diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index 7f7aba06d..a7591c284 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -1,8 +1,12 @@
 # -*- coding: utf-8 -*-
 """Store backfill data."""
+import calendar
 import os
 import glob
-from datetime import datetime
+import re
+import shutil
+from datetime import datetime, timedelta
+from typing import Union
 
 import pandas as pd
 
@@ -11,7 +15,7 @@
 
 gmpr = GeoMapper()
 
-def store_backfill_file(df, _end_date, backfill_dir):
+def store_backfill_file(df, _end_date, backfill_dir, logger):
     """
     Store county level backfill data into backfill_dir.
 
@@ -59,6 +63,7 @@ def store_backfill_file(df, _end_date, backfill_dir):
                         'num_age_0_17', 'den_age_0_17']
     backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
                                     selected_columns]
+    logger.info("Filtering source data", startdate=_start_date, enddate=_end_date)
     backfilldata["lag"] = [(_end_date - x).days for x in backfilldata["time_value"]]
     backfilldata["time_value"] = backfilldata.time_value.dt.strftime("%Y-%m-%d")
     backfilldata["issue_date"] = datetime.strftime(_end_date, "%Y-%m-%d")
@@ -70,19 +75,75 @@ def store_backfill_file(df, _end_date, backfill_dir):
         "state_id": "string"
     })
 
-    path = backfill_dir + \
-        "/quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
+    filename =  "quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
+    path = f"{backfill_dir}/{filename}"
     # Store intermediate file into the backfill folder
-    backfilldata.to_parquet(path, index=False)
+    try:
+        backfilldata.to_parquet(path, index=False)
+        logger.info("Stored source data in parquet", filename=filename)
+    except Exception: # pylint: disable=W0703
+        logger.info("Failed to store source data in parquet")
+    return path
 
-def merge_backfill_file(backfill_dir, backfill_merge_day, today,
-                        test_mode=False, check_nd=25):
+
+def merge_existing_backfill_files(backfill_dir, backfill_file, issue_date, logger):
     """
-    Merge ~4 weeks' backfill data into one file.
+    Merge existing backfill with the patch data included. This function is specifically run for patching.
 
-    Usually this function should merge 28 days' data into a new file so as to
-    save the reading time when running the backfill pipelines. We set a softer
-    threshold to allow flexibility in data delivery.
+    When the indicator fails for some reason or another, there's a gap in the backfill files.
+    The patch to fill in the missing dates happens later down the line when the backfill files are already merged.
+    This function takes the merged files with the missing date, insert the particular date, and merge back the file.
+    Parameters
+    ----------
+    issue_date : datetime
+        The most recent date when the raw data is received
+    backfill_dir : str
+        specified path to store backfill files.
+    backfill_file : str
+        specific file add to merged backfill file.
+    """
+    new_files = glob.glob(backfill_dir + "/quidel_covidtest_*")
+
+    def get_file_with_date(files) -> Union[str, None]:
+        # pylint: disable=R1716
+        for filename in files:
+            # need to only match files with 6 digits for merged files
+            pattern = re.findall(r"_(\d{6,6})\.parquet", filename)
+            if pattern:
+                file_month = datetime.strptime(pattern[0], "%Y%m").replace(day=1)
+                end_date = (file_month + timedelta(days=32)).replace(day=1)
+                if issue_date >= file_month and issue_date < end_date:
+                    return filename
+        # pylint: enable=R1716
+        return ""
+
+    file_name = get_file_with_date(new_files)
+
+    if len(file_name) == 0:
+        logger.info("Issue date has no matching merged files", issue_date=issue_date.strftime("%Y-%m-%d"))
+        return
+
+    logger.info("Adding missing date to merged file", issue_date=issue_date,
+        filename=backfill_file, merged_filename=file_name)
+
+    # Start to merge files
+    merge_file = f"{file_name.split('.')[0]}_after_merge.parquet"
+    try:
+        shutil.copyfile(file_name, merge_file)
+        existing_df = pd.read_parquet(merge_file, engine="pyarrow")
+        df = pd.read_parquet(backfill_file, engine="pyarrow")
+        merged_df = pd.concat([existing_df, df]).sort_values(["time_value", "fips"])
+        merged_df.to_parquet(merge_file, index=False)
+        os.remove(file_name)
+        os.rename(merge_file, file_name)
+    except Exception as e: # pylint: disable=W0703
+        os.remove(merge_file)
+        logger.error(e)
+    return
+
+def merge_backfill_file(backfill_dir, today, logger, test_mode=False):
+    """
+    Merge month's backfill data into one file.
 
