sharing similarities with BA.2 in their spike proteins. The analysis suggested early dispersal of BA.4 from Limpopo to Gauteng in South Africa, followed by international spread to Europe and Asia 3 .
Laboratory studies would later confirm that BA.4 exhibited significant immune escape from neutralizing antibodies generated by previous vaccination or infection. This immune evasion was particularly notable against immunity derived from earlier Omicron BA.1 infections. Research showed that the plasma from triple-vaccinated individuals or those with BA.1 infections had reduced neutralizing activity against BA.4 and BA.5 1 2 .
The functional properties of BA.4 also differed from earlier variants in how it entered human cells. Unlike the Delta variant, which relied heavily on the TMPRSS2 protease for cell entry (facilitating lung infection), BA.4 primarily used the endocytic pathway—an alternative entry mechanism that may contribute to its preference for upper respiratory tract infection and potentially milder clinical presentation 2 .
| Research Tool | Function | Application in BA.4 Investigation |
|---|---|---|
| Illumina MiniSeq Platform | Next-generation sequencing | Viral genome sequencing from patient samples 1 |
| Synthetic RNA Controls | Quality control for diagnostic tests | Verification and validation of RT-PCR and NGS assays 9 |
| SARS-CoV-2 Neutralizing Antibody ELISA Kits | Detection of neutralizing antibodies | Measuring immune responses to BA.4 and other variants 4 |
| Twist Comprehensive Viral Research Panel | Target enrichment for NGS | Detection and characterization of viral samples 9 |
| TaqPath COVID-19 qPCR Assay | SARS-CoV-2 detection with S-gene target | Presumptive identification of BA.4 through SGTF 3 |
Table 3: Essential Research Reagents for SARS-CoV-2 Variant Surveillance
The identification of BA.4 in Guangdong occurred against the backdrop of an ongoing global battle against successively evolving Omicron subvariants. Understanding this case required situating it within the broader narrative of viral evolution and pandemic response.
BA.4 first emerged in South Africa in early 2022, where it initiated the fifth wave of COVID-19 infections. Along with its sister lineage BA.5, BA.4 rapidly displaced the previously dominant BA.2 variant, accounting for over 50% of sequenced cases in South Africa by the first week of April 2022 3 . The rapid growth advantage of BA.4 and BA.5 was estimated at 0.08 and 0.10 per day respectively over BA.2 in South Africa 3 .
By May 2022, when the Guangdong case was detected, BA.4 infections had been reported in at least 20 countries, with the majority (62.39%) still in South Africa 1 . The World Health Organization had issued a reminder on May 4, 2022—the same day the Guangdong case was sequenced—for countries to closely monitor the Omicron BA.4 subvariant due to its potential to drive new infection waves 1 .
The detection of this imported BA.4 case triggered enhanced surveillance measures in China. The country's "zero-COVID" policy at the time relied on early detection and rapid containment of imported cases to prevent domestic transmission. The 14-day quarantine period for international travelers—which enabled detection of this case—proved crucial in identifying this imported instance before community spread could occur 1 .
From a clinical perspective, BA.4 and BA.5 infections tended to manifest differently than earlier variants. Instead of the lower respiratory symptoms that characterized previous strains, these newer subvariants primarily caused upper respiratory symptoms—sore throat, cough, and nasal congestion—similar to common colds. This change in symptom profile was attributed to alterations in how the virus entered cells, with reduced reliance on TMPRSS2 potentially limiting lung infection 2 .
Despite generally causing less severe acute disease than Delta, Omicron subvariants including BA.4 still posed significant health threats, particularly to vulnerable populations. Epidemiological patterns suggested that evolving Omicron subtypes were acquiring characteristics similar to seasonal influenza but with higher mortality rates 2 . Additionally, post-COVID symptoms persisted in a substantial proportion of cases, with studies indicating that 30% to 90% of patients experienced lingering effects up to 6 months after initial illness 2 .
The identification and characterization of China's first imported BA.4 case represents more than just a footnote in pandemic history. It illustrates the critical importance of robust genomic surveillance systems in tracking emerging pathogens. The rapid detection and analysis of this case provided valuable lead time for public health authorities to prepare for potential future waves driven by this variant.
This viral detective story also highlights the ongoing evolutionary arms race between pathogens and human immunity. The mutations that defined BA.4—particularly L452R and F486V—represent the virus's continued efforts to adapt to population immunity while maintaining infectiousness. As one research team noted, "The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir... is potentially contributing to further evolution and dispersal of the virus" 3 .
Nearly three years after this case was detected, COVID-19 continues to evolve, with Omicron lineages successively displacing one another. The scientific infrastructure and knowledge gained from tracking variants like BA.4 have created a foundation for continued surveillance of future viral threats. As the pandemic transitioned to endemicity, the lessons learned from cases like the Guangdong BA.4 importation remain relevant for preparing for whatever viral challenges may emerge next.