     Parameters
     ----------
@@ -90,17 +151,12 @@ def merge_backfill_file(backfill_dir, backfill_merge_day, today,
         The most recent date when the raw data is received
     backfill_dir : str
         specified path to store backfill files.
-    backfill_merge_day: int
-        The day of a week that we used to merge the backfill files. e.g. 0
-        is Monday.
     test_mode: bool
-    check_nd: int
-        The criteria of the number of unmerged files. Ideally, we want the
-        number to be 28, but we use a looser criteria from practical
-        considerations
     """
-    new_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of_*")
+    previous_month = (today.replace(day=1) - timedelta(days=1)).strftime("%Y%m")
+    new_files = glob.glob(backfill_dir + f"/quidel_covidtest_as_of_{previous_month}*")
     if len(new_files) == 0: # if no any daily file is stored
+        logger.info("No new files to merge; skipping merging")
         return
 
     def get_date(file_link):
@@ -110,23 +166,24 @@ def get_date(file_link):
         return datetime.strptime(fn, "%Y%m%d")
 
     date_list = list(map(get_date, new_files))
-    earliest_date = min(date_list)
     latest_date = max(date_list)
 
     # Check whether to merge
     # Check the number of files that are not merged
-    if today.weekday() != backfill_merge_day or (today-earliest_date).days <= check_nd:
+    date_list = list(map(get_date, new_files))
+    num_of_days_in_month = calendar.monthrange(latest_date.year, latest_date.month)[1]
+    if len(date_list) < num_of_days_in_month:
+        logger.info("Not enough days, skipping merging", n_file_days=len(date_list))
         return
 
     # Start to merge files
+    logger.info("Merging files", start_date=date_list[0], end_date=date_list[-1])
     pdList = []
     for fn in new_files:
         df = pd.read_parquet(fn, engine='pyarrow')
         pdList.append(df)
     merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
-    path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
-        datetime.strftime(earliest_date, "%Y%m%d"),
-        datetime.strftime(latest_date, "%Y%m%d"))
+    path = backfill_dir + f"/quidel_covidtest_{datetime.strftime(latest_date, '%Y%m')}.parquet"
     merged_file.to_parquet(path, index=False)
 
     # Delete daily files once we have the merged one.
diff --git a/quidel_covidtest/delphi_quidel_covidtest/constants.py b/quidel_covidtest/delphi_quidel_covidtest/constants.py
index 8e4d37cb2..6caf51863 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/constants.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/constants.py
@@ -1,4 +1,6 @@
 """Registry for constants."""
+from datetime import datetime
+
 # global constants
 MIN_OBS = 50  # minimum number of observations in order to compute a proportion.
 POOL_DAYS = 7  # number of days in the past (including today) to pool over
@@ -49,3 +51,5 @@
     "age_65plus",
     "age_0_17",
 ]
+
+FULL_BKFILL_START_DATE = datetime(2020, 5, 26)
diff --git a/quidel_covidtest/delphi_quidel_covidtest/patch.py b/quidel_covidtest/delphi_quidel_covidtest/patch.py
new file mode 100644
index 000000000..9b5dd1ee8
--- /dev/null
+++ b/quidel_covidtest/delphi_quidel_covidtest/patch.py
@@ -0,0 +1,76 @@
+"""
+This module is used for patching data in the delphi_doctor_visits package.
+
+To use this module, you need to specify the range of issue dates in params.json, like so:
+
+{
+  "common": {
+    ...
+  },
+  "validation": {
+    ...
+  },
+  "patch": {
+    "patch_dir": "/Users/minhkhuele/Desktop/delphi/covidcast-indicators/doctor_visits/AprilPatch",
+    "start_issue": "2024-04-20",
+    "end_issue": "2024-04-21"
+  }
+}
+
+It will generate data for that range of issue dates, and store them in batch issue format:
+[name-of-patch]/issue_[issue-date]/quidel_covidtest/actual_data_file.csv
+"""
+from datetime import datetime, timedelta
+from os import makedirs
+
+from delphi_utils import get_structured_logger, read_params
+
+from .run import run_module
+from .constants import END_FROM_TODAY_MINUS
+
+def patch():
+    """
+    Run the quidel_covidtest indicator for a range of issue dates.
+
+    The range of issue dates is specified in params.json using the following keys:
+    - "patch": Only used for patching data
+        - "start_date": str, YYYY-MM-DD format, first issue date
+        - "end_date": str, YYYY-MM-DD format, last issue date
+        - "patch_dir": str, directory to write all issues output
+    """
+    params = read_params()
+    logger = get_structured_logger("delphi_quidel_covidtest.patch", filename=params["common"]["log_filename"])
+
+    start_issue = datetime.strptime(params["patch"]["start_issue"], "%Y-%m-%d")
+    end_issue = datetime.strptime(params["patch"]["end_issue"], "%Y-%m-%d")
+
+    logger.info(
+        "Starting patching",
+        patch_directory=params["patch"]["patch_dir"],
+        start_issue=start_issue.strftime("%Y-%m-%d"),
+        end_issue=end_issue.strftime("%Y-%m-%d"),
+    )
+    makedirs(params["patch"]["patch_dir"], exist_ok=True)
+    export_day_range = params["indicator"]["export_day_range"]
+
+    current_issue = start_issue
+
+    export_day_range -= END_FROM_TODAY_MINUS
+
+    while current_issue <= end_issue:
+        logger.info("Running issue", issue_date=current_issue.strftime("%Y-%m-%d"))
+
+        current_issue_yyyymmdd = current_issue.strftime("%Y%m%d")
+        current_issue_dir = f"""{params["patch"]["patch_dir"]}/issue_{current_issue_yyyymmdd}/quidel_covidtest"""
+        makedirs(f"{current_issue_dir}", exist_ok=True)
+        params["common"]["export_dir"] = f"""{current_issue_dir}"""
+        calculated_start_date = current_issue - timedelta(export_day_range)
+        calculated_end_date = current_issue
+        params["indicator"]["pull_start_date"] = calculated_start_date.strftime("%Y-%m-%d")
+        params["indicator"]["pull_end_date"] = calculated_end_date.strftime("%Y-%m-%d")
+
+        run_module(params, logger)
+        current_issue += timedelta(days=1)
+
+if __name__ == "__main__":
+    patch()
diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index 560f89456..31704c3fb 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -9,15 +9,17 @@
 import pandas as pd
 import numpy as np
 
-from .constants import AGE_GROUPS
+from .constants import AGE_GROUPS, FULL_BKFILL_START_DATE
 
 
 
-def get_from_s3(start_date, end_date, bucket, logger):
+def get_from_s3(params, start_date, end_date, logger):
     """
     Get raw data from aws s3 bucket.
 
     Args:
+        params: dict
+            read from params.json
         start_date: datetime.datetime
             pull data from file tagged with date on/after the start date
         end_date: datetime.datetime
@@ -30,6 +32,15 @@ def get_from_s3(start_date, end_date, bucket, logger):
         df: pd.DataFrame
         time_flag: datetime.datetime
     """
+    # connect aws s3 bucket
+    aws_access_key_id = params["aws_credentials"]["aws_access_key_id"]
+    aws_secret_access_key = params["aws_credentials"]["aws_secret_access_key"]
+    bucket_name = params["bucket_name"]
+
+    s3 = boto3.resource('s3', aws_access_key_id=aws_access_key_id,
+                        aws_secret_access_key=aws_secret_access_key)
+    bucket = s3.Bucket(bucket_name)
+
     time_flag = None
     selected_columns = ['SofiaSerNum', 'TestDate', 'Facility', 'City',
                                'State', 'Zip', 'PatientAge', 'Result1',
@@ -118,7 +129,7 @@ def fix_date(df, logger):
     df["timestamp"].values[mask] = df["StorageDate"].values[mask]
     return df
 
-def preprocess_new_data(start_date, end_date, params, test_mode, logger):
+def preprocess_new_data(start_date, end_date, params, logger):
     """
     Pull and pre-process Quidel Covid Test data.
 
@@ -133,8 +144,6 @@ def preprocess_new_data(start_date, end_date, params, test_mode, logger):
             pull data from file tagged with date on/before the end date
         params: dict
             read from params.json
-        test_mode: bool
-            pull raw data from s3 or not
         logger: logging.Logger
             The structured logger.
     output:
@@ -142,23 +151,8 @@ def preprocess_new_data(start_date, end_date, params, test_mode, logger):
         time_flag: datetime.date:
             the actual pull end date on which we successfully pull the data
     """
-    if test_mode:
-        test_data_dir = "./test_data/test_data.csv"
-        df, time_flag = pd.read_csv(
-            test_data_dir,
-            parse_dates=["StorageDate", "TestDate"]
-            ), datetime(2020, 8, 17)
-    else:
-        # connect aws s3 bucket
-        aws_access_key_id = params["aws_credentials"]["aws_access_key_id"]
-        aws_secret_access_key = params["aws_credentials"]["aws_secret_access_key"]
-        bucket_name = params["bucket_name"]
-
-        s3 = boto3.resource('s3', aws_access_key_id=aws_access_key_id,
-                            aws_secret_access_key=aws_secret_access_key)
-        bucket = s3.Bucket(bucket_name)
-        # Get new data from s3
-        df, time_flag = get_from_s3(start_date, end_date, bucket, logger)
+    # Get new data from s3
+    df, time_flag = get_from_s3(params, start_date, end_date, logger)
 
     # No new data can be pulled
     if time_flag is None:
@@ -282,13 +276,16 @@ def pull_quidel_covidtest(params, logger):
 
     """
     cache_dir = params["input_cache_dir"]
-
-    test_mode = params["test_mode"]
+    if params["pull_start_date"] == "":
+        params["pull_start_date"] = FULL_BKFILL_START_DATE
 
     # pull new data only that has not been ingested
     previous_df, pull_start_date = check_intermediate_file(
         cache_dir,
-        datetime.strptime(params["pull_start_date"], '%Y-%m-%d'))
+        params["pull_start_date"])
+
+    if params["pull_start_date"] != FULL_BKFILL_START_DATE:
+        pull_start_date = datetime.strptime(params["pull_start_date"], '%Y-%m-%d')
 
     if params["pull_end_date"] == "":
         pull_end_date = datetime.today()
@@ -298,7 +295,7 @@ def pull_quidel_covidtest(params, logger):
     # Pull data from the file at 5 digit zipcode level
     # Use _end_date to check the most recent date that we received data
     df, _end_date = preprocess_new_data(
-            pull_start_date, pull_end_date, params, test_mode, logger)
+            pull_start_date, pull_end_date, params, logger)
 
     # Utilize previously stored data
     if previous_df is not None:
@@ -343,7 +340,7 @@ def check_export_end_date(input_export_end_date, _end_date,
 def check_export_start_date(export_start_date, export_end_date,
                             export_day_range):
     """
-    Ensure that the starte date, end date, and day range are mutually consistent.
+    Ensure that the start date, end date, and day range are mutually consistent.
 
     Parameters:
         export_start_date: str
@@ -359,7 +356,7 @@ def check_export_start_date(export_start_date, export_end_date,
 
     """
     if export_start_date == "":
-        export_start_date = datetime(2020, 5, 26)
+        export_start_date = FULL_BKFILL_START_DATE
     else:
         export_start_date = datetime.strptime(export_start_date, '%Y-%m-%d')
      # Only export data from -50 days to -5 days
diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py
index e6974b6aa..e6f05a45c 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/run.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/run.py
@@ -92,7 +92,7 @@ def generate_and_export_for_parent_geo(geo_groups, geo_data, res_key, smooth, de
                               remove_null_samples=True) # for parent geo, remove null sample size
     return dates
 
-def run_module(params: Dict[str, Any]):
+def run_module(params: Dict[str, Any], logger=None):
     """Run the quidel_covidtest indicator.
 
     The `params` argument is expected to have the following structure:
@@ -117,9 +117,10 @@ def run_module(params: Dict[str, Any]):
         - "test_mode": bool, whether we are running in test mode
     """
     start_time = time.time()
-    logger = get_structured_logger(
-        __name__, filename=params["common"].get("log_filename"),
-        log_exceptions=params["common"].get("log_exceptions", True))
+    if logger is None:
+        logger = get_structured_logger(
+            __name__, filename=params["common"].get("log_filename"),
+            log_exceptions=params["common"].get("log_exceptions", True))
     stats = []
     # Log at program exit in case of an exception, otherwise after successful completion
     atexit.register(log_exit, start_time, stats, logger)
@@ -136,17 +137,14 @@ def run_module(params: Dict[str, Any]):
     # (generate files).
     if params["indicator"].get("generate_backfill_files", True):
         backfill_dir = params["indicator"]["backfill_dir"]
-        backfill_merge_day = params["indicator"]["backfill_merge_day"]
 
-        # Merge 4 weeks' data into one file to save runtime
-        # Notice that here we don't check the _end_date(receive date)
-        # since we always want such merging happens on a certain day of a week
-        merge_backfill_file(backfill_dir, backfill_merge_day, datetime.today())
+        # Merge a month's data into one file to save runtime
+        merge_backfill_file(backfill_dir, datetime.today(), logger)
         if _end_date is None:
             logger.info("The data is up-to-date. Currently, no new data to be ingested.")
             return
         # Store the backfill intermediate file
-        store_backfill_file(df, _end_date, backfill_dir)
+        store_backfill_file(df, _end_date, backfill_dir, logger)
 
     export_end_date = check_export_end_date(
         export_end_date, _end_date, END_FROM_TODAY_MINUS)
@@ -224,7 +222,8 @@ def run_module(params: Dict[str, Any]):
 
     # Export the cache file if the pipeline runs successfully.
     # Otherwise, don't update the cache file
-    update_cache_file(df, _end_date, cache_dir, logger)
+    if not params["common"].get("custom_run", False):
+        update_cache_file(df, _end_date, cache_dir, logger)
     # Log stats now instead of at program exit
     atexit.unregister(log_exit)
     log_exit(start_time, stats, logger)
diff --git a/quidel_covidtest/setup.py b/quidel_covidtest/setup.py
index 82c80832a..8c40e103c 100644
--- a/quidel_covidtest/setup.py
+++ b/quidel_covidtest/setup.py
@@ -7,6 +7,7 @@
     "darker[isort]~=2.1.1",
     "delphi-utils",
     "imap-tools",
+    "mock",
     "numpy",
     "openpyxl",
     "pandas",
diff --git a/quidel_covidtest/tests/conftest.py b/quidel_covidtest/tests/conftest.py
index c5ebcf630..67d4ccbee 100644
--- a/quidel_covidtest/tests/conftest.py
+++ b/quidel_covidtest/tests/conftest.py
@@ -1,16 +1,57 @@
 # -*- coding: utf-8 -*-
-
+from datetime import datetime
 from os.path import join
 import os
+from pathlib import Path
+
+import mock
+import pandas as pd
 import pytest
+from mock.mock import patch
+
+import delphi_quidel_covidtest.run
+
+TEST_DIR = Path(__file__).parent
+SOURCE_DIR = Path(__file__).parent.parent
+@pytest.fixture(scope='session')
+def params():
+    PARAMS = {
+        "common": {
+            "export_dir": f"{TEST_DIR}/receiving"
+        },
+        "indicator": {
+            "static_file_dir": f"{SOURCE_DIR}/static",
+            "input_cache_dir": f"{TEST_DIR}/cache",
+            "backfill_dir": f"{TEST_DIR}/backfill",
+            "backfill_merge_day": 0,
+            "export_start_date": "2020-06-30",
+            "export_end_date": "",
+            "pull_start_date": "2020-07-09",
+            "pull_end_date":"",
+            "export_day_range":40,
+            "aws_credentials": {
+                "aws_access_key_id": "",
+                "aws_secret_access_key": ""
+            },
+            "bucket_name": "",
+            "wip_signal": "",
+            "test_mode": True
+        }
+    }
+    return PARAMS
 
+@pytest.fixture(scope="session", autouse=True)
+def mock_get_from_s3():
+    with patch("delphi_quidel_covidtest.pull.get_from_s3") as m:
+        test_data_dir = "./test_data/test_data.csv"
+        time_flag = datetime(2020, 8, 17)
+        df = pd.read_csv(
+            test_data_dir,
+            parse_dates=["StorageDate", "TestDate"]
+        )
+        m.return_value = df, time_flag
+        yield m
 
 @pytest.fixture(scope="session")
-def clean_receiving_dir():
-    # Clean receiving directory
-    for fname in os.listdir("receiving"):
-        if ".csv" in fname:
-            os.remove(join("receiving", fname))
-    for fname in os.listdir("cache"):
-        if ".csv" in fname:
-            os.remove(join("cache", fname))
+def run_as_module(params, mock_get_from_s3):
+    delphi_quidel_covidtest.run.run_module(params)
diff --git a/quidel_covidtest/tests/test_backfill.py b/quidel_covidtest/tests/test_backfill.py
index 27e0d01bc..9dc45ceb6 100644
--- a/quidel_covidtest/tests/test_backfill.py
+++ b/quidel_covidtest/tests/test_backfill.py
@@ -1,24 +1,20 @@
+import calendar
 import logging
 import os 
 import glob
-from datetime import datetime
-
+from datetime import datetime, timedelta
+from pathlib import Path
 import pandas as pd
 
-from delphi_quidel_covidtest.pull import pull_quidel_covidtest
-
+from delphi_utils.logger import get_structured_logger
 from delphi_quidel_covidtest.backfill import (store_backfill_file,
-                                              merge_backfill_file)
-
-END_FROM_TODAY_MINUS = 5
-EXPORT_DAY_RANGE = 40
+                                              merge_backfill_file, merge_existing_backfill_files)
 
-TEST_LOGGER = logging.getLogger()
-backfill_dir="./backfill"
-
-class TestBackfill:
-    
-    df, _end_date = pull_quidel_covidtest({
+TEST_PATH = Path(__file__).parent
+PARAMS = {
+        "indicator": {
+            "backfill_dir": f"{TEST_PATH}/backfill",
+            "drop_date": "2020-06-11",
             "static_file_dir": "../static",
             "input_cache_dir": "./cache",
             "export_start_date": "2020-06-30",
@@ -29,19 +25,34 @@ class TestBackfill:
                 "aws_access_key_id": "",
                 "aws_secret_access_key": ""
             },
-            "bucket_name": "",
-            "wip_signal": "",
-            "test_mode": True
-        }, TEST_LOGGER)
-    
-    def test_store_backfill_file(self):
-                
-        store_backfill_file(self.df, datetime(2020, 1, 1), backfill_dir)
+        "bucket_name": "",
+        "wip_signal": "",
+        "test_mode": True
+        },
+    }
+DATA_FILEPATH =  f"{PARAMS['indicator']['input_cache_dir']}/pulled_until_20200817.csv"
+backfill_dir = PARAMS["indicator"]["backfill_dir"]
+
+class TestBackfill:
+    _end_date = datetime.strptime(DATA_FILEPATH.split("_")[2].split(".")[0],
+                                        '%Y%m%d') + timedelta(days=1)
+    df = pd.read_csv(DATA_FILEPATH, sep=",", parse_dates=["timestamp"])
+
+    def cleanup(self):
+        for file in glob.glob(f"{backfill_dir}/*.parquet"):
+            os.remove(file)
+            assert file not in os.listdir(backfill_dir)
+
+    def test_store_backfill_file(self, caplog):
+        caplog.set_level(logging.INFO)
+        logger = get_structured_logger()
+
+        store_backfill_file(self.df, datetime(2020, 1, 1), backfill_dir, logger)
         fn = "quidel_covidtest_as_of_20200101.parquet"
         assert fn in os.listdir(backfill_dir)
+        assert "Stored source data in parquet" in caplog.text
         
         backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
-        
         selected_columns = ['time_value', 'fips', 'state_id',
                         'den_total', 'num_total',
                         'num_age_0_4', 'den_age_0_4',
@@ -51,37 +62,36 @@ def test_store_backfill_file(self):
                         'num_age_65plus', 'den_age_65plus',
                         'num_age_0_17', 'den_age_0_17',
                         'lag', 'issue_date']
-        assert set(selected_columns) == set(backfill_df.columns)  
-        
-        os.remove(backfill_dir + "/" + fn)
-        assert fn not in os.listdir(backfill_dir)
-        
-    def test_merge_backfill_file(self):
-        
-        today = datetime.today()
-        fn = "quidel_covidtest_from_20200817_to_20200820.parquet"
+        assert set(selected_columns) == set(backfill_df.columns)
+        assert fn in os.listdir(backfill_dir)
+
+        self.cleanup()
+    def test_merge_backfill_file(self, caplog, monkeypatch):
+        caplog.set_level(logging.INFO)
+        logger = get_structured_logger()
+
+        fn = "quidel_covidtest_202008.parquet"
         assert fn not in os.listdir(backfill_dir)
         
-        # Check the when no daily file stored
+        # Check when no daily file stored
         today = datetime(2020, 8, 20)
-        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
+        merge_backfill_file(backfill_dir, today, logger, test_mode=True)
         assert fn not in os.listdir(backfill_dir)
+        assert "No new files to merge; skipping merging" in caplog.text
         
         for d in range(17, 21):
-            dropdate = datetime(2020, 8, d)        
-            store_backfill_file(self.df, dropdate, backfill_dir)
-                
-        # Check the when the merged file is not generated
-        today = datetime(2020, 8, 20)
-        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
-        assert fn not in os.listdir(backfill_dir)
-        
+            dropdate = datetime(2020, 8, d)
+            store_backfill_file(self.df, dropdate, backfill_dir, logger)
+
          # Generate the merged file, but not delete it
-        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=2)         
+        today = datetime(2020, 9, 1)
+        monkeypatch.setattr(calendar, 'monthrange', lambda x, y: (1, 4))
+        merge_backfill_file(backfill_dir, today, logger, test_mode=True,)
         assert fn in os.listdir(backfill_dir)
+        assert "Merging files" in caplog.text
 
         # Read daily file
-        new_files = glob.glob(backfill_dir + "/quidel_covidtest*.parquet")
+        new_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of*.parquet")
         pdList = []        
         for file in new_files:
             if "from" in file:
@@ -89,9 +99,6 @@ def test_merge_backfill_file(self):
             df = pd.read_parquet(file, engine='pyarrow')
             pdList.append(df)
             os.remove(file)
-        new_files = glob.glob(backfill_dir + "/quidel_covidtest*.parquet")
-        assert len(new_files) == 1
-        
         expected = pd.concat(pdList).sort_values(["time_value", "fips"])
         
         # Read the merged file
@@ -101,6 +108,75 @@ def test_merge_backfill_file(self):
         assert expected.shape[0] == merged.shape[0]
         assert expected.shape[1] == merged.shape[1]
         
-        os.remove(backfill_dir + "/" + fn)
-        assert fn not in os.listdir(backfill_dir)
+        self.cleanup()
+
+    def test_merge_existing_backfill_files(self, caplog, monkeypatch):
+        issue_date = datetime(year=2020, month=7, day=20)
+        issue_date_str = issue_date.strftime("%Y%m%d")
+        caplog.set_level(logging.INFO)
+        logger = get_structured_logger()
+        def prep_backfill_data():
+            # Generate backfill daily files
+            for d in range(18, 24):
+                dropdate = datetime(2020, 7, d)
+                df_part = self.df[self.df['timestamp'] == dropdate]
+                store_backfill_file(df_part, dropdate, backfill_dir, logger)
+
+            today = datetime(2020, 8, 1)
+            # creating expected file
+            monkeypatch.setattr(calendar, 'monthrange', lambda x, y: (1, 4))
+            merge_backfill_file(backfill_dir, today, logger,
+                                test_mode=True)
+            original = f"{backfill_dir}/quidel_covidtest_202007.parquet"
+            os.rename(original, f"{backfill_dir}/expected.parquet")
+
+            # creating backfill without issue date
+            issue_date_filename = f"{backfill_dir}/quidel_covidtest_as_of_{issue_date_str}.parquet"
+            os.remove(issue_date_filename)
+            merge_backfill_file(backfill_dir, today, logger,
+                                test_mode=True)
+
+            old_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of_*")
+            for file in old_files:
+                os.remove(file)
+
+        prep_backfill_data()
+
+        df_to_add = self.df[self.df['timestamp'] == issue_date]
+        file_to_add = store_backfill_file(df_to_add, issue_date, backfill_dir, logger)
+        merge_existing_backfill_files(backfill_dir, file_to_add, issue_date, logger)
+
+        assert "Adding missing date to merged file" in caplog.text
+
+        expected = pd.read_parquet(f"{backfill_dir}/expected.parquet")
+        merged = pd.read_parquet(f"{backfill_dir}/quidel_covidtest_202007.parquet")
+
+        check = pd.concat([merged, expected]).drop_duplicates(keep=False)
+
+        assert len(check) == 0
+        self.cleanup()
+
+
+    def test_merge_existing_backfill_files_no_call(self, caplog):
+        issue_date = datetime(year=2020, month=5, day=20)
+        caplog.set_level(logging.INFO)
+        logger = get_structured_logger()
+        def prep_backfill_data():
+            # Generate backfill daily files
+            for d in range(18, 24):
+                dropdate = datetime(2020, 7, d)
+                df_part = self.df[self.df["timestamp"] == dropdate]
+                store_backfill_file(df_part, dropdate, backfill_dir, logger)
+
+            today = datetime(2020, 8, 1)
+            # creating expected file
+            merge_backfill_file(backfill_dir, today, logger,
+                                test_mode=True)
+
+        prep_backfill_data()
+        file_to_add = store_backfill_file(self.df, issue_date, backfill_dir, logger)
+        merge_existing_backfill_files(backfill_dir, file_to_add, issue_date, logger)
+        assert "Issue date has no matching merged files" in caplog.text
+        self.cleanup()
+
         
diff --git a/quidel_covidtest/tests/test_patch.py b/quidel_covidtest/tests/test_patch.py
new file mode 100644
index 000000000..43b61ec46
--- /dev/null
+++ b/quidel_covidtest/tests/test_patch.py
@@ -0,0 +1,33 @@
+from unittest.mock import patch as mock_patch
+from delphi_quidel_covidtest.patch import patch
+import os
+import shutil
+
+class TestPatchModule:
+    def test_patch(self):
+        with mock_patch('delphi_quidel_covidtest.patch.get_structured_logger') as mock_get_structured_logger, \
+             mock_patch('delphi_quidel_covidtest.patch.read_params') as mock_read_params, \
+             mock_patch('delphi_quidel_covidtest.patch.run_module') as mock_run_module:
+
+            mock_read_params.return_value = {
+                "common": {
+                    "log_filename": "test.log"
+                },
+                "indicator": {
+                    "export_day_range": 40,
+                },
+                "patch": {
+                    "start_issue": "2021-01-01",
+                    "end_issue": "2021-01-02",
+                    "patch_dir": "./patch_dir"
+                }
+            }
+
+            patch()
+
+            assert os.path.isdir('./patch_dir')
+            assert os.path.isdir('./patch_dir/issue_20210101/quidel-covidtest')
+            assert os.path.isdir('./patch_dir/issue_20210102/quidel-covidtest')
+
+            # Clean up the created directories after the test
+            shutil.rmtree(mock_read_params.return_value["patch"]["patch_dir"])
\ No newline at end of file
diff --git a/quidel_covidtest/tests/test_pull.py b/quidel_covidtest/tests/test_pull.py
index a3436392b..8177df1a5 100644
--- a/quidel_covidtest/tests/test_pull.py
+++ b/quidel_covidtest/tests/test_pull.py
@@ -38,8 +38,7 @@ def test_fix_date(self):
                                             datetime(2020, 6, 11), datetime(2020, 7, 2)])
 
 class TestingPullData:
-    def test_pull_quidel_covidtest(self):
-
+    def test_pull_quidel_covidtest(self, mock_get_from_s3):
         df, _ = pull_quidel_covidtest({
             "static_file_dir": "../static",
             "input_cache_dir": "./cache",
diff --git a/quidel_covidtest/tests/test_run.py b/quidel_covidtest/tests/test_run.py
index 4e15bea91..cc054dfc2 100644
--- a/quidel_covidtest/tests/test_run.py
+++ b/quidel_covidtest/tests/test_run.py
@@ -1,49 +1,25 @@
 """Tests for running the quidel covidtest indicator."""
+from itertools import product
+import os
 from os import listdir
 from os.path import join
+from pathlib import Path
 
 import pandas as pd
 import numpy as np
 
 from delphi_utils import add_prefix
 from delphi_quidel_covidtest.constants import PARENT_GEO_RESOLUTIONS, NONPARENT_GEO_RESOLUTIONS, \
-    SENSORS
-from delphi_quidel_covidtest.run import run_module
-
+    SENSORS, AGE_GROUPS
 
 class TestRun:
     """Tests for run_module()."""
 
-    PARAMS = {
-        "common": {
-            "export_dir": "./receiving"
-        },
-        "indicator": {
-            "static_file_dir": "../static",
-            "input_cache_dir": "./cache",
-            "backfill_dir": "./backfill",
-            "backfill_merge_day": 0,
-            "export_start_date": "2020-06-30",
-            "export_end_date": "",
-            "pull_start_date": "2020-07-09",
-            "pull_end_date":"",
-            "export_day_range":40,
-            "aws_credentials": {
-                "aws_access_key_id": "",
-                "aws_secret_access_key": ""
-            },
-            "bucket_name": "",
-            "wip_signal": "",
-            "test_mode": True
-        }
-    }
-
-    def test_output_files(self, clean_receiving_dir):
+    def test_output_files(self, run_as_module, params):
         """Tests that the proper files are output."""
 
         # Test output exists
-        run_module(self.PARAMS)
-        csv_files = [i for i in listdir("receiving") if i.endswith(".csv")]
+        csv_files = [i for i in listdir(params["common"]["export_dir"]) if i.endswith(".csv")]
 
         dates = [
             "20200718",
@@ -52,16 +28,20 @@ def test_output_files(self, clean_receiving_dir):
         ]
         geos = PARENT_GEO_RESOLUTIONS + NONPARENT_GEO_RESOLUTIONS
         sensors = add_prefix(SENSORS,
-                             wip_signal=self.PARAMS["indicator"]["wip_signal"],
+                             wip_signal=params["indicator"]["wip_signal"],
                              prefix="wip_")
+        full_sensor = [f"{sensor}_{age}" for sensor, age in product(sensors, AGE_GROUPS)]
 
         expected_files = []
         for date in dates:
-            for geo in geos:
+            for geo in PARENT_GEO_RESOLUTIONS:
                 for sensor in sensors:
                     expected_files += [date + "_" + geo + "_" + sensor + ".csv"]
+            for geo in NONPARENT_GEO_RESOLUTIONS:
+                for sensor in full_sensor:
+                    expected_files += [date + "_" + geo + "_" + sensor + ".csv"]
 
-        assert set(expected_files).issubset(set(csv_files))
+        assert set(expected_files) == (set(csv_files))
         assert '20200721_state_covid_ag_raw_pct_positive.csv' not in csv_files
         assert '20200722_state_covid_ag_raw_pct_positive.csv' not in csv_files
 
@@ -105,3 +85,8 @@ def test_output_files(self, clean_receiving_dir):
             if ".csv" in fname:
                 flag = 1
         assert flag is not None
+
+        for files in Path(params["common"]["export_dir"]).glob("*.csv"):
+            os.remove(files)
+        for files in Path(params["indicator"]["input_cache_dir"]).glob("*.csv"):
+            os.remove(files)